Merge pull request #2814 from ohcnetwork/develop

Merge Develop To Staging v3.1.0

Makefile

@@ -54,6 +54,11 @@ migrate:
 
 test:
 	docker compose exec backend bash -c "python manage.py test $(path) --keepdb --parallel --shuffle"
+
+test-no-keep:
+	docker compose exec backend bash -c "python manage.py test $(path) --parallel --shuffle"
+
+
 test-coverage:
 	docker compose exec backend bash -c "coverage run manage.py test --settings=config.settings.test --keepdb --parallel --shuffle"
 	docker compose exec backend bash -c "coverage combine || true; coverage xml"

Pipfile

@@ -6,7 +6,7 @@ name = "pypi"
 [packages]
 argon2-cffi = "==23.1.0"
 authlib = "==1.4.0"
-boto3 = "==1.36.7"
+boto3 = "==1.36.12"
 celery = "==5.4.0"
 django = "==5.1.4"
 django-environ = "==0.12.0"
@@ -23,7 +23,7 @@ djangorestframework = "==3.15.2"
 djangorestframework-simplejwt = "==5.4.0"
 dry-rest-permissions = "==0.1.10"
 drf-nested-routers = "==0.94.1"
-drf-spectacular = "==0.27.2"
+drf-spectacular = "==0.28.0"
 gunicorn = "==23.0.0"
 healthy-django = "==0.1.0"
 json-fingerprint = "==0.14.0"
@@ -43,17 +43,17 @@ sentry-sdk = "==2.18.0"
 whitenoise = "==6.8.2"
 django-anymail = {extras = ["amazon-ses"], version = "*"}
 pydantic-extra-types = "2.10.2"
-phonenumberslite = "==8.13.52"
+phonenumberslite = "==8.13.54"
 
 [dev-packages]
 boto3-stubs = { extras = ["s3", "boto3"], version = "*" }
 coverage = "==7.6.10"
-debugpy = "==1.8.11"
+debugpy = "==1.8.12"
 django-coverage-plugin = "==3.1.0"
 django-extensions = "==3.2.3"
 django-silk = "==5.3.2"
 djangorestframework-stubs = "==3.15.2"
-factory-boy = "==3.3.1"
+factory-boy = "==3.3.3"
 freezegun = "==1.5.1"
 ipython = "==8.31.0"
 mypy = "==1.14.1"

care/emr/api/viewsets/allergy_intolerance.py

@@ -1,3 +1,6 @@
+import uuid
+
+from django.db import transaction
 from django_filters import CharFilter, FilterSet
 from django_filters import rest_framework as filters
 from django_filters.rest_framework import DjangoFilterBackend
@@ -68,6 +71,22 @@ def authorize_create(self, instance):
         ):
             raise PermissionDenied("You do not have permission to update encounter")
 
+    def perform_update(self, instance):
+        """
+        Updates need to check if the encounter of the instance has been changed, If, so a copy object needs to be created.
+        """
+        database_copy = AllergyIntolerance.objects.get(id=instance.id)
+        with transaction.atomic():
+            if database_copy.encounter != instance.encounter:
+                database_copy.copied_from = database_copy.id
+                database_copy.id = None
+                database_copy.external_id = uuid.uuid4()
+                database_copy.save()
+                AllergyIntolerance.objects.filter(
+                    encounter=instance.encounter, copied_from=instance.id
+                ).delete()
+            return super().perform_update(instance)
+
     def authorize_update(self, request_obj, model_instance):
         encounter = get_object_or_404(Encounter, external_id=request_obj.encounter)
         if not AuthorizationController.call(
@@ -81,17 +100,31 @@ 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 (
+        queryset = (
             super()
             .get_queryset()
             .filter(patient__external_id=self.kwargs["patient_external_id"])
             .select_related("patient", "encounter", "created_by", "updated_by")
             .order_by("-modified_date")
         )
 
