Dockerize Osler

.circleci/config.yml

@@ -2,7 +2,7 @@ version: 2
 jobs:
   build:
     docker:
-      - image: circleci/python:2.7.15-jessie-browsers
+      - image: circleci/python:3.6.8-stretch-browsers
     steps:
       - checkout
       - run: mkdir test-reports

Dockerfile

@@ -0,0 +1,15 @@
+FROM python:3.7-buster
+
+RUN apt-get update && apt-get upgrade -y && \
+	apt-get install -y git
+
+COPY . /home/gunicorn_user/osler
+WORKDIR /home/gunicorn_user/osler
+
+RUN pip install --upgrade pip --trusted-host pypi.python.org
+RUN pip install --trusted-host pypi.python.org -r requirements-prod.txt
+
+EXPOSE 8000
+
+CMD ["gunicorn", "--chdir", "osler", "--bind", "0.0.0.0:8000", \
+     "osler.gunicorn_wsgi:application", "--log-file", "-", "--log-level", "debug"]

Makefile

@@ -0,0 +1,33 @@
+# makefile
+
+start-dev:
+	docker-compose up
+
+start-prod:
+	docker-compose -f docker-compose.yml -f docker-compose.prod.yml up
+
+stop-compose:
+	@eval docker stop $$(docker ps -a -q)
+	docker-compose down
+
+ssh-nginx:
+	docker exec -it nginx_server bash
+
+ssh-django-web:
+	docker exec -it osler_app bash
+
+ssh-db:
+	docker exec -it osler_db bash
+
+build:
+	docker-compose build
+
+rebuild:
+	docker-compose build --no-cache
+	docker-compose up
+
+test:
+	docker-compose run osler_app python osler/manage.py test
+
+cleanup:
+	docker system prune

config/nginx.conf

@@ -0,0 +1,51 @@
+user  nginx;
+worker_processes  1;
+
+pid        /var/run/nginx.pid;
+error_log /var/log/nginx/error.log warn;
+
+events {
+  worker_connections  1024;  ## Default: 1024, increase if you have lots of clients
+}
+
+http {
+    include       /etc/nginx/mime.types;
+    # fallback in case we can't determine a type
+    default_type  application/octet-stream;
+
+    sendfile        on;
+    #tcp_nopush     on;
+
+    upstream osler_server {
+        server osler_app:8000;
+    }
+
+    server {
+
+        listen 80;
+        # charset utf-8;
+        server_name localhost;
+
+        location = /favicon.ico { access_log off; log_not_found off; }
+
+        location / {
+            proxy_redirect     off;
+            proxy_set_header   Host $host;
+            proxy_set_header   X-Real-IP $remote_addr;
+            proxy_set_header   X-Forwarded-For $proxy_add_x_forwarded_for;
+            proxy_set_header   X-Forwarded-Host $server_name;
+
+            proxy_pass http://osler_server;
+            proxy_redirect off;
+        }
+
+        location /static/ {
+            alias /opt/services/osler/static/;
+        }
+
+        location /media/ {
+            internal;
+            alias /opt/services/osler/media/;
+        }
+    }
+}

