VED-382: Use configurable disease mappings in backend. (#618)

* remock for redis
* clean up test_utils
* PYTHONPATH for builds
* remove relative paths
* remocked batch service
* remock test imm post valid
* remock test_fhir_repo

Author: mfjarvis

.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/mappings.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/constants.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

@@ -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/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

@@ -6,8 +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, [])