VED-382: Use configurable disease mappings in backend.

Author: mfjarvis

backend/src/mappings.py

@@ -126,15 +126,8 @@ def validate(self):
         # Initialise the mandation validation functions
         mandation_functions = MandationFunctions(self.imms, self.vaccine_type)
 
-        # Identify whether to use the vaccine_type_agnostic, or else a vaccine type specific, validation rule set
-        validation_set_to_use = (
-            "vaccine_type_agnostic"
-            if self.vaccine_type in ValidationSets.vaccine_types_which_use_agnostic_set
-            else self.vaccine_type.lower()
-        )
-
         # Obtain the relevant validation set
-        validation_set = getattr(ValidationSets, validation_set_to_use)
+        validation_set = getattr(ValidationSets, self.vaccine_type.lower(), ValidationSets.vaccine_type_agnostic)
 
         # Create an instance of FieldLocations and set dynamic fields
         field_locations = FieldLocations()

backend/src/models/fhir_immunization_post_validators.py

@@ -4,13 +4,13 @@
 
 
 from typing import Union
-from mappings import vaccine_type_mappings
 from .generic_utils import create_diagnostics_error
 from base_utils.base_utils import obtain_field_location
 from models.obtain_field_value import ObtainFieldValue
 from models.field_names import FieldNames
 from models.errors import MandatoryError
 from constants import Urls
+from clients import redis_client
 
 
 def get_target_disease_codes(immunization: dict):
@@ -52,17 +52,14 @@ def convert_disease_codes_to_vaccine_type(disease_codes_input: list) -> Union[st
     Takes a list of disease codes and returns the corresponding vaccine type if found,
     otherwise raises a value error
     """
-    try:
-        return next(
-            vaccine_type
-            for disease_codes, vaccine_type in vaccine_type_mappings
-            if sorted(disease_codes_input) == disease_codes
-        )
-    except Exception as e:
+    key = ":".join(sorted(disease_codes_input))
+    vaccine_type = redis_client.hget("diseases_to_vacc", key)
+    if not vaccine_type:
         raise ValueError(
             f"Validation errors: protocolApplied[0].targetDisease[*].coding[?(@.system=='http://snomed.info/sct')].code - "
             f"{disease_codes_input} is not a valid combination of disease codes for this service"
-        ) from e
+        )
+    return vaccine_type
 
 
 def get_vaccine_type(immunization: dict):

backend/src/models/utils/validation_utils.py

@@ -1,7 +1,6 @@
 """Validation sets for each vaccine type"""
 
 from models.mandation_functions import MandationRules
-from mappings import VaccineTypes
 
 
 class ValidationSets:
@@ -11,7 +10,7 @@ class ValidationSets:
 
     TO ADD A NEW VACCINE TYPE:
     * If the mandation rules for the new vaccine type are identical to the vaccine_type_agnostic rules, then
-      add the vaccine type to the vaccine_types_which_use_agnostic_set list.
+      no action is required.
     * If some of the mandation rules for the new vaccine type are different than the agnostic rules, then create a
       new validation set, with the same name as the vaccine type. This can be done by copying and pasting the
       vaccine_type_agnostic set, and amending any rules as required.
@@ -21,8 +20,6 @@ class ValidationSets:
     def __init__(self) -> None:
         pass
 
-    vaccine_types_which_use_agnostic_set = [VaccineTypes.covid_19, VaccineTypes.flu, VaccineTypes.hpv, VaccineTypes.mmr,VaccineTypes.rsv]
-
     vaccine_type_agnostic = {
         "patient_identifier_value": MandationRules.required,
         "patient_name_given": MandationRules.mandatory,

backend/src/models/validation_sets.py

@@ -6,7 +6,7 @@
 from typing import Optional
 from urllib.parse import parse_qs, urlencode, quote
 
-from mappings import VaccineTypes
+from clients import redis_client
 from models.errors import ParameterException
 
 ParamValue = list[str]
@@ -107,9 +107,11 @@ def process_search_params(params: ParamContainer) -> SearchParams:
                      vaccine_type is not None]
     if len(vaccine_types) < 1:
         raise ParameterException(f"Search parameter {immunization_target_key} must have one or more values.")
-    if any([x not in VaccineTypes().all for x in vaccine_types]):
+
+    valid_vaccine_types = redis_client.hkeys("vacc_to_diseases")
+    if any([x not in valid_vaccine_types for x in vaccine_types]):
         raise ParameterException(
-            f"immunization-target must be one or more of the following: {','.join(VaccineTypes().all)}")
+            f"immunization-target must be one or more of the following: {', '.join(valid_vaccine_types)}")
 