docker-compose.yaml

@@ -0,0 +1,81 @@
+version: "3.2"
+
+services:
+  web:
+    container_name: osler_app
+    build:
+      context: .
+      dockerfile: Dockerfile
+    image: osler
+    stop_signal: SIGINT
+    volumes:
+      - static:/home/gunicorn_user/osler/osler/static
+      - media:/home/gunicorn_user/osler/osler/media
+      - ./logs:/home/gunicorn_user/logs
+    networks:
+      - nginx_network
+      - database_network
+    depends_on:
+      - db
+    environment:
+      DJANGO_DEBUG: 0
+      DJANGO_SETTINGS_MODULE: osler.docker_settings
+      DJANGO_SENDFILE_BACKEND: sendfile.backends.nginx
+      DJANGO_SENDFILE_ROOT: /opt/services/osler/media
+      DJANGO_SENDFILE_URL: /media
+      DJANGO_SECRET_KEY_FILE: /run/secrets/django_secret_key
+      DJANGO_DEBUG_LOG_FILE: /home/gunicorn_user/logs/osler.log
+      DATABASE_PASSWORD_FILE: /run/secrets/database_password
+      DATABASE_BACKEND: django.db.backends.postgresql_psycopg2
+      DATABASE_NAME: osler
+      DATABASE_USER: django
+      DATABASE_PORT: 5432
+      DATABASE_HOST: db
+    secrets:
+      - database_password
+      - django_secret_key
+  db:
+    container_name: osler_db
+    image: postgres
+    restart: always
+    environment:
+      POSTGRES_DB: osler
+      POSTGRES_PASSWORD_FILE: /run/secrets/database_password
+      POSTGRES_USER: django
+    networks:
+      - database_network
+    secrets:
+      - database_password
+  nginx:
+    image: nginx:latest
+    container_name: nginx_server
+    restart: always
+    ports:
+      # - "0.0.0.0:80:80"
+      - 8000:80
+    volumes:
+      - db_data:/var/lib/postgresql/data
+      - ./config/nginx.conf:/etc/nginx/nginx.conf
+      - static:/opt/services/osler/static/
+      - media:/opt/services/osler/media/
+    depends_on:
+      - web
+    networks:
+      - nginx_network
+
+volumes:
+  static:
+  media:
+  db_data:
+
+secrets:
+   database_password:
+     file: config/secrets/database_password.txt
+   django_secret_key:
+     file: config/secrets/django_secret_key.txt
+
+networks:
+  nginx_network:
+    driver: bridge
+  database_network:  # <-- add the bridge
+    driver: bridge

api/test.py → osler/api/test.py

@@ -18,14 +18,15 @@ class APITest(APITestCase):
     def setUp(self):
         workupModels.ClinicType.objects.create(name="Basic Care Clinic")
         workupModels.ClinicDate.objects.create(
-            clinic_type=workupModels.ClinicType.objects.all()[0],
+            clinic_type=workupModels.ClinicType.objects.first(),
             clinic_date=now().date() + datetime.timedelta(days=1))
         workupModels.ClinicDate.objects.create(
-            clinic_type=workupModels.ClinicType.objects.all()[0],
+            clinic_type=workupModels.ClinicType.objects.first(),
             clinic_date=now().date() - datetime.timedelta(days=1))
         workupModels.ClinicDate.objects.create(
-            clinic_type=workupModels.ClinicType.objects.all()[0],
+            clinic_type=workupModels.ClinicType.objects.first(),
             clinic_date=now().date() - datetime.timedelta(days=5))
+
         log_in_provider(self.client, build_provider(["Attending"]))
 
         pt1 = models.Patient.objects.get(pk=1)
@@ -41,52 +42,52 @@ def setUp(self):
             state='BA',
             zip_code='63108',
             pcp_preferred_zip='63018',
-            date_of_birth=datetime.date(1990, 01, 01),
+            date_of_birth=datetime.date(1990, 1, 1),
             patient_comfortable_with_english=False,
-            preferred_contact_method=models.ContactMethod.objects.all()[0],
+            preferred_contact_method=models.ContactMethod.objects.first(),
         )
 
         pt3 = models.Patient.objects.create(
             first_name="Asdf",
             last_name="Lkjh",
             middle_name="Bayer",
             phone='+49 178 236 5288',
-            gender=models.Gender.objects.all()[0],
+            gender=models.Gender.objects.first(),
             address='Schulstrasse 9',
             city='Munich',
             state='BA',
             zip_code='63108',
             pcp_preferred_zip='63018',
-            date_of_birth=datetime.date(1990, 01, 01),
+            date_of_birth=datetime.date(1990, 1, 1),
             patient_comfortable_with_english=False,
-            preferred_contact_method=models.ContactMethod.objects.all()[0],
+            preferred_contact_method=models.ContactMethod.objects.first(),
         )
 
