Merge pull request #1252 from coronasafe/feat/discharge-summary

refactor discharge summary endpoints

.github/workflows/deployment-lambda.yaml

@@ -0,0 +1,64 @@
+name: Lambda Deployment
+
+on:
+  workflow_dispatch:
+
+  pull_request:
+    branches:
+      - devops/lambda-changes
+    paths-ignore:
+      - "docs/**"
+
+jobs:
+
+  build-image:
+    name: Build & Push Staging to container registries
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Docker meta
+        id: meta
+        uses: docker/metadata-action@v4
+        with:
+          images: |
+            ghcr.io/${{ github.repository }}
+          tags: |
+            type=raw,value=${{ github.head_ref}}-${{ github.run_number }}
+            type=raw,value=${{ github.head_ref}}
+
+          flavor: |
+            latest=true
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Cache Docker layers
+        uses: actions/cache@v2
+        with:
+          path: /tmp/.buildx-cache
+          key: ${{ runner.os }}-buildx-${{ hashFiles('r*/base.txt', 'r*/production.txt', 'Dockerfile') }}
+          restore-keys: |
+            ${{ runner.os }}-buildx-
+
+      - name: Login to GitHub Container Registry
+        uses: docker/login-action@v2
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build image
+        uses: docker/build-push-action@v3
+        with:
+          context: .
+          file: lambda_Dockerfile
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          cache-from: type=local,src=/tmp/.buildx-cache
+          cache-to: type=local,mode=max,dest=/tmp/.buildx-cache-new
+
+      - name: Move cache
+        run: |
+          rm -rf /tmp/.buildx-cache
+          mv /tmp/.buildx-cache-new /tmp/.buildx-cache

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ default_stages: [commit]
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.2.0
+    rev: v4.4.0
     hooks:
       - id: check-merge-conflict
       - id: end-of-file-fixer
@@ -12,19 +12,19 @@ repos:
         args: [--markdown-linebreak-ext=md]
 
   - repo: https://github.com/PyCQA/isort
-    rev: 5.10.1
+    rev: 5.11.5
     hooks:
       - id: isort
         additional_dependencies: ["isort[pyproject]"]
 
   - repo: https://github.com/psf/black
-    rev: 22.3.0
+    rev: 23.3.0
     hooks:
       - id: black
         args: ["--config=pyproject.toml"]
 
   - repo: https://github.com/PyCQA/flake8
-    rev: 4.0.1
+    rev: 6.0.0
     hooks:
       - id: flake8
         args: ["--config=.flake8"]

care/facility/api/serializers/facility_capacity.py

@@ -9,6 +9,19 @@ class FacilityCapacitySerializer(serializers.ModelSerializer):
     room_type_text = ChoiceField(choices=ROOM_TYPES, read_only=True, source="room_type")
     id = serializers.UUIDField(source="external_id", read_only=True)
 
+    def validate(self, data):
+        if (
+            data.get("current_capacity")
+            and data.get("total_capacity")
+            and data["current_capacity"] > data["total_capacity"]
+        ):
+            raise serializers.ValidationError(
+                {
+                    "current_capacity": "Current capacity cannot be greater than total capacity."
+                }
+            )
+        return data
+
     class Meta:
         model = FacilityCapacity
         read_only_fields = (

care/facility/api/serializers/patient_consultation.py

@@ -1,5 +1,6 @@
 from datetime import timedelta
 
+from django.db import transaction
 from django.utils.timezone import localtime, now
 from rest_framework import serializers
 from rest_framework.exceptions import ValidationError
@@ -22,6 +23,7 @@
     SuggestionChoices,
 )
 from care.facility.models.patient_consultation import PatientConsultation
+from care.facility.static_data.icd11 import get_icd11_diagnoses_objects_by_ids
 from care.users.api.serializers.user import (
     UserAssignedSerializer,
     UserBaseMinimumSerializer,
@@ -97,23 +99,11 @@ class PatientConsultationSerializer(serializers.ModelSerializer):
         read_only=True
     )
 
