Merge branch 'feature/update-docker-compose' into test

.env.sample

@@ -1,137 +1,7 @@
-# Default values are optimized for production to avoid having to configure
-# much in production.
-#
-# However it should be easy to get going in development too. If you see an
-# uncommented option that means it's either mandatory to set or it's being
-# overwritten in development to make your life easier.
+OP_API_KEY=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb
+OP_API_URL="https://data.bioontology.org"
+STARTER_ONTOLOGY=STY
 
-# Enable BuildKit by default:
-#   https://docs.docker.com/develop/develop-images/build_enhancements
-export DOCKER_BUILDKIT=1
-
-# Rather than use the directory name, let's control the name of the project.
-export COMPOSE_PROJECT_NAME=ontoportal-docker
-
-# In development we want all services to start but in production you don't
-# need the asset watchers to run since assets get built into the image.
-#
-# You can even choose not to run postgres and redis in prod if you plan to use
-# managed cloud services. Everything "just works", even optional depends_on!
-#export COMPOSE_PROFILES=postgres,redis,web,worker,cable
-export COMPOSE_PROFILES=db,cache,assets,web
-
-# If you're running native Linux and your uid:gid isn't 1000:1000 you can set
-# these to match your values before you build your image. You can check what
-# your uid:gid is by running `id` from your terminal.
-#export UID=1000
-#export GID=1000
-
-# You can generate a more secure secret by running: ./run rails secret
-export SECRET_KEY_BASE=insecure_key_for_dev
-
-# Which environment is running? These should be "development" or "production".
-#export RAILS_ENV=production
-#export NODE_ENV=production
-export RAILS_ENV=development
-export NODE_ENV=development
-
-# The bind port for puma.
-#
-# Be warned that if you change this value you'll need to change 8000 in both
-# your Dockerfile and in a few spots in docker-compose.yml due to the nature of
-# how this value can be set (Docker Compose doesn't support nested ENV vars).
-#export PORT=8000
-
-# How many workers and threads should your app use? WEB_CONCURRENCY defaults
-# to the server's CPU count * 2. That is a good starting point. In development
-# it's a good idea to use 1 to avoid race conditions when debugging.
-#export WEB_CONCURRENCY=
-#export RAILS_MAX_THREADS=5
-#export WEB_CONCURRENCY=1
-#export RAILS_MAX_THREADS=1
-
-# You'll always want to set POSTGRES_USER and POSTGRES_PASSWORD since the
-# postgres Docker image uses them for its default database user and password.
-export POSTGRES_USER=hello
-export POSTGRES_PASSWORD=password
-#export POSTGRES_DB=hello
-#export POSTGRES_HOST=postgres
-#export POSTGRES_PORT=5432
-
-# What's your full Redis connection URL? This will be used for caching, Sidekiq,
-# and Action Cable. You can always split them up later.
-#export REDIS_URL=redis://redis:6379/1
-
-# The bind port for puma but for Action Cable.
-#
-# Be warned that if you change this value you'll need to change 28080 in a few
-# spots in docker-compose.yml due to the nature of how this value can be set
-# (Docker Compose doesn't support nested ENV vars).
-#export CABLE_PORT=28080
-
-# The Action Cable address that will be accessible over HTTP. In production
-# you would typically have this reverse proxied to a sub-domain with nginx, in
-# which case you would set something like: ws://cable.example.com
-#
-# This is one case where it defaults to a development value because it's not
-# possible for me to know what domain name you'll be using.
-#export ACTION_CABLE_FRONTEND_URL=ws://localhost:28080
-
-# Comma separated list of RegExp origins to allow connections from for Action
-# Cable. The values will be converted into a proper RegExp, so omit the / /.
-#
-# Examples:
-#   http:\/\/localhost*
-#   http:\/\/example.*,https:\/\/example.*
-#export ACTION_CABLE_ALLOWED_REQUEST_ORIGINS=http:\/\/localhost*
-
-# If this is set then Rails will serve files from public/ in production. You
-# probably don't want this behavior unless you're testing prod mode locally,
-# because nginx would typically serve static files.
-#export RAILS_SERVE_STATIC_FILES=
-
-# Should Docker restart your containers if they go down in unexpected ways?
-#export DOCKER_RESTART_POLICY=unless-stopped
-export DOCKER_RESTART_POLICY=no
-
-# What health check test command do you want to run? In development, having it
-# curl your web server will result in a lot of log spam, so setting it to
-# /bin/true is an easy way to make the health check do basically nothing.
-#export DOCKER_WEB_HEALTHCHECK_TEST=curl localhost:8000/up
-export DOCKER_WEB_HEALTHCHECK_TEST=/bin/true
-
-# What ip:port should be published back to the Docker host for the app server?
-# If you're using Docker Toolbox or a custom VM you can't use 127.0.0.1. This
-# is being overwritten in dev to be compatible with more dev environments.
-#
-# If you have a port conflict because something else is using 8000 then you
-# can either stop that process or change 8000 to be something else.
-#
-# Use the default in production to avoid having puma directly accessible to
-# the internet since it'll very likely be behind nginx or a load balancer.
-#export DOCKER_WEB_PORT_FORWARD=127.0.0.1:8000
-export DOCKER_WEB_PORT_FORWARD=127.0.0.1:3000
-
-# This is the same as above except for Action Cable.
-#export DOCKER_CABLE_PORT_FORWARD=127.0.0.1:28080
-export DOCKER_CABLE_PORT_FORWARD=28080
-
-# What volume path should be used? In dev we want to volume mount everything
-# so that we can develop our code without rebuilding our Docker images.
-#export DOCKER_WEB_VOLUME=./public:/app/public
-
-
-export DOCKER_WEB_VOLUME=.:/app
-
-# What CPU and memory constraints will be added to your services? When left at
-# 0 they will happily use as much as needed.
-# export DOCKER_POSTGRES_CPUS=0
-# export DOCKER_POSTGRES_MEMORY=0
-# export DOCKER_REDIS_CPUS=0
-# export DOCKER_REDIS_MEMORY=0
-# export DOCKER_WEB_CPUS=0
-# export DOCKER_WEB_MEMORY=0
-# export DOCKER_WORKER_CPUS=0
-# export DOCKER_WORKER_MEMORY=0
-# export DOCKER_CABLE_CPUS=0
-# export DOCKER_CABLE_MEMORY=0
+API_IMAGE_REPOSITORY=agroportal
+API_IMAGE_TAG=stage
+API_URL=http://localhost:9393

