Dockerize civic-server

.dockerignore

@@ -0,0 +1,4 @@
+Dockerfile
+.git
+.github
+public

Dockerfile

@@ -0,0 +1,18 @@
+FROM ruby:2
+
+RUN apt-get update
+RUN apt-get install -y rbenv libxml2 libxslt-dev openssl nodejs postgresql-client
+RUN gem install bundler
+
+#RUN mkdir /civic-server
+#RUN cd /civic-server && bundle install
+
+COPY Gemfile /civic-server/Gemfile
+COPY Gemfile.lock /civic-server/Gemfile.lock
+
+RUN cd /civic-server && bundle update --bundler && rbenv rehash && bundle install
+
+COPY $PWD /civic-server
+WORKDIR /civic-server
+
+ENTRYPOINT ["/civic-server/docker-entrypoint.sh"]

Gemfile

@@ -62,3 +62,7 @@ group :development do
   gem 'capistrano-rbenv', '~> 2.0'
   gem 'capistrano-passenger', '~> 0.2.0'
 end
+
+group :production do
+  gem 'puma', '~> 5.6.4'
+end

config/database.yml

@@ -2,7 +2,9 @@ default: &default
   adapter: postgresql
   pool: 5
   encoding: unicode
-  host: localhost
+  host: <%= ENV['DATABASE_HOST'] %>
+  username: <%= ENV['DATABASE_USER'] %>
+  password: <%= ENV['DATABASE_PASSWORD'] %>
 
 development:
   <<: *default

config/environments/production.rb

@@ -36,12 +36,15 @@
 
   # `config.assets.precompile` has moved to config/initializers/assets.rb
 
+  #run background tasks syncronously
+  config.active_job.queue_adapter = :inline
+
   # Specifies the header that your server uses for sending files.
   # config.action_dispatch.x_sendfile_header = "X-Sendfile" # for apache
   # config.action_dispatch.x_sendfile_header = 'X-Accel-Redirect' # for nginx
 
   # Force all access to the app over SSL, use Strict-Transport-Security, and use secure cookies.
-  config.force_ssl = true
+  #config.force_ssl = true
 
   # Set to :debug to see everything in the log.
   config.log_level = :info

docker-compose.yml

@@ -0,0 +1,26 @@
+version: '3'
+
+services:
+  civic:
+    build: .
+    ports:
+      - "3000:3000"
+    environment:
+      RAILS_ENV: production
+      SECRET_KEY_BASE: production_key_eretred547568
+      DATABASE_HOST: db
+      DATABASE_USER: postgres
+      DATABASE_PASSWORD: psw
+    depends_on:
+      - db
+  db:
+    image: postgres:13.5
+    ports:
+      - "5432:5432"
+    environment:
+      POSTGRES_PASSWORD: psw
+    healthcheck:
+      test: "PASSWORD=psw pg_isready -U postgres"
+      interval: 10s
+      timeout: 5s
+      retries: 5

docker-entrypoint.sh

@@ -0,0 +1,33 @@
+#!/usr/bin/env bash
+
+set -e
+set -u # unset variables throw error
+set -o pipefail # pipes fail when partial command fails
+
+bundle update --bundler
+
+# Note: make sure env $DATABASE_* items are set!
+
+# Attempt connect to db and if
+# it fails, then assume db does not exist and
+# db creation should be executed:
+if PGPASSWORD=$DATABASE_PASSWORD psql -lqt -U$DATABASE_USER -h$DATABASE_HOST | cut -d \| -f 1 | grep -q civic; then
+    echo "civic database already exists. Skipping database initialisation."
+else
+    echo "Creating civic database"
+    rake db:create
+
+    echo "Migrating civic database"
+    # migrate:
+    rake db:migrate
+
+    echo "Loading a recent database backup"
+    # unpack ./db/data.sql.gz (required before loading data dump):
+    gunzip ./db/data.sql.gz
+    # load the sanitized version of a recent database backup found in ./db:
+    rake civic:load[force]
+    echo "Done"
+fi
+
+echo "Starting server now. You can test it with e.g. http://localhost:3000/api/genes/3845?identifier_type=entrez_id"
+rails server -b 0.0.0.0