-    def get_icd11_diagnoses_objects_by_ids(self, diagnoses_ids):
-        from care.facility.static_data.icd11 import ICDDiseases
-
-        diagnosis_objects = []
-        for diagnosis in diagnoses_ids:
-            try:
-                diagnosis_object = ICDDiseases.by.id[diagnosis].__dict__
-                diagnosis_objects.append(diagnosis_object)
-            except BaseException:
-                pass
-        return diagnosis_objects
-
     def get_icd11_diagnoses_object(self, consultation):
-        return self.get_icd11_diagnoses_objects_by_ids(consultation.icd11_diagnoses)
+        return get_icd11_diagnoses_objects_by_ids(consultation.icd11_diagnoses)
 
     def get_icd11_provisional_diagnoses_object(self, consultation):
-        return self.get_icd11_diagnoses_objects_by_ids(
+        return get_icd11_diagnoses_objects_by_ids(
             consultation.icd11_provisional_diagnoses
         )
 
@@ -383,6 +373,61 @@ def validate(self, attrs):
         return validated
 
 
+class PatientConsultationDischargeSerializer(serializers.ModelSerializer):
+    discharge_reason = serializers.ChoiceField(
+        choices=DISCHARGE_REASON_CHOICES, required=True
+    )
+    discharge_notes = serializers.CharField(required=True)
+
+    discharge_date = serializers.DateTimeField(required=False)
+    discharge_prescription = serializers.JSONField(required=False)
+    discharge_prn_prescription = serializers.JSONField(required=False)
+
+    death_datetime = serializers.DateTimeField(required=False, allow_null=True)
+    death_confirmed_doctor = serializers.CharField(required=False, allow_null=True)
+
+    class Meta:
+        model = PatientConsultation
+        fields = (
+            "discharge_reason",
+            "discharge_notes",
+            "discharge_date",
+            "discharge_prescription",
+            "discharge_prn_prescription",
+            "death_datetime",
+            "death_confirmed_doctor",
+        )
+
+    def validate(self, attrs):
+        if attrs.get("discharge_reason") == "EXP":
+            if not attrs.get("death_datetime"):
+                raise ValidationError({"death_datetime": "This field is required"})
+            if not attrs.get("death_confirmed_doctor"):
+                raise ValidationError(
+                    {"death_confirmed_doctor": "This field is required"}
+                )
+            attrs["discharge_date"] = now()
+        elif not attrs.get("discharge_date"):
+            raise ValidationError({"discharge_date": "This field is required"})
+        return attrs
+
+    def save(self, **kwargs):
+        with transaction.atomic():
+            instance = super().save(**kwargs)
+            patient: PatientRegistration = instance.patient
+            patient.is_active = False
+            patient.allow_transfer = True
+            patient.review_time = None
+            patient.save(update_fields=["allow_transfer", "is_active", "review_time"])
+            ConsultationBed.objects.filter(
+                consultation=self.instance, end_date__isnull=True
+            ).update(end_date=now())
+            return instance
+
+    def create(self, validated_data):
+        raise NotImplementedError
+
+
 class PatientConsultationIDSerializer(serializers.ModelSerializer):
     consultation_id = serializers.UUIDField(source="external_id", read_only=True)
     patient_id = serializers.UUIDField(source="patient.external_id", read_only=True)

care/facility/api/viewsets/patient.py

@@ -4,11 +4,9 @@
 
 from django.conf import settings
 from django.contrib.postgres.search import TrigramSimilarity
-from django.core.validators import validate_email
 from django.db import models
 from django.db.models import Case, When
 from django.db.models.query_utils import Q
-from django.utils.timezone import localtime, now
 from django_filters import rest_framework as filters
 from djqscsv import render_to_csv_response
 from dry_rest_permissions.generics import DRYPermissionFiltersBase, DRYPermissions
@@ -44,16 +42,14 @@
     DailyRound,
     Facility,
     FacilityPatientStatsHistory,
-    PatientConsultation,
     PatientNotes,
     PatientRegistration,
     PatientSearch,
     ShiftingRequest,
 )
 from care.facility.models.base import covert_choice_dict
-from care.facility.models.bed import AssetBed, ConsultationBed
+from care.facility.models.bed import AssetBed
 from care.facility.models.patient_base import DISEASE_STATUS_DICT
-from care.facility.tasks.patient.discharge_report import generate_discharge_report
 from care.users.models import User
 from care.utils.cache.cache_allowed_facilities import get_accessible_facilities
 from care.utils.filters import CareChoiceFilter, MultiSelectFilter
@@ -397,79 +393,6 @@ def list(self, request, *args, **kwargs):
 
         return super(PatientViewSet, self).list(request, *args, **kwargs)
 
