Merge branch 'master' into development

ontoportal-lirmm · Jun 12, 2024 · cd4f7bb · cd4f7bb
2 parents bfe18b5 + 88c6855
commit cd4f7bb
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Showing 21 changed files with 305 additions and 171 deletions.
diff --git a/.dockerignore b/.dockerignore
@@ -20,3 +20,6 @@ docker-compose.override.yml
 yarn-error.log
 yarn-debug.log*
 .yarn-integrity
+
+config/credentials/*
+config/credentials.yml.enc
diff --git a/.github/workflows/deploy.yml b/.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
diff --git a/.github/workflows/docker-image.yml b/.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

diff --git a/Dockerfile b/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

diff --git a/Gemfile b/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'
@@ -108,8 +108,8 @@ gem 'omniauth'
 gem 'omniauth-rails_csrf_protection'
 gem 'omniauth-github'
 gem 'omniauth-google-oauth2'
-gem 'omniauth-orcid'
 gem 'omniauth-keycloak'
+gem 'omniauth-orcid'
 
 group :staging, :production, :appliance do
   # Application performance monitoring

diff --git a/Gemfile.lock b/Gemfile.lock
@@ -17,67 +17,67 @@ GIT
 GEM
   remote: https://rubygems.org/
   specs:
-    actioncable (7.0.7)
-      actionpack (= 7.0.7)
-      activesupport (= 7.0.7)
+    actioncable (7.0.3)
+      actionpack (= 7.0.3)
+      activesupport (= 7.0.3)
       nio4r (~> 2.0)
       websocket-driver (>= 0.6.1)
-    actionmailbox (7.0.7)
-      actionpack (= 7.0.7)
-      activejob (= 7.0.7)
-      activerecord (= 7.0.7)
-      activestorage (= 7.0.7)
-      activesupport (= 7.0.7)
+    actionmailbox (7.0.3)
+      actionpack (= 7.0.3)
+      activejob (= 7.0.3)
+      activerecord (= 7.0.3)
+      activestorage (= 7.0.3)
+      activesupport (= 7.0.3)
       mail (>= 2.7.1)
       net-imap
       net-pop
       net-smtp
-    actionmailer (7.0.7)
-      actionpack (= 7.0.7)
-      actionview (= 7.0.7)
-      activejob (= 7.0.7)
-      activesupport (= 7.0.7)
+    actionmailer (7.0.3)
+      actionpack (= 7.0.3)
+      actionview (= 7.0.3)
+      activejob (= 7.0.3)
+      activesupport (= 7.0.3)
       mail (~> 2.5, >= 2.5.4)
       net-imap
       net-pop
       net-smtp
       rails-dom-testing (~> 2.0)
-    actionpack (7.0.7)
-      actionview (= 7.0.7)
-      activesupport (= 7.0.7)
-      rack (~> 2.0, >= 2.2.4)
+    actionpack (7.0.3)
+      actionview (= 7.0.3)
+      activesupport (= 7.0.3)
+      rack (~> 2.0, >= 2.2.0)
       rack-test (>= 0.6.3)
       rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.0, >= 1.2.0)
-    actiontext (7.0.7)
-      actionpack (= 7.0.7)
-      activerecord (= 7.0.7)
-      activestorage (= 7.0.7)
-      activesupport (= 7.0.7)
+    actiontext (7.0.3)
+      actionpack (= 7.0.3)
+      activerecord (= 7.0.3)
+      activestorage (= 7.0.3)
+      activesupport (= 7.0.3)
       globalid (>= 0.6.0)
       nokogiri (>= 1.8.5)
-    actionview (7.0.7)
-      activesupport (= 7.0.7)
+    actionview (7.0.3)
+      activesupport (= 7.0.3)
       builder (~> 3.1)
       erubi (~> 1.4)
       rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.1, >= 1.2.0)
-    activejob (7.0.7)
-      activesupport (= 7.0.7)
+    activejob (7.0.3)
+      activesupport (= 7.0.3)
       globalid (>= 0.3.6)
-    activemodel (7.0.7)
-      activesupport (= 7.0.7)
