Merge branch 'develop' into test

.github/workflows/docs.yml

@@ -3,12 +3,12 @@ name: Docs
 on:
   push:
     branches:
-      - master
+      - develop
     paths:
       - "docs/**"
   pull_request:
     branches:
-      - master
+      - develop
     paths:
       - "docs/**"
   workflow_dispatch:
@@ -46,7 +46,7 @@ jobs:
           retention-days: 30
 
   deploy-docs:
-    if: github.repository == 'coronasafe/care' && github.ref == 'refs/heads/master'
+    if: github.repository == 'coronasafe/care' && github.ref == 'refs/heads/develop'
     name: Deploy docs
     runs-on: ubuntu-latest
     needs: build-docs

.github/workflows/linter.yml

@@ -2,7 +2,9 @@ name: Lint Code Base
 
 on:
   pull_request:
-    branches: [master]
+    branches:
+      - develop
+      - staging
   merge_group:
 
 jobs:
@@ -24,7 +26,7 @@ jobs:
       - name: Lint Code Base
         uses: github/super-linter/slim@v5
         env:
-          DEFAULT_BRANCH: master
+          DEFAULT_BRANCH: develop
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           VALIDATE_ALL_CODEBASE: false
           VALIDATE_PYTHON_BLACK: true

.pre-commit-config.yaml

@@ -5,7 +5,7 @@ repos:
     rev: v4.4.0
     hooks:
       - id: no-commit-to-branch
-        args: [--branch, master, --branch, production]
+        args: [--branch, develop, --branch, staging, --branch, production]
       - id: check-merge-conflict
       - id: check-builtin-literals
       - id: mixed-line-ending

.vscode/settings.json

@@ -18,7 +18,7 @@
   },
   "files.trimFinalNewlines": true,
   "files.trimTrailingWhitespace": true,
-  "githubPullRequests.ignoredPullRequestBranches": ["master"],
+  "githubPullRequests.ignoredPullRequestBranches": ["develop", "staging"],
   "python.formatting.blackPath": "${workspaceFolder}/.venv/bin/black",
   "python.formatting.provider": "black",
   "python.languageServer": "Pylance",

CONTRIBUTING.md

@@ -23,7 +23,7 @@ pre-commit install
 
 to run pre-commit on your branch:
 ```bash
-pre-commit run --files $(git diff --name-only master...HEAD)
+pre-commit run --files $(git diff --name-only develop...HEAD)
 ```
 
 #### Using Docker

Pipfile

@@ -6,7 +6,7 @@ name = "pypi"
 [packages]
 argon2-cffi = "==23.1.0"
 authlib = "==1.2.1"
-boto3 = "==1.34.64"
+boto3 = "==1.34.65"
 celery = "==5.3.6"
 django = "==4.2.10"
 django-environ = "==0.11.2"
@@ -23,7 +23,7 @@ django-rest-passwordreset = "==1.3.0"
 django-simple-history = "==3.3.0"
 djangoql = "==0.17.1"
 djangorestframework = "==3.14.0"
-djangorestframework-simplejwt = "==5.3.0"
+djangorestframework-simplejwt = "==5.3.1"
 dry-rest-permissions = "==0.1.10"
 drf-nested-routers = "==0.93.4"
 drf-spectacular = "==0.26.4"
@@ -34,7 +34,7 @@ jsonschema = "==4.20.0"
 jwcrypto = "==1.5.6"
 newrelic = "==9.3.0"
 pillow = "==10.2.0"
-psycopg = "==3.1.14"
+psycopg = "==3.1.18"
 pycryptodome = "==3.20.0"
 pydantic = "==1.10.12" # fix for fhir.resources < 7.0.2
 pyjwt = "==2.8.0"
@@ -48,17 +48,17 @@ redis-om = "==0.2.1"
 
 [dev-packages]
 black = "==23.9.1"
-boto3-stubs = {extras = ["s3", "boto3"], version = "==1.34.64"}
+boto3-stubs = {extras = ["s3", "boto3"], version = "==1.34.65"}
 coverage = "==7.4.0"
-debugpy = "==1.7.0"
+debugpy = "==1.8.1"
 django-coverage-plugin = "==3.1.0"
 django-debug-toolbar = "==4.2.0"
 django-extensions = "==3.2.3"
 django-silk = "==5.0.3"
 django-stubs = "==4.2.4"
 djangorestframework-stubs = "==3.14.2"
 factory-boy = "==3.3.0"
-flake8 = "==6.1.0"
+flake8 = "==7.0.0"
 freezegun = "==1.2.2"
 ipython = "==8.15.0"
 isort = "==5.12.0"