-    @action(detail=True, methods=["POST"])
-    def discharge_patient(self, request, *args, **kwargs):
-        discharged = bool(request.data.get("discharge", False))
-        patient = self.get_object()
-        patient.is_active = discharged
-        patient.allow_transfer = not discharged
-        patient.review_time = None
-        patient.save(update_fields=["allow_transfer", "is_active", "review_time"])
-        last_consultation = (
-            PatientConsultation.objects.filter(patient=patient).order_by("-id").first()
-        )
-        current_time = localtime(now())
-        if last_consultation:
-            reason = request.data.get("discharge_reason")
-            notes = request.data.get("discharge_notes", "")
-            if reason not in DISCHARGE_REASONS:
-                raise serializers.ValidationError(
-                    {"discharge_reason": "discharge reason is not valid"}
-                )
-            discharge_date = request.data.get("discharge_date", "")
-            last_consultation.discharge_reason = reason
-            last_consultation.discharge_notes = notes
-            if last_consultation.discharge_date is None:
-                if discharge_date:
-                    last_consultation.discharge_date = discharge_date
-                else:
-                    last_consultation.discharge_date = current_time
-            last_consultation.current_bed = None
-            if reason == "EXP":
-                death_datetime = request.data.get("death_datetime")
-                death_confirmed_doctor = request.data.get("death_confirmed_doctor")
-                if death_datetime is None:
-                    raise serializers.ValidationError(
-                        {"death_datetime": "Please provide death date and time"}
-                    )
-                if death_confirmed_doctor is None:
-                    raise serializers.ValidationError(
-                        {"death_confirmed_doctor": "Please provide doctor details"}
-                    )
-                last_consultation.death_datetime = death_datetime
-                last_consultation.death_confirmed_doctor = death_confirmed_doctor
-            if reason == "REC":
-                discharge_prescription = request.data.get("discharge_prescription", [])
-                discharge_prn_prescription = request.data.get(
-                    "discharge_prn_prescription", []
-                )
-                if discharge_date is None:
-                    raise serializers.ValidationError(
-                        {"discharge_date": "Please set the discharge date"}
-                    )
-                last_consultation.discharge_prescription = discharge_prescription
-                last_consultation.discharge_prn_prescription = (
-                    discharge_prn_prescription
-                )
-                last_consultation.discharge_date = discharge_date
-            last_consultation.save()
-            ConsultationBed.objects.filter(
-                consultation=last_consultation, end_date__isnull=True
-            ).update(end_date=current_time)
-
-        return Response(status=status.HTTP_200_OK)
-
-    @action(detail=True, methods=["POST"])
-    def discharge_summary(self, request, *args, **kwargs):
-        patient = self.get_object()
-        email = request.data.get("email", "")
-        try:
-            validate_email(email)
-        except Exception:
-            email = request.user.email
-        generate_discharge_report.delay(patient.id, email)
-        return Response(status=status.HTTP_200_OK)
-
     @action(detail=True, methods=["POST"])
     def transfer(self, request, *args, **kwargs):
         patient = PatientRegistration.objects.get(
@@ -481,9 +404,9 @@ def transfer(self, request, *args, **kwargs):
                 {"Patient": "Cannot Transfer Patient , Source Facility Does Not Allow"},
                 status=status.HTTP_406_NOT_ACCEPTABLE,
             )
-        patient.is_active = True
         patient.allow_transfer = False
-        serializer = self.get_serializer(patient, data=request.data)
+        patient.is_active = True
+        serializer = self.get_serializer_class()(patient, data=request.data)
         serializer.is_valid(raise_exception=True)
         serializer.save()
 
@@ -497,10 +420,7 @@ def transfer(self, request, *args, **kwargs):
             ~Q(status__in=[30, 50, 80]), patient=patient
         ):
             shifting_request.status = 30
-            shifting_request.comments = (
-                shifting_request.comments
-                + f"\n The shifting request was auto rejected by the system as the patient was moved to {patient.facility.name}"
-            )
+            shifting_request.comments = f"{shifting_request.comments}\n The shifting request was auto rejected by the system as the patient was moved to {patient.facility.name}"
             shifting_request.save(update_fields=["status", "comments"])
         return Response(data=response_serializer.data, status=status.HTTP_200_OK)