Cleanup postgis dependencies

.github/workflows/deployment.yaml

@@ -29,11 +29,11 @@ jobs:
     if: github.ref == 'refs/heads/production'
     runs-on: ubuntu-latest
     env:
-      DATABASE_URL: postgis://postgres:postgres@localhost:5432/care
+      DATABASE_URL: postgres://postgres:postgres@localhost:5432/care
     name: Test
     services:
       db:
-        image: postgis/postgis:latest
+        image: postgres:latest
         env:
           POSTGRES_USER: postgres
           POSTGRES_PASSWORD: postgres
@@ -89,7 +89,7 @@ jobs:
       - name: Install dependencies
         run: |
           sudo apt-get update
-          sudo apt-get install binutils libproj-dev gdal-bin -y
+          sudo apt-get install binutils libproj-dev libjpeg-dev zlib1g-dev -y
           pip install --upgrade pip
           pip install -r requirements/local.txt
 

.github/workflows/tests.yml

@@ -7,10 +7,10 @@ jobs:
   test:
     runs-on: ubuntu-latest
     env:
-      DATABASE_URL: postgis://postgres:postgres@localhost:5432/care
+      DATABASE_URL: postgres://postgres:postgres@localhost:5432/care
     services:
       db:
-        image: postgis/postgis:latest
+        image: postgres:latest
         env:
           POSTGRES_USER: postgres
           POSTGRES_PASSWORD: postgres
@@ -51,7 +51,7 @@ jobs:
       - name: Install system packages
         run: |
           sudo apt-get update
-          sudo apt-get install binutils libproj-dev gdal-bin -y
+          sudo apt-get install binutils libproj-dev libjpeg-dev zlib1g-dev -y
 
       - name: Install CI dependencies
         run: |

.gitignore

@@ -152,7 +152,7 @@ typings/
 
 ### VisualStudioCode template
 .vscode/*
-!.vscode/settings.json
+# !.vscode/settings.json
 !.vscode/tasks.json
 !.vscode/launch.json
 !.vscode/extensions.json
@@ -344,12 +344,10 @@ care/media/*
 .envs/*
 !.envs/.local/
 
-.vscode
-.idea/
 test_db
 
 celerybeat-schedule
 
 config/settings/local.py
 
-secrets.sh
+secrets.sh

.vscode/launch.json

@@ -0,0 +1,30 @@
+{
+  // Use IntelliSense to learn about possible attributes.
+  // Hover to view descriptions of existing attributes.
+  // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+  "version": "0.2.0",
+  "configurations": [
+    {
+      "name": "Docker: Django",
+      "type": "python",
+      "request": "attach",
+      "pathMappings": [
+        {
+          "localRoot": "${workspaceFolder}",
+          "remoteRoot": "/app"
+        }
+      ],
+      "port": 9876,
+      "host": "127.0.0.1",
+    },
+    {
+      "name": "Python: Django",
+      "type": "python",
+      "request": "launch",
+      "program": "${workspaceFolder}/manage.py",
+      "args": ["runserver"],
+      "django": true,
+      "justMyCode": false
+    },
+  ]
+}

CONTRIBUTING.rst

@@ -39,7 +39,7 @@ Troubleshooting Local Setup
 If you're on Mac and you have installed Postgres.app Run:
 `export PATH=$PATH:/Applications/Postgres.app/Contents/Versions/14/bin`
 
-If you're pip install is failing on Pillow Consider installing 
+If you're pip install is failing on Pillow Consider installing
 
 `brew install libjpeg libtiff little-cms2 openjpeg webp`
 
@@ -147,16 +147,6 @@ Login to the postgres shell and run:
 
 You may replace `care` with the database name of your preference
 
-You also might have to install PostGIS scripts.
-
-* Linux users can install PostGIS scripts by running ::
-
-    $ sudo apt install postgresql-<version>-postgis-scripts
-
-* Windows users can install
-    - PostGIS through Application Stack Builder which is installed along PostgreSQL using standard PostgreSQL installer.
-    - OSGeo4W from this site_.
-
 Then follow the steps listed here_.
 