README.md

@@ -36,10 +36,11 @@ You can find the docs at https://care-be-docs.coronasafe.network
 
 ### Staging Deployments
 
-Staging instances for testing are automatically deployed on every commit to the `master` branch. The staging instances
-are available at:
+Dev and staging instances for testing are automatically deployed on every commit to the `develop` and `staging` branches.
+The staging instances are available at:
 
 - https://careapi.ohc.network
+- https://careapi-staging.ohc.network
 
 ### Self hosting
 

care/facility/api/viewsets/patient.py

@@ -416,6 +416,14 @@ def get_serializer_class(self):
         else:
             return self.serializer_class
 
+    def filter_queryset(self, queryset: QuerySet) -> QuerySet:
+        if self.action == "list" and settings.CSV_REQUEST_PARAMETER in self.request.GET:
+            for backend in (PatientDRYFilter, filters.DjangoFilterBackend):
+                queryset = backend().filter_queryset(self.request, queryset, self)
+            return queryset.filter(last_consultation__discharge_date__isnull=True)
+
+        return super().filter_queryset(queryset)
+
     def list(self, request, *args, **kwargs):
         """
         Patient List

care/facility/migrations/0421_merge_20240318_1434.py

@@ -0,0 +1,14 @@
+# Generated by Django 4.2.10 on 2024-03-18 09:04
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("facility", "0415_alter_dailyround_consciousness_level_and_more"),
+        ("facility", "0415_consultationclinician_and_more"),
+        ("facility", "0415_rename_dosage_prescription_base_dosage_and_more"),
+        ("facility", "0420_migrate_shifting_facility_type"),
+    ]
+
+    operations = []

care/facility/models/file_upload.py

@@ -38,8 +38,10 @@ class FileCategory(enum.Enum):
     FileTypeChoices = [(e.value, e.name) for e in FileType]
     FileCategoryChoices = [(e.value, e.name) for e in FileCategory]
 
-    name = models.CharField(max_length=2000)
-    internal_name = models.CharField(max_length=2000)
+    name = models.CharField(max_length=2000)  # name should not contain file extension
+    internal_name = models.CharField(
+        max_length=2000
+    )  # internal_name should include file extension
     associating_id = models.CharField(max_length=100, blank=False, null=False)
     upload_completed = models.BooleanField(default=False)
     is_archived = models.BooleanField(default=False)

care/facility/tests/test_patient_consultation_api.py

@@ -1,10 +1,12 @@
 import datetime
+from unittest.mock import patch
 
 from django.utils.timezone import make_aware
 from rest_framework import status
 from rest_framework.test import APITestCase
 
 from care.facility.api.serializers.patient_consultation import MIN_ENCOUNTER_DATE
+from care.facility.models.file_upload import FileUpload
 from care.facility.models.icd11_diagnosis import (
     ConditionVerificationStatus,
     ICD11Diagnosis,
@@ -224,6 +226,32 @@ def test_discharge_as_recovered_with_expired_fields(self):
         self.assertIsNone(consultation.death_datetime)
         self.assertIsNot(consultation.death_confirmed_doctor, "Dr. Test")
 
+    def discharge_summary(self, consultation, **kwargs):
+        return self.client.post(
+            f"{self.get_url(consultation)}generate_discharge_summary/", kwargs, "json"
+        )
+
+    def test_discharge_summary(self):
+        consultation = self.create_admission_consultation(
+            suggestion=SuggestionChoices.A,
+            encounter_date=make_aware(datetime.datetime(2020, 4, 1, 15, 30, 00)),
+        )
+        with patch.object(FileUpload, "put_object"):
+            self.discharge_summary(
+                consultation,
+                new_discharge_reason=NewDischargeReasonEnum.RECOVERED,
+                discharge_date="2020-04-02T15:30:00Z",
+                discharge_notes="Discharge as recovered after admission before future",
+            )
+
+        file_res = FileUpload.objects.filter(
+            associating_id=consultation.external_id,
+            upload_completed=True,
+            is_archived=False,
+        )
+        uploaded_file = file_res[0]
+        self.assertFalse(uploaded_file.name.endswith(".pdf"))
+
     def test_referred_to_external_null(self):
         consultation = self.create_admission_consultation(
             suggestion=SuggestionChoices.A,