     # date.from
     date_froms = params.get(date_from_key, [])

backend/src/parameter_parser.py

@@ -1,4 +1,12 @@
 import os
 import sys
+from unittest.mock import patch
+
+from tests.utils.mock_redis import MockRedisClient
 
 sys.path.append(f"{os.path.dirname(os.path.abspath(__file__))}/../src")
+
+# TODO - probably shouldn't do this here. Mock in individual tests instead for clarity.
+#  I tried setUpModule() but that wasn't called from __init__.py
+redis_patcher = patch("clients.redis_client", MockRedisClient())
+redis_patcher.start()

backend/tests/__init__.py

@@ -28,7 +28,6 @@
     IdentifierDuplicationError,
 )
 from tests.utils.immunization_utils import create_covid_19_immunization
-from mappings import VaccineTypes
 from parameter_parser import patient_identifier_system, process_search_params
 from tests.utils.generic_utils import load_json_data
 from tests.utils.values_for_tests import ValidValues
@@ -133,7 +132,7 @@ def test_get_imms_by_identifer_header_missing(self):
         response = self.controller.get_immunization_by_identifier(lambda_event)
 
         self.assertEqual(response["statusCode"], 403)
-    
+
     @patch("fhir_controller.get_supplier_permissions")
     def test_not_found_for_identifier(self, mock_get_permissions):
         """it should return not-found OperationOutcome if it doesn't exist"""
@@ -165,7 +164,7 @@ def test_not_found_for_identifier(self, mock_get_permissions):
 
         imms = identifier.replace("|", "#")
         # When
-        
+
         response = self.controller.get_immunization_by_identifier(lambda_event)
 
         # Then
@@ -403,7 +402,7 @@ def test_validate_immunization_identifier_having_whitespace(self):
         self.assertEqual(response["statusCode"], 400)
         outcome = json.loads(response["body"])
         self.assertEqual(outcome["resourceType"], "OperationOutcome")
-    
+
     @patch("fhir_controller.get_supplier_permissions")
     def test_validate_imms_id_invalid_vaccinetype(self, mock_get_permissions):
         """it should validate lambda's Immunization id"""
@@ -704,7 +703,7 @@ def test_validate_immunization_identifier_having_whitespace(self):
         self.assertEqual(response["statusCode"], 400)
         outcome = json.loads(response["body"])
         self.assertEqual(outcome["resourceType"], "OperationOutcome")
-   
+
     @patch("fhir_controller.get_supplier_permissions")
     def test_validate_imms_id_invalid_vaccinetype(self, mock_get_permissions):
         """it should validate lambda's Immunization id"""
@@ -786,7 +785,7 @@ def test_get_imms_by_id_unauthorised_vax_error(self,mock_permissions):
         # Then
         mock_permissions.assert_called_once_with("test")
         self.assertEqual(response["statusCode"], 403)
-    
+
     @patch("fhir_controller.get_supplier_permissions")
     def test_get_imms_by_id_no_vax_permission(self, mock_permissions):
         """it should return Immunization Id if it exists"""
@@ -1108,7 +1107,7 @@ def test_update_immunization_UnauthorizedVaxError(self, mock_get_supplier_permis
         response = self.controller.update_immunization(aws_event)
         mock_get_supplier_permissions.assert_called_once_with("Test")
         self.assertEqual(response["statusCode"], 403)
-    
+
     @patch("fhir_controller.get_supplier_permissions")
     def test_update_immunization_UnauthorizedVaxError_check_for_non_batch(self, mock_get_supplier_permissions):
         """it should not update the Immunization record"""
@@ -1539,7 +1538,7 @@ def test_immunization_exception_not_found(self, mock_get_permissions):
         body = json.loads(response["body"])
         self.assertEqual(body["resourceType"], "OperationOutcome")
         self.assertEqual(body["issue"][0]["code"], "not-found")
-    
+
     @patch("fhir_controller.get_supplier_permissions")
     def test_immunization_unhandled_error(self, mock_get_supplier_permissions):
         """it should return server-error OperationOutcome if service throws UnhandledResponseError"""
@@ -1577,12 +1576,12 @@ def setUp(self):
     @patch("fhir_controller.get_supplier_permissions")
     def test_get_search_immunizations(self, mock_get_supplier_permissions):
         """it should search based on patient_identifier and immunization_target"""
-        
+
         mock_get_supplier_permissions.return_value = ["covid19:search"]
         search_result = Bundle.construct()
         self.service.search_immunizations.return_value = search_result
 
-        vaccine_type = VaccineTypes().all[0]
+        vaccine_type = "COVID19"
         params = f"{self.immunization_target_key}={vaccine_type}&" + urllib.parse.urlencode(
             [(f"{self.patient_identifier_key}", f"{self.patient_identifier_valid_value}")]
         )
@@ -1616,7 +1615,7 @@ def test_get_search_immunizations_vax_permission_check(self, mock_get_supplier_p
         search_result = Bundle.construct()
         self.service.search_immunizations.return_value = search_result
 
