Merge to master - Release 2.7.0.3 - New UI, Multilingual integration, New metadata mode and docker images

.env.sample

@@ -1,137 +1,43 @@
-# 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.
+##################### UI configuration ####################
+RAILS_ENV=development
+SITE=Testportal
+ORG=LIRMM
+ORG_URL=http://www.lirmm.fr
 
-# Enable BuildKit by default:
-#   https://docs.docker.com/develop/develop-images/build_enhancements
-export DOCKER_BUILDKIT=1
+UI_URL=http://localhost:3000
+API_URL=http://localhost:9393
+API_KEY=
 
-# Rather than use the directory name, let's control the name of the project.
-export COMPOSE_PROJECT_NAME=ontoportal-docker
+UI_THEME=ontoportal
 
-# 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
+BIOMIXER_URL=
+BIOMIXER_APIKEY=
 
-# 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
+ANNOTATOR_URL=
 
-# You can generate a more secure secret by running: ./run rails secret
-export SECRET_KEY_BASE=insecure_key_for_dev
+FAIRNESS_DISABLED=false
+FAIRNESS_URL=
 
-# 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
+NCBO_ANNOTATORPLUS_ENABLED=false
+NCBO_ANNOTATOR_URL=
+NCBO_API_KEY=
 
-# 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
+[email protected]
+RELEASE_VERSION="OntoPortal Appliance 3.0.1"
 
-# 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
+ANALYTICS_ID=
+USE_RECAPTCHA=false
+####################  Buidling the API for running tests ####################
+## An ontology that will be imported in the starting of the API server
+STARTER_ONTOLOGY=STY
+## API key of a remote API used to download the starter ontology
+OP_API_KEY=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb
+## API url of the remote API used to download the starter ontology
+OP_API_URL="https://data.bioontology.org"
 
-# 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
+## Image repositroy from which the ontoportal api will be built
+API_IMAGE_REPOSITORY=agroportal
+## Image tag/version from which the ontoportal api will be built
+API_IMAGE_TAG=development
 
-# 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

.github/workflows/docker-image-arm.yml

@@ -0,0 +1,56 @@
+name: Docker branch Images build - ARM version
+
+on:
+  push:
+    branches:
+      - development
+      - stage
+      - test
+  release:
+    types: [ published ]
+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@f4ef78c080cd8ba55a85445d5b36e214a81df20a
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@65b78e6e13532edd9afa3aa52ac7964289d1a9c1
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v4
+        with:
+          images: | 
+            agroportal/ontoportal_web_ui-arm
+            ghcr.io/${{ github.repository }}-arm
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v4
+        with:
+          context: .
+          platforms: linux/arm64
+          build-args: |
+            RUBY_VERSION=2.7.8
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}-${{ env.BRANCH_NAME }}-arm64
+          labels: ${{ steps.meta.outputs.labels }}
+

.github/workflows/docker-image.yml

@@ -0,0 +1,55 @@
+name: Docker branch Images build
+
+on:
+  push:
+    branches:
+      - development
+      - stage
+      - test
+  release:
+    types: [ published ]
+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@f4ef78c080cd8ba55a85445d5b36e214a81df20a
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@65b78e6e13532edd9afa3aa52ac7964289d1a9c1
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v4
+        with:
+          images: |
+            agroportal/ontoportal_web_ui
+            ghcr.io/${{ github.repository }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v4
+        with:
+          context: .
+          platforms: linux/amd64
+          build-args: |
+            RUBY_VERSION=2.7.8
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

.github/workflows/tests-real-data-stageportal.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 (stageportal) tests CI"
+
+on:
+  push:
+  pull_request_target:
+    types: [ opened, reopened ]
+env:
+  API_URL: https://data.stageportal.lirmm.fr/ # or ${{ secrets.API_URL }}
+  API_KEY: 1de0a270-29c5-4dda-b043-7c3580628cd5 # public apikey or ${{ 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-real-data-testportal.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 (testportal) tests CI"
+
+on:
+  push:
+  pull_request_target:
+    types: [ opened, reopened ]
+env:
+  API_URL: https://data.testportal.lirmm.fr/ # or ${{ secrets.API_URL }}
+  API_KEY: 1de0a270-29c5-4dda-b043-7c3580628cd5 # public apikey or ${{ 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