Add chronic condition api (#2775)

Add chronic condition api (#2775)

care/audit_log/middleware.py

@@ -16,7 +16,7 @@ class RequestInformation(NamedTuple):
     exception: Exception | None
 
 
-logger = logging.getLogger(__name__)
+logger = logging.getLogger("audit_log")
 
 
 class AuditLogMiddleware:

care/emr/api/viewsets/allergy_intolerance.py

@@ -67,7 +67,6 @@ def authorize_create(self, instance):
             "can_write_patient_obj", self.request.user, self.get_patient_obj()
         ):
             raise PermissionDenied("You do not have permission to update encounter")
-        # TODO If there is an encounter, check access to the encounter
 
     def get_queryset(self):
         if not AuthorizationController.call(

care/emr/api/viewsets/base.py

@@ -145,13 +145,14 @@ def perform_update(self, instance):
                     updated_by=self.request.user,
                 )
 
-    def clean_update_data(self, request_data):
+    def clean_update_data(self, request_data, keep_fields: set | None = None):
         if type(request_data) is list:
             return request_data
-        request_data.pop("id", None)
-        request_data.pop("external_id", None)
-        request_data.pop("patient", None)
-        request_data.pop("encounter", None)
+        ignored_fields = {"id", "external_id", "patient", "encounter"}
+        if keep_fields:
+            ignored_fields = ignored_fields - set(keep_fields)
+        for field in ignored_fields:
+            request_data.pop(field, None)
         return request_data
 
     def update(self, request, *args, **kwargs):

care/emr/api/viewsets/condition.py

@@ -1,22 +1,34 @@
-from django.shortcuts import get_object_or_404
 from django_filters import CharFilter, FilterSet, UUIDFilter
 from django_filters.rest_framework import DjangoFilterBackend
-from rest_framework.exceptions import ValidationError
+from rest_framework.exceptions import PermissionDenied, ValidationError
+from rest_framework.generics import get_object_or_404
 
-from care.emr.api.viewsets.base import EMRModelViewSet, EMRQuestionnaireResponseMixin
+from care.emr.api.viewsets.base import (
+    EMRBaseViewSet,
+    EMRCreateMixin,
+    EMRListMixin,
+    EMRModelViewSet,
+    EMRQuestionnaireResponseMixin,
+    EMRRetrieveMixin,
+    EMRUpdateMixin,
+    EMRUpsertMixin,
+)
 from care.emr.api.viewsets.encounter_authz_base import EncounterBasedAuthorizationBase
 from care.emr.models.condition import Condition
 from care.emr.models.encounter import Encounter
+from care.emr.models.patient import Patient
 from care.emr.registries.system_questionnaire.system_questionnaire import (
     InternalQuestionnaireRegistry,
 )
 from care.emr.resources.condition.spec import (
     CategoryChoices,
+    ChronicConditionUpdateSpec,
+    ConditionReadSpec,
     ConditionSpec,
-    ConditionSpecRead,
-    ConditionSpecUpdate,
+    ConditionUpdateSpec,
 )
 from care.emr.resources.questionnaire.spec import SubjectType
+from care.security.authorization import AuthorizationController
 
 
 class ValidateEncounterMixin:
@@ -54,8 +66,8 @@ class SymptomViewSet(
 ):
     database_model = Condition
     pydantic_model = ConditionSpec
-    pydantic_read_model = ConditionSpecRead
-    pydantic_update_model = ConditionSpecUpdate
+    pydantic_read_model = ConditionReadSpec
+    pydantic_update_model = ConditionUpdateSpec
     # Filters
     filterset_class = ConditionFilters
     filter_backends = [DjangoFilterBackend]
@@ -94,8 +106,8 @@ class DiagnosisViewSet(
 ):
     database_model = Condition
     pydantic_model = ConditionSpec
-    pydantic_read_model = ConditionSpecRead
-    pydantic_update_model = ConditionSpecUpdate
+    pydantic_read_model = ConditionReadSpec
+    pydantic_update_model = ConditionUpdateSpec
 
     # Filters
     filterset_class = ConditionFilters
@@ -125,3 +137,72 @@ def get_queryset(self):
 
 
 InternalQuestionnaireRegistry.register(DiagnosisViewSet)
+
+
+class ChronicConditionViewSet(
+    EMRQuestionnaireResponseMixin,
+    EMRCreateMixin,
+    EMRRetrieveMixin,
+    EMRUpdateMixin,
+    EMRListMixin,
+    EMRBaseViewSet,
+    EMRUpsertMixin,
+):
+    database_model = Condition
+    pydantic_model = ConditionSpec
+    pydantic_read_model = ConditionReadSpec
+    pydantic_update_model = ChronicConditionUpdateSpec
+
+    # Filters
+    filterset_class = ConditionFilters
+    filter_backends = [DjangoFilterBackend]
+    # Questionnaire Spec
+    questionnaire_type = "chronic_condition"
+    questionnaire_title = "Chronic Condition"
+    questionnaire_description = "Chronic Condition"
+    questionnaire_subject_type = SubjectType.patient.value
+
+    def get_patient_obj(self):
+        return get_object_or_404(
+            Patient, external_id=self.kwargs["patient_external_id"]
+        )
+
+    def authorize_create(self, instance):
+        if not AuthorizationController.call(
+            "can_write_patient_obj", self.request.user, self.get_patient_obj()
+        ):
+            raise PermissionDenied("You do not have permission to update encounter")
+
+    def authorize_update(self, request_obj, model_instance):
+        encounter = get_object_or_404(Encounter, external_id=request_obj.encounter)
+        if not AuthorizationController.call(
+            "can_update_encounter_obj",
+            self.request.user,
+            encounter,
+        ):
+            raise PermissionDenied("You do not have permission to update encounter")
+
+    def perform_create(self, instance):
+        instance.category = CategoryChoices.chronic_condition.value
+        super().perform_create(instance)
+
+    def clean_update_data(self, request_data):
+        return super().clean_update_data(request_data, keep_fields={"encounter"})
+
+    def get_queryset(self):
+        if not AuthorizationController.call(
+            "can_view_clinical_data", self.request.user, self.get_patient_obj()
+        ):
+            raise PermissionDenied("Permission denied for patient data")
+        return (
+            super()
+            .get_queryset()
+            .filter(
+                patient__external_id=self.kwargs["patient_external_id"],
+                category=CategoryChoices.chronic_condition.value,
+            )
+            .select_related("patient", "encounter", "created_by", "updated_by")
+        )
+
+
+InternalQuestionnaireRegistry.register(ChronicConditionViewSet)

