Merge pull request #14 from ncbo/master

Sync: bring OntoPortal up-to-date with BioPortal releases 6.13.0 and 6.13.1
ncbo · Sep 30, 2023 · 58f038e · 58f038e
2 parents ccac202 + b45ed09
commit 58f038e
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Showing 26 changed files with 252 additions and 128 deletions.
diff --git a/.github/workflows/brakeman-analysis.yml b/.github/workflows/brakeman-analysis.yml
@@ -22,12 +22,10 @@ jobs:
     # Customize the ruby version depending on your needs
     - name: Setup Ruby
       uses: ruby/setup-ruby@v1
-      with:
-        ruby-version: '2.7'
 
     - name: Setup Brakeman
       env:
-        BRAKEMAN_VERSION: '5.4.0' # SARIF support is provided in Brakeman version 4.10+
+        BRAKEMAN_VERSION: '6.0.1' # SARIF support is provided in Brakeman version 4.10+
       run: |
         gem install brakeman --version $BRAKEMAN_VERSION
 

diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
@@ -59,7 +59,6 @@ jobs:
     - uses: actions/checkout@v3
     - uses: ruby/setup-ruby@v1
       with:
-        ruby-version: 2.7.7 # 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
@@ -75,7 +74,7 @@ jobs:
         mkdir -p ~/.ssh
         ssh-keyscan -H ${{ secrets.SSH_JUMPHOST }} > ~/.ssh/known_hosts
       shell: bash
-    - uses: miloserdow/capistrano-deploy@master
+    - uses: miloserdow/capistrano-deploy@v3
       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/.gitignore b/.gitignore
@@ -25,8 +25,6 @@ config/deploy/*
 /public/assets/
 nohup.out
 
-.ruby-version
-
 # Ignore editor files
 .idea
 *.swp

diff --git a/.ruby-version b/.ruby-version
@@ -0,0 +1 @@
+3.0.6
diff --git a/Capfile b/Capfile
@@ -15,16 +15,15 @@ require 'capistrano/deploy'
 #   https://github.com/capistrano/rails
 #
 # require 'capistrano/rvm'
-# require 'capistrano/rbenv'
+require 'capistrano/rbenv'
 # require 'capistrano/chruby'
 require 'capistrano/bundler'
 require "capistrano/scm/git"
 install_plugin Capistrano::SCM::Git
 #require 'capistrano/rails/assets'
 #require 'capistrano/rails/migrations'
 require 'capistrano/rails'
-require 'capistrano/yarn'
 require 'capistrano/locally'
-
+require 'capistrano/yarn'
 # Loads custom tasks from `lib/capistrano/tasks' if you have any defined.
 Dir.glob('lib/capistrano/tasks/*.cap').each { |r| import r }
diff --git a/Gemfile b/Gemfile
@@ -34,7 +34,7 @@ gem 'haml', '~> 5.1'
 gem 'i18n'
 gem 'iconv'
 gem 'multi_json'
-gem 'mysql2', '0.5.2'
+gem 'mysql2', '0.5.5'
 gem 'oj'
 gem 'open_uri_redirections'
 gem 'pry'
@@ -44,6 +44,7 @@ gem 'rails_autolink'
 gem 'rdoc'
 gem 'recaptcha', '~> 5.9.0'
 gem 'rest-client'
+gem 'rexml', '~> 3'
 gem 'stackprof', require: false
 gem 'thin'
 gem 'will_paginate', '~> 3.0'
@@ -61,8 +62,9 @@ end
 group :development do
   # Capistrano Deployment
   gem 'bcrypt_pbkdf', '>= 1.0', '< 2.0', require: false # https://github.com/miloserdow/capistrano-deploy/issues/42
-  gem 'capistrano', '~> 3.11', require: false
+  gem 'capistrano', '~> 3.17', require: false
   gem 'capistrano-bundler', require: false
+  gem 'capistrano-rbenv', require: false
   gem 'capistrano-locally', require: false
   gem 'capistrano-passenger', require: false
   gem 'capistrano-rails', '~> 1.4', require: false