+        if not AuthorizationController.call(
+            "can_view_clinical_data", self.request.user, self.get_patient_obj()
+        ):
+            encounter = Encounter.objects.filter(
+                external_id=self.request.GET.get("encounter")
+            ).first()
+
+            # Check for encounter access
+            if not encounter or not AuthorizationController.call(
+                "can_view_encounter_obj", self.request.user, encounter
+            ):
+                raise PermissionDenied("Permission denied to user")
+            queryset = queryset.filter(encounter=encounter)
+
+        else:
+            queryset = queryset.filter(copied_from__isnull=True)
+        return queryset
+
 
 InternalQuestionnaireRegistry.register(AllergyIntoleranceViewSet)

care/emr/api/viewsets/location.py

@@ -43,6 +43,14 @@
 class FacilityLocationFilter(filters.FilterSet):
     parent = filters.UUIDFilter(field_name="parent__external_id")
     name = filters.CharFilter(field_name="name", lookup_expr="icontains")
+    mode = filters.CharFilter(field_name="mode", lookup_expr="iexact")
+    availability_status = filters.CharFilter(
+        field_name="availability_status", lookup_expr="iexact"
+    )
+    operational_status = filters.CharFilter(
+        field_name="operational_status", lookup_expr="iexact"
+    )
+    status = filters.CharFilter(field_name="status", lookup_expr="iexact")
 
 
 class FacilityLocationViewSet(EMRModelViewSet):

care/emr/api/viewsets/medication_administration.py

@@ -9,6 +9,7 @@
 from care.emr.resources.medication.administration.spec import (
     MedicationAdministrationReadSpec,
     MedicationAdministrationSpec,
+    MedicationAdministrationUpdateSpec,
 )
 from care.emr.resources.questionnaire.spec import SubjectType
 
@@ -25,6 +26,7 @@ class MedicationAdministrationViewSet(
 ):
     database_model = MedicationAdministration
     pydantic_model = MedicationAdministrationSpec
+    pydantic_update_model = MedicationAdministrationUpdateSpec
     pydantic_read_model = MedicationAdministrationReadSpec
     questionnaire_type = "medication_administration"
     questionnaire_title = "Medication Administration"

care/emr/api/viewsets/questionnaire.py

@@ -67,6 +67,7 @@ class QuestionnaireFilter(filters.FilterSet):
     title = filters.CharFilter(field_name="title", lookup_expr="icontains")
     subject_type = filters.CharFilter(field_name="subject_type", lookup_expr="iexact")
     tag_slug = QuestionnaireTagSlugFilter(field_name="tag_slug")
+    status = filters.CharFilter(field_name="status", lookup_expr="iexact")
 
 
 class QuestionnaireViewSet(EMRModelViewSet):

care/emr/api/viewsets/scheduling/schedule.py

@@ -15,6 +15,7 @@
 from care.emr.models.scheduling.booking import TokenSlot
 from care.emr.models.scheduling.schedule import Availability, Schedule
 from care.emr.resources.scheduling.schedule.spec import (
+    AvailabilityCreateSpec,
     AvailabilityForScheduleSpec,
     ScheduleCreateSpec,
     ScheduleReadSpec,
@@ -132,7 +133,8 @@ def get_queryset(self):
 
 class AvailabilityViewSet(EMRCreateMixin, EMRDestroyMixin, EMRBaseViewSet):
     database_model = Availability
-    pydantic_model = AvailabilityForScheduleSpec
+    pydantic_model = AvailabilityCreateSpec
+    pydantic_retrieve_model = AvailabilityForScheduleSpec
 
     def get_facility_obj(self):
         return get_object_or_404(
@@ -164,6 +166,10 @@ def get_queryset(self):
             .order_by("-modified_date")
         )
 