 Setting up Pre-Commit
@@ -218,8 +208,6 @@ In the virtualenv shell type the following commands also::
 
  export DATABASE_URL=postgres://postgres:<password>@127.0.0.1:5432/care
 
- export TEST_POSTGIS_URL="postgis://postgres:<password>@127.0.0.1:5432/care"
-
 You may replace 'care' with the database you have created before.
 
 After doing this you can type the following command::

Dockerfile

@@ -12,7 +12,7 @@ ARG BUILD_ENVIRONMENT=production
 # Install apt packages
 RUN apt-get update && apt-get install --no-install-recommends -y \
   # dependencies for building Python packages
-  build-essential libgdal-dev \
+  build-essential libjpeg-dev zlib1g-dev \
   # psycopg2 dependencies
   libpq-dev
 
@@ -44,8 +44,6 @@ RUN addgroup --system django \
 RUN apt-get update && apt-get install --no-install-recommends -y \
   # psycopg2 dependencies
   libpq-dev \
-  # PostGIS dependencies
-  libgdal-dev \
   # Translations dependencies
   gettext \
   # Msic

config/settings/base.py

@@ -6,9 +6,6 @@
 from datetime import timedelta
 
 import environ
-from healthy_django.healthcheck.celery_queue_length import (
-    DjangoCeleryQueueLengthHealthCheck,
-)
 from healthy_django.healthcheck.django_cache import DjangoCacheHealthCheck
 from healthy_django.healthcheck.django_database import DjangoDatabaseHealthCheck
 
@@ -53,7 +50,6 @@
 
 DATABASES = {"default": env.db("DATABASE_URL", default="postgres:///care")}
 DATABASES["default"]["ATOMIC_REQUESTS"] = True
-# DATABASES["default"]["ENGINE"] = "django.contrib.gis.db.backends.postgis"
 DATABASES["default"]["CONN_MAX_AGE"] = 300
 
 # URLS
@@ -424,8 +420,12 @@ def GETKEY(group, request):
 OTP_LENGTH = 5
 
 # ICD
-ICD_SCRAPER_ROOT_CONCEPTS_URL = "https://icd.who.int/browse11/l-m/en/JsonGetRootConcepts"
-ICD_SCRAPER_CHILD_CONCEPTS_URL = "https://icd.who.int/browse11/l-m/en/JsonGetChildrenConcepts"
+ICD_SCRAPER_ROOT_CONCEPTS_URL = (
+    "https://icd.who.int/browse11/l-m/en/JsonGetRootConcepts"
+)
+ICD_SCRAPER_CHILD_CONCEPTS_URL = (
+    "https://icd.who.int/browse11/l-m/en/JsonGetChildrenConcepts"
+)
 
 # SMS
 USE_SMS = False

config/settings/deployment.py

@@ -27,6 +27,7 @@
 
 # DATABASES
 # ------------------------------------------------------------------------------
+# TODO: rename POSTGIS_URL to DATABASE_URL
 DATABASES["default"] = env.db("POSTGIS_URL")  # noqa F405
 DATABASES["default"]["ATOMIC_REQUESTS"] = True  # noqa F405
 DATABASES["default"]["CONN_MAX_AGE"] = env.int("CONN_MAX_AGE", default=60)  # noqa F405

