Merge branch 'development' into test

.env.sample

@@ -1,7 +1,43 @@
+##################### UI configuration ####################
+RAILS_ENV=development
+SITE=Testportal
+ORG=LIRMM
+ORG_URL=http://www.lirmm.fr
+
+UI_URL=http://localhost:3000
+API_URL=http://localhost:9393
+API_KEY=
+
+UI_THEME=ontoportal
+
+BIOMIXER_URL=
+BIOMIXER_APIKEY=
+
+ANNOTATOR_URL=
+
+FAIRNESS_DISABLED=false
+FAIRNESS_URL=
+
+NCBO_ANNOTATORPLUS_ENABLED=false
+NCBO_ANNOTATOR_URL=
+NCBO_API_KEY=
+
+SUPPORT_EMAIL=[email protected]
+RELEASE_VERSION="OntoPortal Appliance 3.0.1"
+
+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"
-STARTER_ONTOLOGY=STY
 
+## Image repositroy from which the ontoportal api will be built
 API_IMAGE_REPOSITORY=agroportal
-API_IMAGE_TAG=stage
-API_URL=http://localhost:9393
+## Image tag/version from which the ontoportal api will be built
+API_IMAGE_TAG=development
+
+

.github/workflows/deploy.yml

@@ -9,6 +9,7 @@
 # GH_PAT - github Personal Access Token for accessing private config repo
 #
 # SSH_JUMPHOST - ssh jump/proxy host though which deployments have to though if UI nodes live on private network.
+# SSH_JUMPHOST_USER - username  to use to connect to the ssh jump/proxy.
 #
 # DEPLOY_ENC_KEY - key for decrypting deploymnet ssh key residing in config/
 # this SSH key is used for accessing jump host, UI nodes, and private github repo.
@@ -17,26 +18,27 @@ name: Capistrano Deployment
 # Controls when the action will run.
 on:
   push:
-    branches: [ development staging ]
+    branches: [ stage test]
   # Allows running this workflow manually from the Actions tab
   workflow_dispatch:
     inputs:
       BRANCH:
         description: 'Branch/tag to deploy'
         options:
-          - development
-          - staging
+          - stage
+          - test
           - master
-        default: staging
+        default: test
         required: true
       environment:
         description: 'target environment to deploy to'
         type: choice
         options:
-          - development
           - staging
           - production
-        default: staging
+          - appliance
+          - test
+        default: test
 jobs:
   deploy:
     runs-on: ubuntu-latest
@@ -55,6 +57,13 @@ jobs:
 
         USER_INPUT_ENVIRONMENT=${{ inputs.environment }}
         echo "TARGET=${USER_INPUT_ENVIRONMENT:-staging}" >> $GITHUB_ENV
+        
+        CONFIG_REPO=${{ secrets.CONFIG_REPO }}
+        GH_PAT=${{ secrets.GH_PAT }}
+        echo "PRIVATE_CONFIG_REPO=https://${GH_PAT}@github.com/${CONFIG_REPO}" >> $GITHUB_ENV
+        
+        echo "SSH_JUMPHOST=${{ secrets.SSH_JUMPHOST }}" >> $GITHUB_ENV
+        echo "SSH_JUMPHOST_USER=${{ secrets.SSH_JUMPHOST_USER }}" >> $GITHUB_ENV
     # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
     - uses: actions/checkout@v3
     - uses: ruby/setup-ruby@v1
@@ -69,6 +78,13 @@ jobs:
         path:  deploy_config
     - name: copy-deployment-config
       run:  cp -r deploy_config/ontoportal_web_ui/${{ inputs.environment }}/* .
+      # add ssh hostkey so that capistrano doesn't complain
+    - name: Add jumphost's hostkey to Known Hosts
+      run: |
+        mkdir -p ~/.ssh
+        echo "${{ secrets.SSH_JUMPHOST }}"
+        ssh-keyscan -H ${{ secrets.SSH_JUMPHOST }} > ~/.ssh/known_hosts
+      shell: bash
     - uses: miloserdow/capistrano-deploy@master
       with:
         target: ${{ env.TARGET }} # which environment to deploy

.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: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v4
+        with:
+          images: | 
+            agroportal/ontoportal_web_ui
+            ghcr.io/${{ github.repository }}
+
+      - 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