+    def clean_create_data(self, request_data):
+        request_data["schedule"] = self.kwargs["schedule_external_id"]
+        return request_data
+
     def perform_create(self, instance):
         schedule = self.get_schedule_obj()
         instance.schedule = schedule

care/emr/api/viewsets/user.py

@@ -72,8 +72,9 @@ def perform_create(self, instance):
 
     def authorize_update(self, request_obj, model_instance):
         if self.request.user.is_superuser:
-            return True
-        return self.request.user.id == model_instance.id
+            return
+        if not self.request.user.id == model_instance.id:
+            raise PermissionDenied("You do not have permission to update this user")
 
     def authorize_create(self, instance):
         if not AuthorizationController.call("can_create_user", self.request.user):

care/emr/migrations/0016_allergyintolerance_copied_from.py

@@ -0,0 +1,18 @@
+# Generated by Django 5.1.4 on 2025-02-04 17:40
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('emr', '0015_facilitylocation_availability_status_and_more'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='allergyintolerance',
+            name='copied_from',
+            field=models.BigIntegerField(blank=True, default=None, null=True),
+        ),
+    ]

care/emr/models/allergy_intolerance.py

@@ -15,3 +15,6 @@ class AllergyIntolerance(EMRBaseModel):
     recorded_date = models.DateTimeField(null=True, blank=True)
     last_occurrence = models.DateTimeField(null=True, blank=True)
     note = models.TextField(null=True, blank=True)
+    copied_from = models.BigIntegerField(
+        default=None, null=True, blank=True
+    )  # If True, the record is a copy maintained of the given ID

care/emr/resources/allergy_intolerance/spec.py

@@ -123,6 +123,7 @@ class AllergyIntoleranceReadSpec(BaseAllergyIntoleranceSpec):
     recorded_date: datetime.datetime | None = None
     created_by: dict = {}
     updated_by: dict = {}
+    note: str | None = None
 
     @classmethod
     def perform_extra_serialization(cls, mapping, obj):

care/emr/resources/encounter/constants.py

@@ -59,7 +59,7 @@ class DischargeDispositionChoices(str, Enum):
 
 class DietPreferenceChoices(str, Enum):
     vegetarian = "vegetarian"
-    diary_free = "diary_free"
+    dairy_free = "dairy_free"
     nut_free = "nut_free"
     gluten_free = "gluten_free"
     vegan = "vegan"

care/emr/resources/encounter/spec.py

@@ -4,7 +4,12 @@
 from django.utils import timezone
 from pydantic import UUID4, BaseModel, model_validator
 
-from care.emr.models import Encounter, EncounterOrganization, TokenBooking
+from care.emr.models import (
+    Encounter,
+    EncounterOrganization,
+    FacilityLocationEncounter,
+    TokenBooking,
+)
 from care.emr.models.patient import Patient
 from care.emr.resources.base import EMRResource
 from care.emr.resources.encounter.constants import (
@@ -17,10 +22,12 @@
 )
 from care.emr.resources.facility.spec import FacilityBareMinimumSpec
 from care.emr.resources.facility_organization.spec import FacilityOrganizationReadSpec
-from care.emr.resources.location.spec import FacilityLocationListSpec
+from care.emr.resources.location.spec import (
+    FacilityLocationEncounterListSpecWithLocation,
+    FacilityLocationListSpec,
+)
 from care.emr.resources.patient.spec import PatientListSpec
 from care.emr.resources.scheduling.slot.spec import TokenBookingReadSpec
-from care.emr.resources.user.spec import UserSpec
 from care.facility.models import Facility
 
 
@@ -118,6 +125,7 @@ class EncounterRetrieveSpec(EncounterListSpec):
     updated_by: dict = {}
     organizations: list[dict] = []
     current_location: dict | None = None
+    location_history: list[dict] = []
 
     @classmethod
     def perform_extra_serialization(cls, mapping, obj):
@@ -136,7 +144,10 @@ def perform_extra_serialization(cls, mapping, obj):
             mapping["current_location"] = FacilityLocationListSpec.serialize(
                 obj.current_location
             ).to_json()
-        if obj.created_by:
-            mapping["created_by"] = UserSpec.serialize(obj.created_by)
-        if obj.updated_by:
-            mapping["updated_by"] = UserSpec.serialize(obj.updated_by)
+        mapping["location_history"] = [
+            FacilityLocationEncounterListSpecWithLocation.serialize(i)
+            for i in FacilityLocationEncounter.objects.filter(encounter=obj).order_by(
+                "-created_date"
+            )
+        ]
+        cls.serialize_audit_users(mapping, obj)

care/emr/resources/location/spec.py

@@ -161,6 +161,26 @@ class FacilityLocationEncounterUpdateSpec(FacilityLocationEncounterBaseSpec):
     end_datetime: datetime.datetime | None = None
 