-        vaccine_type = VaccineTypes().all[0]
+        vaccine_type = "COVID19"
         lambda_event = {
             "SupplierSystem": "test",
             "multiValueQueryStringParameters": {
@@ -1639,7 +1638,7 @@ def test_get_search_immunizations_for_unauthorized_vaccine_type_search(self, moc
         bundle = Bundle.parse_obj(search_result)
         self.service.search_immunizations.return_value = bundle
 
-        vaccine_type = VaccineTypes().all[0], VaccineTypes().all[1]
+        vaccine_type = "COVID19", "FLU"
         vaccine_type = ",".join(vaccine_type)
 
         lambda_event = {
@@ -1693,7 +1692,7 @@ def test_get_search_immunizations_for_unauthorized_vaccine_type_search_403(self,
         mock_get_supplier_permissions.return_value = []
         self.service.search_immunizations.return_value = bundle
 
-        vaccine_type = VaccineTypes().all[0], VaccineTypes().all[1]
+        vaccine_type = "COVID19", "FLU"
         vaccine_type = ",".join(vaccine_type)
 
         lambda_event = {
@@ -1718,7 +1717,7 @@ def test_get_search_immunizations_unauthorized(self, mock_get_supplier_permissio
         mock_get_supplier_permissions.return_value = []
         self.service.search_immunizations.return_value = search_result
 
-        vaccine_type = VaccineTypes().all[0]
+        vaccine_type = "COVID19"
         params = f"{self.immunization_target_key}={vaccine_type}&" + urllib.parse.urlencode(
             [(f"{self.patient_identifier_key}", f"{self.patient_identifier_valid_value}")]
         )
@@ -1742,7 +1741,7 @@ def test_post_search_immunizations(self,mock_get_supplier_permissions):
         search_result = Bundle.construct()
         self.service.search_immunizations.return_value = search_result
 
-        vaccine_type = VaccineTypes().all[0]
+        vaccine_type = "COVID19"
         params = f"{self.immunization_target_key}={vaccine_type}&" + urllib.parse.urlencode(
             [(f"{self.patient_identifier_key}", f"{self.patient_identifier_valid_value}")]
         )
@@ -1761,7 +1760,7 @@ def test_post_search_immunizations(self,mock_get_supplier_permissions):
             "headers": {"Content-Type": "application/x-www-form-urlencoded", "SupplierSystem": "Test"},
             "body": base64_encoded_body,
         }
-        
+
         # When
         response = self.controller.search_immunizations(lambda_event)
         # Then
@@ -1781,7 +1780,7 @@ def test_post_search_immunizations_for_unauthorized_vaccine_type_search(self,moc
         self.service.search_immunizations.return_value = bundle
         mock_get_supplier_permissions.return_value = ["covid19:search"]
 
-        vaccine_type = VaccineTypes().all[0], VaccineTypes().all[1]
+        vaccine_type = "COVID19", "FLU"
         vaccine_type = ",".join(vaccine_type)
         # Construct the application/x-www-form-urlencoded body
         body = {
@@ -1846,7 +1845,7 @@ def test_post_search_immunizations_for_unauthorized_vaccine_type_search_403(self
         mock_get_supplier_permissions.return_value = []
         self.service.search_immunizations.return_value = bundle
 
-        vaccine_type = VaccineTypes().all[0], VaccineTypes().all[1]
+        vaccine_type = "COVID19", "FLU"
         vaccine_type = ",".join(vaccine_type)
 
         # Construct the application/x-www-form-urlencoded body
@@ -1916,7 +1915,7 @@ def test_search_immunizations_returns_400_on_passing_superseded_nhs_number(self,
         self.service.search_immunizations.return_value = search_result
         mock_get_supplier_permissions.return_value = ["covid19:search"]
 
-        vaccine_type = VaccineTypes().all[0]
+        vaccine_type = "COVID19"
         lambda_event = {
             "headers": {
                 "Content-Type": "application/x-www-form-urlencoded",
@@ -1943,7 +1942,7 @@ def test_search_immunizations_returns_200_remove_vaccine_not_done(self, mock_get
         bundle = Bundle.parse_obj(search_result)
         mock_get_supplier_permissions.return_value = ["covid19:search"]
         self.service.search_immunizations.return_value = bundle
-        vaccine_type = VaccineTypes().all[0]
+        vaccine_type = "COVID19"
         lambda_event = {
             "headers": {
                 "Content-Type": "application/x-www-form-urlencoded",
@@ -1967,7 +1966,7 @@ def test_search_immunizations_returns_200_remove_vaccine_not_done(self, mock_get
     def test_self_link_excludes_extraneous_params(self, mock_get_supplier_permissions):
         search_result = Bundle.construct()
         self.service.search_immunizations.return_value = search_result
-        vaccine_type = VaccineTypes().all[0]
+        vaccine_type = "COVID19"
         mock_get_supplier_permissions.return_value = ["covid19:search"]
         params = f"{self.immunization_target_key}={vaccine_type}&" + urllib.parse.urlencode(
             [(f"{self.patient_identifier_key}", f"{self.patient_identifier_valid_value}")]