         pt4 = models.Patient.objects.create(
             first_name="No",
             last_name="Action",
             middle_name="Item",
             phone='+12 345 678 9000',
-            gender=models.Gender.objects.all()[0],
+            gender=models.Gender.objects.first(),
             address='Schulstrasse 9',
             city='Munich',
             state='BA',
             zip_code='63108',
             pcp_preferred_zip='63018',
-            date_of_birth=datetime.date(1990, 01, 01),
+            date_of_birth=datetime.date(1990, 1, 1),
             patient_comfortable_with_english=False,
-            preferred_contact_method=models.ContactMethod.objects.all()[0],
+            preferred_contact_method=models.ContactMethod.objects.first(),
         )
 
         # Give pt2 a workup one day later.
         workupModels.Workup.objects.create(
-            clinic_day=workupModels.ClinicDate.objects.all()[0], # one day later
+            clinic_day=workupModels.ClinicDate.objects.first(), # one day later
             chief_complaint="SOB",
             diagnosis="MI",
             HPI="", PMH_PSH="", meds="", allergies="", fam_hx="", soc_hx="",
             ros="", pe="", A_and_P="",
-            author=models.Provider.objects.all()[0],
-            author_type=models.ProviderType.objects.all()[0],
+            author=models.Provider.objects.first(),
+            author_type=models.ProviderType.objects.first(),
             patient=pt2)
 
         # Give pt3 a workup one day ago.
@@ -96,8 +97,8 @@ def setUp(self):
             diagnosis="MI",
             HPI="", PMH_PSH="", meds="", allergies="", fam_hx="", soc_hx="",
             ros="", pe="", A_and_P="",
-            author=models.Provider.objects.all()[0],
-            author_type=models.ProviderType.objects.all()[0],
+            author=models.Provider.objects.first(),
+            author_type=models.ProviderType.objects.first(),
             patient=pt3)
 
 
@@ -108,38 +109,38 @@ def setUp(self):
             diagnosis="MI",
             HPI="", PMH_PSH="", meds="", allergies="", fam_hx="", soc_hx="",
             ros="", pe="", A_and_P="",
-            author=models.Provider.objects.all()[0],
-            author_type=models.ProviderType.objects.all()[0],
+            author=models.Provider.objects.first(),
+            author_type=models.ProviderType.objects.first(),
             patient=pt1,
             signer=models.Provider.objects.all().filter(
             clinical_roles=models.ProviderType.objects.all().filter(
                 short_name="Attending")[0])[0])
 
         # make pt1 have and AI due tomorrow
         pt1_ai = models.ActionItem.objects.create(
-            author=models.Provider.objects.all()[0],
-            author_type=models.ProviderType.objects.all()[0],
-            instruction=models.ActionInstruction.objects.all()[0],
+            author=models.Provider.objects.first(),
+            author_type=models.ProviderType.objects.first(),
+            instruction=models.ActionInstruction.objects.first(),
             due_date=now().date()+datetime.timedelta(days=1),
             comments="",
             priority=True,
             patient=pt1)
 
         # make pt2 have an AI due yesterday
         pt2_ai = models.ActionItem.objects.create(
-            author=models.Provider.objects.all()[0],
-            author_type=models.ProviderType.objects.all()[0],
-            instruction=models.ActionInstruction.objects.all()[0],
+            author=models.Provider.objects.first(),
+            author_type=models.ProviderType.objects.first(),
+            instruction=models.ActionInstruction.objects.first(),
             due_date=now().date()-datetime.timedelta(days=1),
             comments="",
             priority=True,
             patient=pt2)
 