 
+class FacilityLocationEncounterListSpec(FacilityLocationEncounterBaseSpec):
+    encounter: UUID4
+    start_datetime: datetime.datetime
+    end_datetime: datetime.datetime | None = None
+    status: str
+
+    @classmethod
+    def perform_extra_serialization(cls, mapping, obj):
+        mapping["id"] = obj.external_id
+
+
+class FacilityLocationEncounterListSpecWithLocation(FacilityLocationEncounterListSpec):
+    location: dict
+
+    @classmethod
+    def perform_extra_serialization(cls, mapping, obj):
+        super().perform_extra_serialization(mapping, obj)
+        mapping["location"] = FacilityLocationListSpec.serialize(obj.location).to_json()
+
+
 class FacilityLocationEncounterReadSpec(FacilityLocationEncounterBaseSpec):
     encounter: UUID4
     start_datetime: datetime.datetime

care/emr/resources/medication/administration/spec.py

@@ -142,10 +142,8 @@ class BaseMedicationAdministrationSpec(EMRResource):
     occurrence_period_start: datetime = Field(
         description="When the medication was administration started",
     )
-    occurrence_period_end: datetime | None = Field(
-        None,
-        description="When the medication administration ended. If not provided, it is assumed to be ongoing",
-    )
+    occurrence_period_end: datetime | None = None
+
     recorded: datetime | None = Field(
         None,
         description="When administration was recorded",
@@ -167,10 +165,7 @@ class BaseMedicationAdministrationSpec(EMRResource):
         description="The dosage of the medication",
     )
 
-    note: str | None = Field(
-        None,
-        description="Any additional notes about the medication",
-    )
+    note: str | None = None
 
 
 class MedicationAdministrationSpec(BaseMedicationAdministrationSpec):
@@ -217,6 +212,15 @@ def perform_extra_deserialization(self, is_update, obj):
             obj.request = MedicationRequest.objects.get(external_id=self.request)
 
 
+class MedicationAdministrationUpdateSpec(EMRResource):
+    __model__ = MedicationAdministration
+    __exclude__ = ["patient", "encounter", "request"]
+
+    status: MedicationAdministrationStatus
+    note: str | None = None
+    occurrence_period_end: datetime | None = None
+
+
 class MedicationAdministrationReadSpec(BaseMedicationAdministrationSpec):
     created_by: UserSpec = dict
 

care/emr/resources/questionnaire/utils.py

@@ -225,21 +225,22 @@ def create_observation_spec(questionnaire, responses, parent_id=None):
         for value in responses[questionnaire["id"]].values:
             observation = spec.copy()
             observation["id"] = str(uuid.uuid4())
-            if questionnaire["type"] == QuestionType.choice.value and value.value_code:
-                observation["value"] = {
-                    "value_code": (value.value_code.model_dump(exclude_defaults=True))
-                }
+            if questionnaire["type"] == QuestionType.choice.value and value.code:
+                observation["value"] = value.value_code.model_dump(
+                    exclude_defaults=True
+                )
+
             elif (
                 questionnaire["type"] == QuestionType.quantity.value
                 and value.value_quantity
             ):
-                observation["value"] = {
-                    "value_quantity": (
-                        value.value_quantity.model_dump(exclude_defaults=True)
-                    )
-                }
+                observation["value"] = value.value_quantity.model_dump(
+                    exclude_defaults=True
+                )
             elif value:
                 observation["value"] = {"value": value.value}
+                if "unit" in questionnaire:
+                    observation["value"]["unit"] = questionnaire["unit"]
             if responses[questionnaire["id"]].note:
                 observation["note"] = responses[questionnaire["id"]].note
         if parent_id: