VED-382: Use configurable disease mappings in backend.

.github/workflows/sonarcloud.yml

@@ -59,6 +59,8 @@ jobs:
       - name: Run unittest with recordforwarder-coverage
         working-directory: backend
         id: recordforwarder
+        env:
+          PYTHONPATH: ${{ github.workspace }}/backend/src:${{ github.workspace }}/backend/tests
         continue-on-error: true
         run: |
           poetry env use 3.11
@@ -90,6 +92,8 @@ jobs:
 
       - name: Run unittest with coverage-fhir-api
         working-directory: backend
+        env:
+          PYTHONPATH: ${{ github.workspace }}/backend/src:${{ github.workspace }}/backend/tests
         id: fhirapi
         continue-on-error: true
         run: |

.gitignore

@@ -29,3 +29,4 @@ openapi.json
 !**/.vscode/settings.json.default
 
 devtools/volume/
+backend/tests/.coverage

ack_backend/tests/test_splunk_logging.py

@@ -19,7 +19,7 @@
 from tests.utils_for_ack_backend_tests.utils_for_ack_backend_tests import generate_event
 
 with patch.dict("os.environ", MOCK_ENVIRONMENT_DICT):
-    from src.ack_processor import lambda_handler
+    from ack_processor import lambda_handler
 
 s3_client = boto3_client("s3")
 

backend/Makefile

@@ -6,6 +6,6 @@ package: build
 	docker run --rm -v $(shell pwd)/build:/build imms-lambda-build
 
 test:
-	python -m unittest
+	@PYTHONPATH=src:tests python -m unittest
 
 .PHONY: build package test

backend/src/models/constants.py

@@ -39,3 +39,7 @@ class Constants:
     }
 
     ALLOWED_CONTAINED_RESOURCES = {"Practitioner", "Patient"}
+
+    SUPPLIER_PERMISSIONS_KEY = "supplier_permissions"
+    VACCINE_TYPE_TO_DISEASES_HASH_KEY = "vacc_to_diseases"
+    DISEASES_TO_VACCINE_TYPE_HASH_KEY = "diseases_to_vacc"

backend/src/models/fhir_immunization_post_validators.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/utils/validation_utils.py

@@ -2,15 +2,15 @@
 
 import json
 
-
 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 models.constants import Constants
+from clients import redis_client
 
 
 def get_target_disease_codes(immunization: dict):
@@ -52,17 +52,15 @@ 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(Constants.DISEASES_TO_VACCINE_TYPE_HASH_KEY, 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/validation_sets.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/parameter_parser.py

@@ -6,8 +6,9 @@
 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
+from models.constants import Constants
 
 ParamValue = list[str]
 ParamContainer = dict[str, ParamValue]
@@ -107,9 +108,11 @@ 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(Constants.VACCINE_TYPE_TO_DISEASES_HASH_KEY)
+    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/tests/__init__.py

@@ -1,4 +0,0 @@
-import os
-import sys
-
-sys.path.append(f"{os.path.dirname(os.path.abspath(__file__))}/../src")

backend/tests/test_fhir_batch_repository.py

@@ -9,6 +9,7 @@
 from models.errors import IdentifierDuplicationError, ResourceNotFoundError, UnhandledResponseError, ResourceFoundError
 from fhir_batch_repository import ImmunizationBatchRepository, create_table
 from tests.utils.immunization_utils import create_covid_19_immunization_dict
+
 imms_id = str(uuid4())
 
 
@@ -28,6 +29,12 @@ def setUp(self):
         self.table.query = MagicMock(return_value={})
         self.immunization = create_covid_19_immunization_dict(imms_id)
         self.table.update_item = MagicMock(return_value = {"ResponseMetadata": {"HTTPStatusCode": 200}})
+        self.redis_patcher = patch("models.utils.validation_utils.redis_client")
+        self.mock_redis_client = self.redis_patcher.start()
+
+    def tearDown(self):
+        self.redis_patcher.stop()
+        return super().tearDown()
 
 class TestCreateImmunization(TestImmunizationBatchRepository): 
 
