Merge branch 'development' into ecoportal

.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