care/facility/utils/reports/discharge_summary.py

@@ -178,7 +178,7 @@ def generate_and_upload_discharge_summary(consultation: PatientConsultation):
     try:
         current_date = timezone.now()
         summary_file = FileUpload(
-            name=f"discharge_summary-{consultation.patient.name}-{current_date}.pdf",
+            name=f"discharge_summary-{consultation.patient.name}-{current_date}",
             internal_name=f"{uuid4()}.pdf",
             file_type=FileUpload.FileType.DISCHARGE_SUMMARY.value,
             associating_id=consultation.external_id,

data/dummy/users.json

@@ -768,5 +768,75 @@
             "groups": [],
             "user_permissions": []
         }
+    },
+    {
+        "model": "users.user",
+        "pk": 23,
+        "fields": {
+            "password": "argon2$argon2id$v=19$m=102400,t=2,p=8$WDE0YXVzR1dIV09zNWJZalF4QzdXSw$ZTpeDj5sbB3TKfu0DEJ5EkQnL3EmM2vGgvdx+Qt2sAw",
+            "last_login": "2024-03-18 17:04:08.753272+00",
+            "is_superuser": false,
+            "first_name": "Dummy",
+            "last_name": "Nurse",
+            "email": "dummynurse1@test.com",
+            "is_staff": false,
+            "is_active": true,
+            "date_joined": "2024-03-08 06:31:23.199154+00",
+            "username": "dummynurse1",
+            "user_type": 14,
+            "created_by": 1,
+            "ward": null,
+            "local_body": null,
+            "district": 7,
+            "state": 1,
+            "phone_number": "+918878825662",
+            "alt_phone_number": "+918878825662",
+            "gender": 2,
+            "age": 21,
+            "home_facility": 1,
+            "verified": true,
+            "deleted": false,
+            "pf_endpoint": null,
+            "pf_p256dh": null,
+            "pf_auth": null,
+            "asset": null,
+            "groups": [],
+            "user_permissions": []
+        }
+    },
+    {
+        "model": "users.user",
+        "pk": 24,
+        "fields": {
+            "password": "argon2$argon2id$v=19$m=102400,t=2,p=8$WlVSNkdVTEd4Vkgzako3SHUxT0xJag$b5A8WE7JdwlysGuiJPwoQneBQHtzjWTs3Br0VnX3XRc",
+            "last_login": "2024-03-12 16:34:18.859463+00",
+            "is_superuser": false,
+            "first_name": "Dummy",
+            "last_name": "Nurse",
+            "email": "dummynurse2@test.com",
+            "is_staff": false,
+            "is_active": true,
+            "date_joined": "2024-03-08 06:32:12.270135+00",
+            "username": "dummynurse2",
+            "user_type": 14,
+            "created_by": 1,
+            "ward": null,
+            "local_body": null,
+            "district": 7,
+            "state": 1,
+            "phone_number": "+918744587566",
+            "alt_phone_number": "+918744587566",
+            "gender": 1,
+            "age": 35,
+            "home_facility": 1,
+            "verified": true,
+            "deleted": false,
+            "pf_endpoint": null,
+            "pf_p256dh": null,
+            "pf_auth": null,
+            "asset": null,
+            "groups": [],
+            "user_permissions": []
+        }
     }
 ]

docs/github-repo/configuration.rst

@@ -3,7 +3,9 @@ GitHub Repository
 
 The Github Repo available here_ contains the source code for the care project, Apart from the secrets configured at runtime, the exact copy is deployed in production.
 
-The :code:`master` branch auto deploys to the Development instance and is regarded as the Beta version of the application.
+The :code:`develop` branch auto deploys to the Development instance and is regarded as the Beta version of the application.
+
+The :code:`staging` branch auto deploys to the Staging instance and is regarded as the Release Candidate version of the application.
 
 The :code:`production` branch auto deploys to Production instance and is regarded as the Stable version of the application.