.github/workflows/docker-dev-release.yml

@@ -0,0 +1,45 @@
+name: Docker branch Images build
+
+on:
+  push:
+    branches:
+      - development
+      - stage
+      - test
+
+jobs:
+  push_to_registry:
+    name: Push Docker branch image to Docker Hub
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v3
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v2
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v4
+        with:
+          images: agroportal/ontoportal_web_ui
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v4
+        with:
+          context: .
+          platforms: linux/amd64,linux/arm64
+          build-args: |
+            RUBY_VERSION=2.7
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

.github/workflows/tests-real-data.yml

@@ -0,0 +1,52 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+# This workflow will download a prebuilt Ruby version, install dependencies and run tests with Rake
+# For more information see: https://github.com/marketplace/actions/setup-ruby-jruby-and-truffleruby
+name: "Run remote API tests CI"
+
+on:
+  push:
+  pull_request_target:
+    types: [ opened, reopened ]
+env:
+  API_URL: ${{ secrets.API_URL }}
+  API_KEY: ${{ secrets.API_KEY }}
+  BIOMIXER_URL: ${{ secrets.BIOMIXER_URL }}
+  FAIRNESS_URL: ${{ secrets.FAIRNESS_URL }}
+  ANNOTATOR_URL: ${{ secrets.ANNOTATOR_URL }}
+  DB_HOST: 127.0.0.1
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    services:
+      mysql:
+        image: mysql:8.0
+        ports:
+          - "3306:3306"
+        env:
+          MYSQL_ROOT_PASSWORD: root
+      memcached:
+        image: memcached:1.6
+        ports:
+          - 11211:11211
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+      # Add or replace dependency steps here
+      - name: Install Ruby and gems
+        uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: 2.7.8
+          bundler-cache: true
+      # Add or replace database setup steps here
+      - name: set up config file
+        run: cp config/database.yml.sample config/database.yml
+      - name: Set up database schema
+        run: RAILS_ENV=test bin/rails db:setup
+      - name: Set up yarn
+        run: yarn install
+      # Add or replace test runners here
+      - name: Run tests
+        run:  RAILS_ENV=test bin/rails test test/controllers/* -v