         # make pt3 have an AI that during the test will be marked done
         pt3_ai = models.ActionItem.objects.create(
-            author=models.Provider.objects.all()[0],
-            author_type=models.ProviderType.objects.all()[0],
-            instruction=models.ActionInstruction.objects.all()[0],
+            author=models.Provider.objects.first(),
+            author_type=models.ProviderType.objects.first(),
+            instruction=models.ActionInstruction.objects.first(),
             due_date=now().date()-datetime.timedelta(days=15),
             comments="",
             patient=pt3)
@@ -149,16 +150,19 @@ def test_api_list_patients_by_last_name(self):
         url = reverse("pt_list_api") # Way to have this here and not repeat this line? Reverse is called in every test now
 
         # Test last_name ordering
-        data = {'sort':'last_name'}
+        data = {'sort': 'last_name'}
         response = self.client.get(reverse("pt_list_api"), data, format='json')
         self.assertEqual(response.status_code, status.HTTP_200_OK)
-        self.assertLessEqual(response.data[0]['last_name'],response.data[1]['last_name'])
-        self.assertLessEqual(response.data[1]['last_name'],response.data[2]['last_name'])
-        self.assertLessEqual(response.data[2]['last_name'],response.data[3]['last_name'])
+        self.assertLessEqual(response.data[0]['last_name'],
+                             response.data[1]['last_name'])
+        self.assertLessEqual(response.data[1]['last_name'],
+                             response.data[2]['last_name'])
+        self.assertLessEqual(response.data[2]['last_name'],
+                             response.data[3]['last_name'])
 
     def test_api_list_patients_by_latest_activity(self):
         # Test workup/intake ordering.
-        data = {'sort':'latest_workup'}
+        data = {'sort': 'latest_workup'}
         response = self.client.get(reverse("pt_list_api"), data, format='json')
         self.assertEqual(response.status_code, status.HTTP_200_OK)
         self.assertNotEqual(response.data[0]['latest_workup'], None) # pt2, workup date now()+1day
@@ -167,9 +171,15 @@ def test_api_list_patients_by_latest_activity(self):
         self.assertNotEqual(response.data[3]['latest_workup'], None) # pt1, workup date now()-5days
 
         # Check that dates are correcly sorted
-        self.assertGreaterEqual(response.data[0]['latest_workup']['clinic_day']['clinic_date'],response.data[1]['history']['last']['history_date'])
-        self.assertGreaterEqual(response.data[1]['history']['last']['history_date'],response.data[2]['latest_workup']['clinic_day']['clinic_date'])
-        self.assertGreaterEqual(response.data[2]['latest_workup']['clinic_day']['clinic_date'],response.data[3]['latest_workup']['clinic_day']['clinic_date'])
+        self.assertGreaterEqual(
+            response.data[0]['latest_workup']['clinic_day']['clinic_date'],
+            response.data[1]['history']['last']['history_date'])
+        self.assertGreaterEqual(
+            response.data[1]['history']['last']['history_date'],
+            response.data[2]['latest_workup']['clinic_day']['clinic_date'])
+        self.assertGreaterEqual(
+            response.data[2]['latest_workup']['clinic_day']['clinic_date'],
+            response.data[3]['latest_workup']['clinic_day']['clinic_date'])
 
     def test_api_list_patients_with_unsigned_workup(self):
         # Test for unsigned_workup
@@ -225,7 +235,7 @@ def test_api_list_patients_with_inactive_action_item(self):
         self.assertEqual(len(response.data), 1)
         self.assertEqual(response.data[0]['id'], pt1.id)
 
-        pt3_ai.mark_done(models.Provider.objects.all()[0])
+        pt3_ai.mark_done(models.Provider.objects.first())
         pt3_ai.save()
 
         # Test now only has pt2

appointment/models.py → osler/appointment/models.py

@@ -47,7 +47,7 @@ class Meta:
 
     history = HistoricalRecords()
 
-    def __unicode__(self):
+    def __str__(self):
         return "Appointment ({type}) for {name} on {date}".format(
             type=self.verbose_appointment_type(),
             name=self.patient.name(),