config/settings/local.py

@@ -1,5 +1,3 @@
-import os
-
 from .base import *  # noqa
 from .base import env
 
@@ -9,11 +7,19 @@
 DEBUG = env.bool("DJANGO_DEBUG", True)
 ALLOWED_HOSTS = ["*"]
 # https://docs.djangoproject.com/en/dev/ref/settings/#secret-key
-SECRET_KEY = env("DJANGO_SECRET_KEY", default="eXZQzOzx8gV38rDG0Z0fFZWweUGl3LwMZ9aTKqJiXQTI0nKMh0Z7sbHfqT8KFEnd",)
+SECRET_KEY = env(
+    "DJANGO_SECRET_KEY",
+    default="eXZQzOzx8gV38rDG0Z0fFZWweUGl3LwMZ9aTKqJiXQTI0nKMh0Z7sbHfqT8KFEnd",
+)
 # The first key will be used to encrypt all new data, and decryption of existing values will be attempted
 # with all given keys in order. This is useful for key rotation: place a new key at the head of the list
 # for use with all new or changed data, but existing values encrypted with old keys will still be accessible
-FERNET_KEYS = [env("FERNET_SECRET_KEY_1", default="f685a83652d782188382a3f2696e623a764c8012b1488d2fc5bc6460cddc7878")]
+FERNET_KEYS = [
+    env(
+        "FERNET_SECRET_KEY_1",
+        default="f685a83652d782188382a3f2696e623a764c8012b1488d2fc5bc6460cddc7878",
+    )
+]
 # https://docs.djangoproject.com/en/dev/ref/settings/#allowed-hostsRUNSERVER_PLUS_PRINT_SQL_TRUNCATE
 
 # CACHES
@@ -64,19 +70,6 @@
 # https://django-extensions.readthedocs.io/en/latest/installation_instructions.html#configuration
 INSTALLED_APPS += ["django_extensions"]  # noqa F405
 
-# Required for gis on windows platform
-# Make sure to install OSGeo4W from https://trac.osgeo.org/osgeo4w/
-if os.name == "nt":
-    import platform
-
-    OSGEO4W = r"C:\OSGeo4W"
-    if "64" in platform.architecture()[0]:
-        OSGEO4W += "64"
-    assert os.path.isdir(OSGEO4W), "Directory does not exist: " + OSGEO4W
-    os.environ["OSGEO4W_ROOT"] = OSGEO4W
-    os.environ["GDAL_DATA"] = OSGEO4W + r"\share\gdal"
-    os.environ["PROJ_LIB"] = OSGEO4W + r"\share\proj"
-    os.environ["PATH"] = OSGEO4W + r"\bin;" + os.environ["PATH"]
 
 # Your stuff...
 # ------------------------------------------------------------------------------
@@ -94,8 +87,12 @@
 
 # Simple JWT
 SIMPLE_JWT = {
-    "ACCESS_TOKEN_LIFETIME": timedelta(minutes=env("JWT_ACCESS_TOKEN_LIFETIME", default=1000000000)),
-    "REFRESH_TOKEN_LIFETIME": timedelta(minutes=env("JWT_REFRESH_TOKEN_LIFETIME", default=3000000000)),
+    "ACCESS_TOKEN_LIFETIME": timedelta(  # noqa
+        minutes=env("JWT_ACCESS_TOKEN_LIFETIME", default=1000000000)
+    ),
+    "REFRESH_TOKEN_LIFETIME": timedelta(  # noqa
+        minutes=env("JWT_REFRESH_TOKEN_LIFETIME", default=3000000000)
+    ),
     "ROTATE_REFRESH_TOKENS": True,
 }
 

config/settings/test.py

@@ -60,7 +60,6 @@
 
 DATABASES = {"default": env.db("DATABASE_URL", default="postgres:///care-test")}
 DATABASES["default"]["ATOMIC_REQUESTS"] = True
-# DATABASES["default"]["ENGINE"] = "django.contrib.gis.db.backends.postgis"
 
 # https://whitenoise.evans.io/en/stable/django.html#whitenoise-makes-my-tests-run-slow
 WHITENOISE_AUTOREFRESH = True

docker-compose.local.yaml

@@ -7,33 +7,34 @@ networks:
 services:
   db:
     container_name: care_db
-    image: postgres
+    image: postgres:latest
     restart: always
     env_file:
       - ./docker/.local.env
     volumes:
       - postgres-data:/var/lib/postgresql/data
 