.github/workflows/tests.yml

@@ -4,28 +4,30 @@
 # documentation.
 # This workflow will download a prebuilt Ruby version, install dependencies and run tests with Rake
 # For more information see: https://github.com/marketplace/actions/setup-ruby-jruby-and-truffleruby
-name: "Ruby on Rails CI"
+name: "Run local API tests CI"
 
 on:
   push:
   pull_request_target:
     types: [ opened, reopened ]
 env:
-  API_URL: ${{ secrets.API_URL }}
-  API_KEY: ${{ secrets.API_KEY }}
+  API_URL: http://localhost:9393
+  REMOTE_API_KEY: 8b5b7825-538d-40e0-9e9e-5ab9274a9aeb
+  REMOTE_API_URL: https://data.bioontology.org
   BIOMIXER_URL: ${{ secrets.BIOMIXER_URL }}
   FAIRNESS_URL: ${{ secrets.FAIRNESS_URL }}
   ANNOTATOR_URL: ${{ secrets.ANNOTATOR_URL }}
+  DB_HOST: 127.0.0.1
 jobs:
   test:
     runs-on: ubuntu-latest
     services:
       mysql:
-        image: mysql:latest
+        image: mysql:8.0
         ports:
           - "3306:3306"
         env:
-          MYSQL_ROOT_PASSWORD: 'bp_user'
+          MYSQL_ROOT_PASSWORD: root
       memcached:
         image: memcached:1.6
         ports:
@@ -39,6 +41,10 @@ jobs:
         with:
           ruby-version: 2.7.8
           bundler-cache: true
+
+      - name: Run OntoPortal API
+        run: bin/run_api -k ${{ env.REMOTE_API_KEY }} -r agroportal -t stage -s STY -u ${{ env.REMOTE_API_URL }}
+
       # Add or replace database setup steps here
       - name: set up config file
         run: cp config/database.yml.sample config/database.yml
@@ -48,4 +54,4 @@ jobs:
         run: yarn install
       # Add or replace test runners here
       - name: Run tests
-        run: RAILS_ENV=test bin/rails test -v
+        run:  RAILS_ENV=test bin/rails test -v

Dockerfile

@@ -1,50 +1,55 @@
-FROM ruby:2.7.5-alpine AS app
-
+# Make sure it matches the Ruby version in .ruby-version and Gemfile
+ARG RUBY_VERSION=3.2.0
+FROM ruby:${RUBY_VERSION}-alpine
+
+# Install libvips for Active Storage preview support
+RUN apk add --no-cache build-base \
+                       libxml2-dev \
+                       libxslt-dev \
+                       mariadb-dev \
+                       git \
+                       tzdata \
+                       nodejs yarn \
+                       less \
+                       bash \
+                       docker \
+                       docker-compose \
+    && mkdir /node_modules
+
+# Rails app lives here
 WORKDIR /app
 
-ARG UID=1000
-ARG GID=1000
-
-RUN apk add --no-cache \
-    build-base \
-    libxml2-dev \
-    libxslt-dev \
-    mariadb-dev \
-    git \
-    nodejs \
-    tzdata \
-    yarn \
-    less \
-  && addgroup --gid ${GID} ruby \
-  && adduser  -u ${UID} -G ruby -D  ruby \
-  && chown ruby:ruby -R /app \
-  && mkdir /node_modules \
-  && chown ruby:ruby -R /node_modules /app
-
-USER ruby
-
-COPY --chown=ruby:ruby bin/ ./bin
-RUN chmod 0755 bin/*
-
+# Set production environment
 ARG RAILS_ENV="production"
+ARG BUNDLE_WITHOUT="development test"
 
-ENV RAILS_ENV="${RAILS_ENV}" \
-    NODE_ENV="${NODE_ENV}" \
-    PATH="${PATH}:/home/ruby/.local/bin:/node_modules/.bin" \
-    USER="ruby" \
-    BUNDLE_PATH=/usr/local/bundle
-
-COPY --chown=ruby:ruby Gemfile* ./
-RUN bundle install --jobs "$(nproc)"
-RUN gem install rails 
+ENV RAILS_LOG_TO_STDOUT="1" \
+    RAILS_SERVE_STATIC_FILES="true" \
+    RAILS_ENV="${RAILS_ENV}" \
+    BUNDLE_PATH=/usr/local/bundle \
+    BUNDLE_WITHOUT="${BUNDLE_WITHOUT}"
 
+RUN gem update --system && \
+    gem install bundler
 
+COPY Gemfile* .
+RUN bundle install
 
 RUN echo "--modules-folder /node_modules" > .yarnrc
-COPY --chown=ruby:ruby package.json *yarn* ./
+COPY package.json *yarn* ./
 RUN yarn install
 
+COPY . .
+
+# Precompile bootsnap code for faster boot times
+RUN bundle exec bootsnap precompile --gemfile app/ lib/
+
+# Precompiling assets for production without requiring secret RAILS_MASTER_KEY
+COPY ./config/database.yml.sample ./config/database.yml
+RUN SECRET_KEY_BASE_DUMMY=1 RAILS_ENV=test bundle exec rails assets:precompile
+
 
+ENV BINDING="0.0.0.0"
 EXPOSE 3000
 
-CMD ["sh"]
+CMD ["bash"]