diff --git a/Gemfile.lock b/Gemfile.lock
@@ -77,19 +77,20 @@ GEM
       minitest (>= 5.1)
       tzinfo (~> 2.0)
       zeitwerk (~> 2.3)
-    addressable (2.8.4)
+    addressable (2.8.5)
       public_suffix (>= 2.0.2, < 6.0)
-    airbrussh (1.4.1)
+    airbrussh (1.4.2)
       sshkit (>= 1.6.1, != 1.7.0)
     ast (2.4.2)
     autoprefixer-rails (10.4.13.0)
       execjs (~> 2)
+    base64 (0.1.1)
     bcrypt_pbkdf (1.1.0)
     bootstrap (4.1.3)
       autoprefixer-rails (>= 6.0.3)
       popper_js (>= 1.12.9, < 2)
       sass (>= 3.5.2)
-    brakeman (5.4.1)
+    brakeman (6.0.1)
     builder (3.2.4)
     capistrano (3.17.3)
       airbrussh (>= 1.0.0)
@@ -102,9 +103,12 @@ GEM
       capistrano (~> 3.0)
     capistrano-passenger (0.2.1)
       capistrano (~> 3.0)
-    capistrano-rails (1.6.2)
+    capistrano-rails (1.6.3)
       capistrano (~> 3.1)
       capistrano-bundler (>= 1.1, < 3)
+    capistrano-rbenv (2.2.0)
+      capistrano (~> 3.1)
+      sshkit (~> 1.3)
     capistrano-yarn (2.0.2)
       capistrano (~> 3.0)
     capybara (3.39.2)
@@ -132,7 +136,7 @@ GEM
     erubi (1.12.0)
     erubis (2.7.0)
     eventmachine (1.2.7)
-    excon (0.100.0)
+    excon (0.102.0)
     execjs (2.8.1)
     faraday (2.7.10)
       faraday-net_http (>= 2.0, < 3.1)
@@ -147,7 +151,7 @@ GEM
     flamegraph (0.9.5)
     globalid (1.1.0)
       activesupport (>= 5.0)
-    graphql (2.0.22)
+    graphql (2.0.26)
     graphql-client (0.18.0)
       activesupport (>= 3.0)
       graphql
@@ -165,13 +169,14 @@ GEM
     i18n (1.14.1)
       concurrent-ruby (~> 1.0)
     iconv (1.0.8)
-    jquery-rails (4.5.1)
+    jquery-rails (4.6.0)
       rails-dom-testing (>= 1, < 3)
       railties (>= 4.2.0)
       thor (>= 0.14, < 2.0)
     jquery-ui-rails (6.0.1)
       railties (>= 3.2.16)
     json (2.6.3)
+    language_server-protocol (3.17.0.3)
     listen (3.8.0)
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
@@ -187,15 +192,15 @@ GEM
     marcel (1.0.2)
     matrix (0.4.2)
     method_source (1.0.0)
-    mime-types (3.4.1)
+    mime-types (3.5.1)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2023.0218.1)
-    mini_mime (1.1.2)
-    minitest (5.18.1)
+    mime-types-data (3.2023.0808)
+    mini_mime (1.1.5)
+    minitest (5.19.0)
     multi_json (1.15.0)
     multipart-post (2.3.0)
-    mysql2 (0.5.2)
-    net-imap (0.3.6)
+    mysql2 (0.5.5)
+    net-imap (0.3.7)
       date
       net-protocol
     net-pop (0.1.2)
@@ -206,15 +211,17 @@ GEM
       net-ssh (>= 2.6.5, < 8.0.0)
     net-smtp (0.3.3)
       net-protocol
-    net-ssh (7.1.0)
+    net-ssh (7.2.0)
     netrc (0.11.0)
-    newrelic_rpm (9.2.2)
+    newrelic_rpm (9.4.2)
     nio4r (2.5.9)
-    nokogiri (1.15.2-x86_64-darwin)
+    nokogiri (1.15.4-arm64-darwin)
+      racc (~> 1.4)
+    nokogiri (1.15.4-x86_64-darwin)
       racc (~> 1.4)
-    nokogiri (1.15.2-x86_64-linux)
+    nokogiri (1.15.4-x86_64-linux)
       racc (~> 1.4)
-    oj (3.15.0)
+    oj (3.16.0)
     open_uri_redirections (0.2.1)
     parallel (1.23.0)
     parser (3.2.2.3)
@@ -225,10 +232,10 @@ GEM
       coderay (~> 1.1)
       method_source (~> 1.0)
     psych (3.3.4)
-    public_suffix (5.0.1)
+    public_suffix (5.0.3)
     racc (1.7.1)
-    rack (2.2.7)
-    rack-mini-profiler (3.1.0)
+    rack (2.2.8)
+    rack-mini-profiler (3.1.1)
       rack (>= 1.2.0)
     rack-test (2.1.0)
       rack (>= 1.3)
@@ -247,8 +254,9 @@ GEM
       bundler (>= 1.15.0)
       railties (= 6.1.7.3)
       sprockets-rails (>= 2.0.0)
-    rails-dom-testing (2.0.3)
-      activesupport (>= 4.2.0)
+    rails-dom-testing (2.2.0)
+      activesupport (>= 5.0.0)
+      minitest
       nokogiri (>= 1.6)
     rails-html-sanitizer (1.6.0)
       loofah (~> 2.21)
@@ -277,13 +285,13 @@ GEM
       http-cookie (>= 1.0.2, < 2.0)
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
-    rexml (3.2.5)
+    rexml (3.2.6)
     rspec-core (3.12.2)
       rspec-support (~> 3.12.0)
     rspec-expectations (3.12.3)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.12.0)
-    rspec-mocks (3.12.5)
+    rspec-mocks (3.12.6)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.12.0)
     rspec-rails (6.0.3)
@@ -294,22 +302,24 @@ GEM
       rspec-expectations (~> 3.12)
       rspec-mocks (~> 3.12)
       rspec-support (~> 3.12)
-    rspec-support (3.12.0)
-    rubocop (1.52.1)
+    rspec-support (3.12.1)
+    rubocop (1.56.2)
+      base64 (~> 0.1.1)
       json (~> 2.3)
+      language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
       parser (>= 3.2.2.3)
       rainbow (>= 2.2.2, < 4.0)
       regexp_parser (>= 1.8, < 3.0)
       rexml (>= 3.2.5, < 4.0)
-      rubocop-ast (>= 1.28.0, < 2.0)
+      rubocop-ast (>= 1.28.1, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 2.4.0, < 3.0)
     rubocop-ast (1.29.0)
       parser (>= 3.2.1.0)
     ruby-progressbar (1.13.0)
     ruby2_keywords (0.0.5)
-    ruby_parser (3.20.2)
+    ruby_parser (3.20.3)
       sexp_processor (~> 4.16)
     sass (3.7.4)
       sass-listen (~> 4.0.0)
@@ -332,7 +342,7 @@ GEM
       actionpack (>= 5.2)
       activesupport (>= 5.2)
       sprockets (>= 3.0.0)
-    sshkit (1.21.4)
+    sshkit (1.21.5)
       net-scp (>= 1.1.2)
       net-ssh (>= 2.8.0)
     stackprof (0.2.25)
@@ -343,7 +353,7 @@ GEM
       rack (>= 1, < 3)
     thor (1.2.2)
     tilt (2.2.0)
-    timeout (0.3.2)
+    timeout (0.4.0)
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
     uglifier (4.2.0)
@@ -352,27 +362,29 @@ GEM
       unf_ext
     unf_ext (0.0.8.2)
     unicode-display_width (2.4.2)
-    websocket-driver (0.7.5)
+    websocket-driver (0.7.6)
       websocket-extensions (>= 0.1.0)
     websocket-extensions (0.1.5)
     will_paginate (3.3.1)
     xpath (3.2.0)
       nokogiri (~> 1.8)
-    zeitwerk (2.6.8)
+    zeitwerk (2.6.11)
 