+  redis:
+    container_name: care_redis
+    image: redis:alpine
+    restart: always
+
   backend:
     container_name: care
     build:
       context: .
       dockerfile: docker/DevDockerfile
     env_file:
       - ./docker/.local.env
-    command: python manage.py runserver 0.0.0.0:9000
+    entrypoint: ["bash", "docker/docker-entrypoint.sh"]
     ports:
       - "9000:9000"
+      - "9876:9876" #debugpy
     depends_on:
       - db
     volumes:
       - .:/app
 
-  redis:
-    container_name: care_redis
-    image: redis:alpine
-    restart: always
-
   celery:
     container_name: care_celery
     build:

docker/.local.env

@@ -1,12 +1,12 @@
-DEBUG=True
 POSTGRES_USER=postgres
 POSTGRES_PASSWORD=postgres
 POSTGRES_HOST=db
 POSTGRES_DB=care
 POSTGRES_PORT=5432
 DATABASE_URL=postgres://postgres:postgres@db:5432/care
-TEST_POSTGIS_URL=postgis://postgres:postgres@db:5432/care
 CELERY_BROKER_URL=redis://redis:6379/0
 
+DJANGO_DEBUG=False
+
 FILE_UPLOAD_BUCKET=patient-bucket
 FACILITY_S3_BUCKET=facility-bucket

docker/DevDockerfile

@@ -1,17 +1,26 @@
-FROM python:3.8.9-slim-buster
+FROM python:3.10-slim-bullseye
 
 # These two environment variables prevent __pycache__/ files.
 # since ipython is already present in required, you might as well use it
 ENV PYTHONUNBUFFERED 1 PYTHONDONTWRITEBYTECODE 1 PYTHONBREAKPOINT=ipython
 
-RUN : \
-  && apt-get update \
-  && DEBIAN_FRONTEND=noninteractive apt-get install -y \
-    --no-install-recommends \
-    python3-dev \
-    build-essential \
-  && rm -rf /var/lib/apt/lists/* \
-  &&:
+# Install required system dependencies
+RUN apt-get update && apt-get install --no-install-recommends -y \
+  # dependencies for building Python packages
+  build-essential libjpeg-dev zlib1g-dev \
+  # psycopg2 dependencies
+  libpq-dev \
+  # Translations dependencies
+  gettext \
+  # Msic
+  wget gnupg \
+  # Install Chrome
+  && wget -q -O - https://dl-ssl.google.com/linux/linux_signing_key.pub | apt-key add - \
+  && echo "deb http://dl.google.com/linux/chrome/deb/ stable main" >> /etc/apt/sources.list.d/google.list \
+  && apt-get update && apt-get -y install google-chrome-stable \
+  # cleaning up unused files
+  && apt-get purge -y --auto-remove -o APT::AutoRemove::RecommendsImportant=false \
+  && rm -rf /var/lib/apt/lists/*
 
 # Copy the requirements folder to ensure they are cached
 COPY requirements ./requirements
@@ -27,4 +36,4 @@ COPY . /app
 
 WORKDIR /app
 
-ENTRYPOINT ["bash", "docker/docker-entrypoint.sh"]
+# ENTRYPOINT ["bash", "docker/docker-entrypoint.sh"]

docker/docker-entrypoint.sh

@@ -6,4 +6,8 @@ python manage.py migrate
 
 echo "All migrations have been made successfully"
 
-python manage.py runserver_plus 0.0.0.0:9000
+if ["${DJANGO_DEBUG,,}" == "true"]; then
+  python -m debugpy --wait-for-client --listen 0.0.0.0:9876 manage.py runserver_plus 0.0.0.0:9000
+else
+  python manage.py runserver 0.0.0.0:9000
+fi