-    activerecord (7.0.7)
-      activemodel (= 7.0.7)
-      activesupport (= 7.0.7)
-    activestorage (7.0.7)
-      actionpack (= 7.0.7)
-      activejob (= 7.0.7)
-      activerecord (= 7.0.7)
-      activesupport (= 7.0.7)
+    activemodel (7.0.3)
+      activesupport (= 7.0.3)
+    activerecord (7.0.3)
+      activemodel (= 7.0.3)
+      activesupport (= 7.0.3)
+    activestorage (7.0.3)
+      actionpack (= 7.0.3)
+      activejob (= 7.0.3)
+      activerecord (= 7.0.3)
+      activesupport (= 7.0.3)
       marcel (~> 1.0)
       mini_mime (>= 1.1.0)
-    activesupport (7.0.7)
+    activesupport (7.0.3)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 1.6, < 2)
       minitest (>= 5.1)
@@ -325,7 +325,7 @@ GEM
       rack (>= 1.2, < 4)
       snaky_hash (~> 2.0)
       version_gem (~> 1.1)
-    oj (3.16.3)
+    oj (3.16.4)
       bigdecimal (>= 3.0)
     omniauth (2.1.2)
       hashie (>= 3.4.6)
@@ -373,20 +373,20 @@ GEM
       rack (~> 2.2, >= 2.2.4)
     rack-test (2.1.0)
       rack (>= 1.3)
-    rails (7.0.7)
-      actioncable (= 7.0.7)
-      actionmailbox (= 7.0.7)
-      actionmailer (= 7.0.7)
-      actionpack (= 7.0.7)
-      actiontext (= 7.0.7)
-      actionview (= 7.0.7)
-      activejob (= 7.0.7)
-      activemodel (= 7.0.7)
-      activerecord (= 7.0.7)
-      activestorage (= 7.0.7)
-      activesupport (= 7.0.7)
+    rails (7.0.3)
+      actioncable (= 7.0.3)
+      actionmailbox (= 7.0.3)
+      actionmailer (= 7.0.3)
+      actionpack (= 7.0.3)
+      actiontext (= 7.0.3)
+      actionview (= 7.0.3)
+      activejob (= 7.0.3)
+      activemodel (= 7.0.3)
+      activerecord (= 7.0.3)
+      activestorage (= 7.0.3)
+      activesupport (= 7.0.3)
       bundler (>= 1.15.0)
-      railties (= 7.0.7)
+      railties (= 7.0.3)
     rails-dom-testing (2.2.0)
       activesupport (>= 5.0.0)
       minitest
@@ -397,9 +397,9 @@ GEM
     rails-i18n (7.0.9)
       i18n (>= 0.7, < 2)
       railties (>= 6.0.0, < 8)
-    railties (7.0.7)
-      actionpack (= 7.0.7)
-      activesupport (= 7.0.7)
+    railties (7.0.3)
+      actionpack (= 7.0.3)
+      activesupport (= 7.0.3)
       method_source
       rake (>= 12.2)
       thor (~> 1.0)
@@ -593,7 +593,7 @@ DEPENDENCIES
   mysql2
   net-ftp (~> 0.2.0)
   net-http (~> 0.3.2)
-  newrelic_rpm
+  newrelic_rpm (< 9.10.0)
   oj
   omniauth
   omniauth-github
@@ -604,7 +604,7 @@ DEPENDENCIES
   ontologies_api_client!
   pry
   puma (~> 5.0)
-  rails (= 7.0.7)
+  rails (= 7.0.3)
   rails-i18n (~> 7.0.0)
   recaptcha (~> 5.9.0)
   rest-client

diff --git a/app/assets/stylesheets/ontologies.scss b/app/assets/stylesheets/ontologies.scss
@@ -195,7 +195,7 @@ $widget-table-border-color: #EFEFEF;
 #bd_content .sidebar {
   overflow-x: auto;
   white-space: nowrap;
-  min-width: 35%;
+  min-width: 29%;
 }
 
 #search_box:focus {

diff --git a/app/controllers/concerns/submission_filter.rb b/app/controllers/concerns/submission_filter.rb
@@ -236,7 +236,7 @@ def ontology_hash(ont, submissions)
     o[:individual_count_formatted] = number_with_delimiter(o[:individual_count], delimiter: ',')
 
     o[:note_count] = ont.notes&.length || 0
-    o[:project_count] = ont.projects&.length ||
+    o[:project_count] = ont.projects&.length || 0
     o[:popularity] = @analytics[ont.acronym] || 0
     o[:rank] = sub&[:rank] || 0