MAINT: Update docker-compose.yml to version 3

.circleci/config.yml

@@ -38,6 +38,8 @@ jobs:
           name: Set-up dockereve
           command: |
             mkdir -p dockereve-master/nginx/.ssl
+            mkdir -p /tmp/log
+            ln -s /tmp/log ./log
             touch dockereve-master/nginx/.ssl/mriqcep.crt
             touch dockereve-master/nginx/.ssl/mriqcep.key
             docker pull mongo:latest 
@@ -46,7 +48,25 @@ jobs:
             docker-compose -f dockereve-master/docker-compose.yml build
       - run:
           name: Start server
-          command: docker-compose -f dockereve-master/docker-compose.yml up -d
+          command: |
+            docker system prune -f
+            docker-compose -f dockereve-master/docker-compose.yml up
+          background: true
+
+      - run:
+          name: Check Swagger frontend is up
+          command: |
+            sleep 10
+            curl -i http://localhost:8080/
+
+      - run:
+          name: Check BOLD endpoint is up
+          command: |
+            curl -i -H "Content-Type: application/json" http://localhost:5000/api/v1/bold
+
+      - store_artifacts:
+          path: /tmp/log/
+
       - run:
           name: Test MRIQC WebAPI
           command: python3 test/testGetPost.py

dockereve-master/.env

@@ -2,4 +2,4 @@ MONGODB_HOST=mongodb
 MONGODB_PORT=27017
 
 API_TOKEN=<secret_token>
-API_URL=http://localhost/docs/api
+API_URL=http://localhost/docs/api/api-docs

dockereve-master/docker-compose.yml

@@ -1,42 +1,66 @@
-nginx:
-    image: nginx
+version: '3.6'
+
+services:
+  nginx:
+    image: nginx:latest
     restart: always
     ports:
-        - 80:80
-        - 443:443
+      - "80:80"
+      - "443:443"
     volumes:
-        - /www/static
-        - ./uwsgi_params.par:/etc/nginx/uwsgi_params.par:ro
-        - ./nginx/nginx.conf:/etc/nginx/nginx.conf:ro
-        - ./nginx/.ssl:/etc/ssl/certs/
-    volumes_from:
-        - eve
-    links:
-        - eve:eve
-        - swagger_ui:swagger_ui
+      - ./uwsgi_params.par:/etc/nginx/uwsgi_params.par:ro
+      - ./nginx/nginx.conf:/etc/nginx/nginx.conf:ro
+      - ./nginx/.ssl:/etc/ssl/certs/
+      - eve:/www/static
+    depends_on:
+      - endpoints
+      - frontend
+    networks:
+      - mynet
 
-swagger_ui:
+  frontend:
     image: swaggerapi/swagger-ui:latest
-    env_file: .env
+    hostname: frontend
+    env_file:
+        - .env
+    ports:
+      - "8080:8080"
+    depends_on:
+      - mongodb
+    networks:
+      - mynet
 
-eve:
+  endpoints:
     restart: always
-    env_file: .env
+    hostname: endpoints
+    env_file:
+        - .env
     build: eve-app
-    expose:
-        - 5000
     ports:
-        - 5000
+      - "5000:5000"
     volumes:
-        - ./eve-app:/usr/src/app 
-        - /usr/src/app/static
-    links:
-        - mongodb
-    command: /usr/local/bin/gunicorn -w 2 -b :5000 app:app
+      - ./eve-app/settings.py:/usr/src/app/settings.py
+      - ./log/:/var/log/
+      - eve:/usr/src/app/static
+      # - /usr/src/app/static
+    command: /usr/local/bin/gunicorn -w 2 --access-logfile /var/log/gunicorn.log -b :5000 app:app
+    depends_on:
+      - mongodb
+    networks:
+      - mynet
+
+  mongodb:
+    image: mongo:latest
+    container_name: mongodb
+    hostname: mongodb
+    ports:
+      - "27017:27017"
+    networks:
+      - mynet
+
+networks:
+  mynet:
+    driver: bridge
 
-mongodb:
-  image: mongo
-  expose:
-    - 27017
-  ports:
-    - 27017
+volumes:
+  eve:

dockereve-master/eve-app/Dockerfile

@@ -1,13 +1,9 @@
-FROM python:3.6-onbuild
+FROM python:3.7-slim
 
 WORKDIR /usr/src/app
 
 ADD . /usr/src/app
 
 RUN pip3 install -r requirements.txt
 RUN pip3 install pytest
-RUN sed -i 's/\[scheme\]/\["https"\]/' /usr/local/lib/python3.6/site-packages/eve_swagger/objects.py
-
-#EXPOSE 5000
-#CMD ["python3", "server.py"]
-
+RUN sed -i 's/\[scheme\]/\["https"\]/' /usr/local/lib/python3.7/site-packages/eve_swagger/objects.py

dockereve-master/eve-app/settings.py

@@ -551,8 +551,10 @@
     'URL_PREFIX': 'api',
     'API_VERSION': 'v1',
     'ALLOWED_FILTERS': ['*'],
-    'MONGO_HOST': os.environ.get('MONGODB_HOST', ''),
-    'MONGO_PORT': int(os.environ.get('MONGODB_PORT', 27017)),
+    'MONGO_URI': (
+        f"mongodb://{os.environ.get('MONGODB_HOST', 'localhost')}"
+        f":{os.environ.get('MONGODB_PORT', '27017')}"
+    ),
     'MONGO_DBNAME': 'mriqc_api',
     'PUBLIC_METHODS': ['GET'],
     'PUBLIC_ITEM_METHODS': ['GET'],

dockereve-master/nginx/nginx.conf

@@ -10,27 +10,38 @@ events {
 }
 
 http {
+    upstream eve-endpoint {
+        server endpoints:5000;
+    }
+
     server {
         listen 80;
         listen [::]:80 ;
         server_name 34.224.227.208;
 
+        location = /docs/api/api-docs {
+            proxy_pass http://eve-endpoint/docs/api/api-docs;
+            proxy_set_header Host $host;
+            proxy_set_header X-Real-IP $remote_addr;
+            proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+        }
+
         location = /docs/api {
-            proxy_pass http://eve:5000/docs/api;
+            proxy_pass http://eve-endpoint/docs/api;
             proxy_set_header Host $host;
             proxy_set_header X-Real-IP $remote_addr;
             proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
         }
 
         location /api {
-            proxy_pass http://eve:5000;
+            proxy_pass http://eve-endpoint/api;
             proxy_set_header Host $host;
             proxy_set_header X-Real-IP $remote_addr;
             proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
         }
 
         location / {
-            proxy_pass http://swagger_ui:8080/;
+            proxy_pass http://frontend:8080/;
             proxy_set_header Host $host;
             proxy_set_header X-Real-IP $remote_addr;
             proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;