Merge branch 'master' into development

.dockerignore

@@ -20,3 +20,6 @@ docker-compose.override.yml
 yarn-error.log
 yarn-debug.log*
 .yarn-integrity
+
+config/credentials/*
+config/credentials.yml.enc

.github/workflows/deploy.yml

@@ -18,27 +18,28 @@ name: Capistrano Deployment
 # Controls when the action will run.
 on:
   push:
-    branches: [ stage test]
+    branches:
+      - stage
+      - test
   # Allows running this workflow manually from the Actions tab
   workflow_dispatch:
     inputs:
       BRANCH:
-        description: 'Branch/tag to deploy'
+        description: "Branch/tag to deploy"
         options:
           - stage
           - test
           - master
-        default: test
+        default: stage
         required: true
       environment:
-        description: 'target environment to deploy to'
+        description: "target environment to deploy to"
         type: choice
         options:
           - staging
-          - production
-          - appliance
+          - agroportal
           - test
-        default: test
+        default: stage
 jobs:
   deploy:
     runs-on: ubuntu-latest
@@ -47,45 +48,45 @@ jobs:
       PRIVATE_CONFIG_REPO: ${{ format('[email protected]:{0}.git', secrets.CONFIG_REPO) }}
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
-    - name: set branch/tag and environment to deploy from inputs
-      run: |
-        # workflow_dispatch default input doesn't get set on push so we need to set defaults
-        # via shell parameter expansion
-        # https://dev.to/mrmike/github-action-handling-input-default-value-5f2g
-        USER_INPUT_BRANCH=${{ inputs.branch }}
-        echo "BRANCH=${USER_INPUT_BRANCH:github.head_ref:-master}" >> $GITHUB_ENV
+      - name: set branch/tag and environment to deploy from inputs
+        run: |
+          # workflow_dispatch default input doesn't get set on push so we need to set defaults
+          # via shell parameter expansion
+          # https://dev.to/mrmike/github-action-handling-input-default-value-5f2g
+          USER_INPUT_BRANCH=${{ inputs.branch }}
+          echo "BRANCH=${USER_INPUT_BRANCH:github.head_ref:-master}" >> $GITHUB_ENV
 
-        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
-      with:
-        ruby-version: 2.7.6 # Not needed with a .ruby-version file
-        bundler-cache: true # runs 'bundle install' and caches installed gems automatically
-    - name: get-deployment-config
-      uses: actions/checkout@v3
-      with:
-        repository: ${{ secrets.CONFIG_REPO }} # repository containing deployment settings
-        token: ${{ secrets.GH_PAT }} # `GH_PAT` is a secret that contains your PAT
-        path:  deploy_config
-    - name: copy-deployment-config
-      run:  cp -r deploy_config/ontoportal_web_ui/${{ 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
-        deploy_key: ${{ secrets.DEPLOY_ENC_KEY }} # Name of the variable configured in Settings/Secrets of your github project
+          USER_INPUT_ENVIRONMENT=${{ 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
+        with:
+          ruby-version: 2.7.6 # Not needed with a .ruby-version file
+          bundler-cache: true # runs 'bundle install' and caches installed gems automatically
+      - name: get-deployment-config
+        uses: actions/checkout@v3
+        with:
+          repository: ${{ secrets.CONFIG_REPO }} # repository containing deployment settings
+          token: ${{ secrets.GH_PAT }} # `GH_PAT` is a secret that contains your PAT
+          path: deploy_config
+      - name: copy-deployment-config
+        run: cp -r deploy_config/ontoportal_web_ui/${{ 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
+          deploy_key: ${{ secrets.DEPLOY_ENC_KEY }} # Name of the variable configured in Settings/Secrets of your github project

.github/workflows/docker-image.yml

@@ -3,11 +3,12 @@ name: Docker branch Images build
 on:
   push:
     branches:
+      - master
       - development
       - stage
       - test
   release:
-    types: [ published ]
+    types: [published]
 jobs:
   push_to_registry:
     name: Push Docker branch image to Docker Hub

Dockerfile

@@ -38,10 +38,14 @@ RUN yarn install && yarn build
 
 
 
+RUN cp config/bioportal_config_env.rb.sample config/bioportal_config_production.rb
+RUN cp config/bioportal_config_env.rb.sample config/bioportal_config_development.rb
+RUN cp config/database.yml.sample config/database.yml
+
 # Precompile bootsnap code for faster boot times
 RUN bundle exec bootsnap precompile --gemfile app/ lib/
 
-# RUN SECRET_KEY_BASE_DUMMY="1" ./bin/rails assets:precompile
+RUN SECRET_KEY_BASE_DUMMY="1" ./bin/rails assets:precompile
 
 ENV BINDING="0.0.0.0"
 EXPOSE 3000

Gemfile

@@ -2,7 +2,7 @@ source 'https://rubygems.org'
 
 # Main Rails gem
 # Bundle edge Rails instead: gem 'rails', github: 'rails/rails'
-gem 'rails', '7.0.7'
+gem 'rails', '7.0.3'
 
 # JavaScript bundling for Rails
 gem 'jsbundling-rails'
@@ -96,7 +96,8 @@ gem 'flag-icons-rails', '~> 3.4'
 gem 'iso-639', '~> 0.3.6'
 
 # Custom API client
-gem 'ontologies_api_client', git: 'https://github.com/ontoportal-lirmm/ontologies_api_ruby_client.git', branch: 'development'
+gem 'ontologies_api_client', git: 'https://github.com/ontoportal-lirmm/ontologies_api_ruby_client.git',
+                             branch: 'development'
 
 # Ruby 2.7.8 pinned gems (to remove when migrating to Ruby >= 3.0)
 gem 'ffi', '~> 1.16.3'
@@ -105,15 +106,15 @@ gem 'net-http', '~> 0.3.2'
 
 # Multi-Provider Authentication
 gem 'omniauth'
-gem 'omniauth-rails_csrf_protection'
 gem 'omniauth-github'
 gem 'omniauth-google-oauth2'
-gem 'omniauth-orcid'
 gem 'omniauth-keycloak'
+gem 'omniauth-orcid'
+gem 'omniauth-rails_csrf_protection'
 
 group :staging, :production, :appliance do
   # Application performance monitoring
-  gem 'newrelic_rpm'
+  gem 'newrelic_rpm', '< 9.10.0'
 
   # Error monitoring
   gem 'bugsnag', '~> 6.26'
@@ -151,9 +152,9 @@ group :development do
 
   # Internationalization tasks
   # gem 'i18n-debug'
+  gem 'deepl-rb'
   gem 'i18n-tasks'
   gem 'i18n-tasks-csv', '~> 1.1'
-  gem 'deepl-rb'
 
   # Email preview in the browser
   gem 'letter_opener_web', '~> 2.0'