 PLATFORMS
+  arm64-darwin-22
   x86_64-darwin-21
   x86_64-linux
 
 DEPENDENCIES
   bcrypt_pbkdf (>= 1.0, < 2.0)
   bootstrap (~> 4.1.0)
   brakeman
-  capistrano (~> 3.11)
+  capistrano (~> 3.17)
   capistrano-bundler
   capistrano-locally
   capistrano-passenger
   capistrano-rails (~> 1.4)
+  capistrano-rbenv
   capistrano-yarn
   capybara
   chart-js-rails
@@ -389,7 +401,7 @@ DEPENDENCIES
   jquery-ui-rails
   listen
   multi_json
-  mysql2 (= 0.5.2)
+  mysql2 (= 0.5.5)
   newrelic_rpm
   oj
   ontologies_api_client!
@@ -402,6 +414,7 @@ DEPENDENCIES
   rdoc
   recaptcha (~> 5.9.0)
   rest-client
+  rexml (~> 3)
   rspec-rails
   rubocop
   sass-rails (~> 5.0)
@@ -412,4 +425,4 @@ DEPENDENCIES
   will_paginate (~> 3.0)
 
 BUNDLED WITH
-   2.3.22
+   2.4.18
diff --git a/app/assets/stylesheets/bioportal.scss b/app/assets/stylesheets/bioportal.scss
@@ -1039,9 +1039,6 @@ button.fg-button-menu, button.fg-button {
  ************************************/
 .pop_window {
 }
-div.subdomain_info a.pop_window {
-  font-size: inherit;
-}
 
 /************************************
  * Help text at top of tabs