care/emr/migrations/0012_alter_condition_encounter.py

@@ -0,0 +1,19 @@
+# Generated by Django 5.1.4 on 2025-01-24 07:58
+
+import django.db.models.deletion
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('emr', '0011_medicationrequest_requester'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='condition',
+            name='encounter',
+            field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='emr.encounter'),
+        ),
+    ]

care/emr/models/condition.py

@@ -11,7 +11,9 @@ class Condition(EMRBaseModel):
     code = models.JSONField(default=dict, null=False, blank=False)
     body_site = models.JSONField(default=dict, null=False, blank=False)
     patient = models.ForeignKey("emr.Patient", on_delete=models.CASCADE)
-    encounter = models.ForeignKey("emr.Encounter", on_delete=models.CASCADE)
+    encounter = models.ForeignKey(
+        "emr.Encounter", on_delete=models.CASCADE, null=True, blank=True
+    )
     onset = models.JSONField(default=dict)
     abatement = models.JSONField(default=dict)
     recorded_date = models.DateTimeField(null=True, blank=True)

care/emr/resources/condition/spec.py

@@ -2,6 +2,7 @@
 from enum import Enum
 
 from pydantic import UUID4, Field, field_validator
+from rest_framework.generics import get_object_or_404
 
 from care.emr.fhir.schema.base import Coding
 from care.emr.models.condition import Condition
@@ -96,7 +97,7 @@ def perform_extra_deserialization(self, is_update, obj):
             obj.patient = obj.encounter.patient
 
 
-class ConditionSpecRead(BaseConditionSpec):
+class ConditionReadSpec(BaseConditionSpec):
     """
     Validation for deeper models may not be required on read, Just an extra optimisation
     """
@@ -119,15 +120,16 @@ class ConditionSpecRead(BaseConditionSpec):
     @classmethod
     def perform_extra_serialization(cls, mapping, obj):
         mapping["id"] = obj.external_id
-        mapping["encounter"] = obj.encounter.external_id
+        if obj.encounter:
+            mapping["encounter"] = obj.encounter.external_id
 
         if obj.created_by:
             mapping["created_by"] = UserSpec.serialize(obj.created_by)
         if obj.updated_by:
             mapping["updated_by"] = UserSpec.serialize(obj.updated_by)
 
 
-class ConditionSpecUpdate(BaseConditionSpec):
+class ConditionUpdateSpec(BaseConditionSpec):
     clinical_status: ClinicalStatusChoices | None = None
     verification_status: VerificationStatusChoices
     severity: SeverityChoices | None = None
@@ -142,3 +144,11 @@ def validate_code(cls, code: int):
         return validate_valueset(
             "code", cls.model_fields["code"].json_schema_extra["slug"], code
         )
+
+
+class ChronicConditionUpdateSpec(ConditionUpdateSpec):
+    encounter: UUID4
+
+    def perform_extra_deserialization(self, is_update, obj):
+        if self.encounter:
+            obj.encounter = get_object_or_404(Encounter, external_id=self.encounter)

care/emr/tests/test_booking_api.py

@@ -1,5 +1,6 @@
 from datetime import UTC, datetime, timedelta
 
+from django.test.utils import ignore_warnings
 from django.urls import reverse
 
 from care.emr.models import (
@@ -20,6 +21,7 @@
 from config.patient_otp_authentication import PatientOtpObject
 
 
+@ignore_warnings(category=RuntimeWarning, message=r".*received a naive datetime.*")
 class TestBookingViewSet(CareAPITestBase):
     def setUp(self):
         super().setUp()
@@ -376,6 +378,7 @@ def test_list_available_users(self):
         self.assertGreaterEqual(len(response.data["users"]), 1)
 
 
+@ignore_warnings(category=RuntimeWarning, message=r".*received a naive datetime.*")
 class TestSlotViewSetAppointmentApi(CareAPITestBase):
     def setUp(self):
         super().setUp()
@@ -582,6 +585,7 @@ def test_over_booking_a_slot(self):
         self.assertContains(response, status_code=400, text="Slot is already full")
 
 
+@ignore_warnings(category=RuntimeWarning, message=r".*received a naive datetime.*")
 class TestSlotViewSetSlotStatsApis(CareAPITestBase):
     def setUp(self):
         super().setUp()
@@ -932,6 +936,7 @@ def test_availability_heatmap_slots_same_as_get_slots_for_day_with_exceptions(se
             self.assertEqual(slot_stats["total_slots"], total_slots_for_day)
 
 
+@ignore_warnings(category=RuntimeWarning, message=r".*received a naive datetime.*")
 class TestOtpSlotViewSet(CareAPITestBase):
     def setUp(self):
         super().setUp()