@@ -41,6 +48,7 @@ def modify_immunization(self, remove_nhs):
 
     def create_immunization_test_logic(self, is_present, remove_nhs):
         """Common logic for testing immunization creation."""
+        self.mock_redis_client.hget.side_effect = ['COVID19']
         self.modify_immunization(remove_nhs)
 
         self.repository.create_immunization(
@@ -65,18 +73,16 @@ def create_immunization_test_logic(self, is_present, remove_nhs):
 
     def test_create_immunization_with_nhs_number(self):
         """Test creating Immunization with NHS number."""
-
         self.create_immunization_test_logic(is_present=True, remove_nhs=False)
 
     def test_create_immunization_without_nhs_number(self):
         """Test creating Immunization without NHS number."""
-
+        
         self.create_immunization_test_logic(is_present=False, remove_nhs=True)    
 
 
     def test_create_immunization_duplicate(self):
         """it should not create Immunization since the request is duplicate"""
-
         self.table.query = MagicMock(return_value={
             "id": imms_id,
             "identifier": [{"system": "test-system", "value": "12345"}],

backend/tests/test_fhir_batch_service.py

@@ -1,16 +1,34 @@
 import unittest
 import uuid
 from copy import deepcopy
-from unittest.mock import Mock, create_autospec
+from unittest.mock import Mock, create_autospec, patch
 from tests.utils.immunization_utils import  create_covid_19_immunization_dict_no_id
 from models.errors import CustomValidationError
 from models.fhir_immunization import ImmunizationValidator
 from fhir_batch_repository import ImmunizationBatchRepository
 from fhir_batch_service import ImmunizationBatchService
 
-class TestCreateImmunizationBatchService(unittest.TestCase):
+
+class TestFhirBatchServiceBase(unittest.TestCase):
+    """Base class for all tests to set up common fixtures"""
 
     def setUp(self):
+        super().setUp()
+        self.redis_patcher = patch("models.utils.validation_utils.redis_client")
+        self.mock_redis_client = self.redis_patcher.start()
+        self.logger_info_patcher = patch("logging.Logger.info")
+        self.mock_logger_info = self.logger_info_patcher.start()
+
+    def tearDown(self):
+        self.redis_patcher.stop()
+        self.logger_info_patcher.stop()
+        super().tearDown()
+
+
+class TestCreateImmunizationBatchService(TestFhirBatchServiceBase):
+
+    def setUp(self):
+        super().setUp()
         self.mock_repo = create_autospec(ImmunizationBatchRepository)
         self.mock_validator = create_autospec(ImmunizationValidator)
         self.mock_table = Mock()
@@ -19,6 +37,14 @@ def setUp(self):
             self.mock_repo, ImmunizationValidator(add_post_validators=False)
         )
 
+    def tearDown(self):
+        super().tearDown()
+        self.mock_repo.reset_mock()
+        self.mock_validator.reset_mock()
+        self.mock_table.reset_mock()
+        self.service = None
+        self.pre_validate_fhir_service = None
+
     def test_create_immunization_valid(self):
         """it should create Immunization and return imms id location"""
 
@@ -57,6 +83,7 @@ def test_create_immunization_post_validation_error(self):
         bad_target_disease_imms = deepcopy(valid_imms)
         bad_target_disease_imms["protocolApplied"][0]["targetDisease"][0]["coding"][0]["code"] = "bad-code"
         expected_msg = "protocolApplied[0].targetDisease[*].coding[?(@.system=='http://snomed.info/sct')].code - ['bad-code'] is not a valid combination of disease codes for this service"
+        self.mock_redis_client.hget.return_value = None  # Reset mock for invalid cases
         with self.assertRaises(CustomValidationError) as error:
             self.pre_validate_fhir_service.create_immunization(
                 immunization=bad_target_disease_imms, 
@@ -69,9 +96,10 @@ def test_create_immunization_post_validation_error(self):
         self.mock_repo.create_immunization.assert_not_called() 
 
 
-class TestUpdateImmunizationBatchService(unittest.TestCase):
+class TestUpdateImmunizationBatchService(TestFhirBatchServiceBase):
 
     def setUp(self):
+        super().setUp()
         self.mock_repo = create_autospec(ImmunizationBatchRepository)
         self.mock_validator = create_autospec(ImmunizationValidator)
         self.mock_table = Mock()
@@ -80,6 +108,14 @@ def setUp(self):
             self.mock_repo, ImmunizationValidator(add_post_validators=False)
         )
 
+    def tearDown(self):
+        super().tearDown()
+        self.mock_repo.reset_mock()
+        self.mock_validator.reset_mock()
+        self.mock_table.reset_mock()
+        self.service = None
+        self.pre_validate_fhir_service = None
+
     def test_update_immunization_valid(self):
         """it should update Immunization and return imms id"""
 
@@ -114,6 +150,8 @@ def test_update_immunization_pre_validation_error(self):
     def test_update_immunization_post_validation_error(self):
         """it should return error since it got failed in initial validation"""
 
+        self.mock_redis_client.hget.return_value = None  # Reset mock for invalid cases
+
         valid_imms = create_covid_19_immunization_dict_no_id()
         bad_target_disease_imms = deepcopy(valid_imms)
         bad_target_disease_imms["protocolApplied"][0]["targetDisease"][0]["coding"][0]["code"] = "bad-code"