Merge all dev, prod, pre-prod code. Use docker compose profiles to bu…

…ild and start the correct containers

.github/workflows/deploy-preprod-to-azure.yaml → .github/workflows/deploy-preprod-to-azurevm.yaml

@@ -6,14 +6,14 @@ on:
 
 jobs:
   deployment:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
 
     steps:
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Copy files using SCP
-        uses: appleboy/scp-action@master
+        uses: appleboy/scp-action@v0.1.7
         with:
           host: ${{ secrets.PANKB_PREPROD_HOST }}
           username: ${{ secrets.PANKB_PREPROD_SSH_USERNAME }}
@@ -22,7 +22,7 @@ jobs:
           target: "/projects/pankb_web/django_project"
 
       - name: Create the .env file and (re-)start containers over SSH
-        uses: appleboy/ssh-action@master
+        uses: appleboy/ssh-action@v0.1.7
         with:
           host: ${{ secrets.PANKB_PREPROD_HOST }}
           username: ${{ secrets.PANKB_PREPROD_SSH_USERNAME }}

.github/workflows/deploy-prod-to-azurevm.yml

@@ -6,14 +6,14 @@ on:
 
 jobs:
   deployment:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
 
     steps:
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Copy files using SCP
-        uses: appleboy/scp-action@master
+        uses: appleboy/scp-action@@v0.1.7
         with:
           host: ${{ secrets.PANKB_PROD_HOST }}
           username: ${{ secrets.PANKB_PROD_SSH_USERNAME }}
@@ -22,7 +22,7 @@ jobs:
           target: "/projects/pankb_web/django_project"
 
       - name: Create the .env file and (re-)start containers over SSH
-        uses: appleboy/ssh-action@master
+        uses: appleboy/ssh-action@@v0.1.7
         with:
           host: ${{ secrets.PANKB_PROD_HOST }}
           username: ${{ secrets.PANKB_PROD_SSH_USERNAME }}

CHANGELOG.md

@@ -5,6 +5,26 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/)
 and this project adheres to [Semantic Versioning](http://semver.org/).
 =======
 
+## PanKB v3.1.0 - 10.12.2024
+ - Removed djongo as a dependency
+ - Upgraded to django v5.1
+ - Used multiple gunicorn workers
+
+## PanKB v3.0.0 - 10.12.2024
+ - Improved layout/styling
+ - Improved interfacing between the Pipeline, Azure and MongoDB.
+ - Improved handling of isolation sources/countries.
+ - Integration of Aaron’s improved phylotree.
+ - Improved KEGG pathway links.
+ - iModulonDB interoperability and NCBI locus tag mapping.
+ - Dynamic loading + server side processing of large datatables.
+ - Search now immediately loads all other results, whilst the genes table shows a loading symbol.
+ - Added a “Genomes” page for each species.
+ - Improved loading speeds for many pages, including the overview pages for species.
+ - Added a panning mode to the phylotree to enable users to navigate the tree more easily.
+ - Many small improvements...
+
+
 ## PanKB v2.0.0 - 15.07.2024
 
 ### Added

README.md

@@ -1,4 +1,4 @@
-# PanKB Website (PROD)
+# PanKB Website
 <b>The dynamic Python-based version of the website. The Django framework is used as the back-end. Data about organisms, genes, genomes, locus_tags and KEGG pathways are stored in a database (in a cloud-based Azure Cosmos DB for MongoDB). The Microsoft Azure Blob Storage is still used as a data lake to store static unstructured or semi-structured data, e.g., plots, bibliome and phylogenetic trees (i.e., data that are not used by search or any other scripts generating dynamic content).</b>
 
 ## Contributors

docker-compose.yml

@@ -22,14 +22,45 @@ services:
     networks:
       - pankb-net
 
-  nginx:
-    container_name: pankb-nginx
+  nginx_dev:
+    profiles:
+      - dev
+    container_name: pankb-nginx-dev
+    build:
+      context: ./nginx
+      args:
+        - PANKB_SERVER_TYPE=dev
+    image: pankb_nginx_dev:latest
+    restart: always       # for the container to be up and running again even after the VM is brought down
+    volumes:
+      - ./static:/static  # a folder, where the static content will be served from
+    ports:
+      - 80:80
+    networks:
+      - pankb-net
+
+  nginx_prod:
+    profiles:
+      - prod
+    container_name: pankb-nginx-prod
     build: ./nginx
-    image: pankb_nginx:latest
+    image: pankb_nginx_prod:latest
     restart: always       # for the container to be up and running again even after the VM is brought down
     volumes:
       - ./static:/static  # a folder, where the static content will be served from
+      - ./certbot/www/:/var/www/certbot/:ro      # a mounted folder that links nginx with certbot
+      - ./certbot/conf/live/pankb.org/fullchain.pem:/etc/nginx/ssl/live/pankb.org/fullchain.pem        # the SSL certificate
+      - ./certbot/conf/live/pankb.org/privkey.pem:/etc/nginx/ssl/live/pankb.org/privkey.pem            # the SSL private key
     ports:
       - 80:80
+      - 443:443
     networks:
       - pankb-net
+
+  certbot:
+    profiles:
+      - prod
+    image: certbot/certbot:latest
+    volumes:
+      - ./certbot/www/:/var/www/certbot/:rw
+      - ./certbot/conf/:/etc/letsencrypt/:rw

nginx/Dockerfile

@@ -1,3 +1,5 @@
 FROM nginx:1.19.0-alpine
+ARG PANKB_SERVER_TYPE=prod
 
-COPY ./default.conf /etc/nginx/conf.d/default.conf
+COPY ./default-$PANKB_SERVER_TYPE.conf /etc/nginx/conf.d/default.conf
+RUN [ "$PANKB_SERVER_TYPE" == "prod" ] && mkdir -p /etc/nginx/ssl/live/pankb.org || echo "Not in production"

nginx/default-prod.conf

@@ -0,0 +1,43 @@
+upstream django {
+        server django_gunicorn:8000;
+}
+
+
+server {
+        listen 80;
+        listen [::]:80;
+
+        server_name pankb.org www.pankb.org;
+        server_tokens off;
+
+        location /.well-known/acme-challenge/ {
+                root /var/www/certbot;
+        }
+
+        location /static/ {
+                alias /static/;
+        }
+
+        location / {
+                return 301 https://$server_name$request_uri;
+        }
+}
+
+
+server {
+        listen 443 default_server ssl http2;
+        listen [::]:443 ssl http2;
+
+        server_name pankb.org www.pankb.org;
+
+        ssl_certificate /etc/nginx/ssl/live/pankb.org/fullchain.pem;
+        ssl_certificate_key /etc/nginx/ssl/live/pankb.org/privkey.pem;
+
+        location /static/ {
+                alias /static/;
+        }
+
+        location / {
+                proxy_pass http://django;
+        }
+}