Merge pull request #10 from ncbo/master

Sync: bring OntoPortal up-to-date with BioPortal releases 6.8.2 and onward

.github/workflows/brakeman-analysis.yml

@@ -17,17 +17,17 @@ jobs:
     steps:
     # Checkout the repository to the GitHub Actions runner
     - name: Checkout
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
 
     # Customize the ruby version depending on your needs
     - name: Setup Ruby
-      uses: actions/setup-ruby@v1
+      uses: ruby/setup-ruby@v1
       with:
         ruby-version: '2.7'
 
     - name: Setup Brakeman
       env:
-        BRAKEMAN_VERSION: '4.10' # SARIF support is provided in Brakeman version 4.10+
+        BRAKEMAN_VERSION: '5.4.0' # SARIF support is provided in Brakeman version 4.10+
       run: |
         gem install brakeman --version $BRAKEMAN_VERSION
 
@@ -39,6 +39,7 @@ jobs:
 
     # Upload the SARIF file generated in the previous step
     - name: Upload SARIF
-      uses: github/codeql-action/upload-sarif@v1
+      uses: github/codeql-action/upload-sarif@v2
       with:
         sarif_file: output.sarif.json
+

.github/workflows/deploy.yml

@@ -52,11 +52,14 @@ jobs:
 
         USER_INPUT_ENVIRONMENT=${{ inputs.environment }}
         echo "TARGET=${USER_INPUT_ENVIRONMENT:-staging}" >> $GITHUB_ENV
+    - name: provide info on deployment branch/target
+      run: |     
+       echo  "deploying ${BRANCH} branch/tag to ${TARGET} environment"
     # 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
+        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

Gemfile

@@ -1,7 +1,9 @@
+# frozen_string_literal: true
+
 source 'https://rubygems.org'
 
 # Bundle edge Rails instead: gem 'rails', github: 'rails/rails'
-gem 'rails', '6.0.4.1'
+gem 'rails', '6.1.5.1'
 
 gem 'sass-rails', '~> 5.0'
 gem 'uglifier', '>= 1.0.3'
@@ -27,15 +29,16 @@ gem 'select2-rails'
 gem 'cube-ruby', require: 'cube'
 gem 'dalli'
 gem 'flamegraph'
+gem 'graphql-client'
 gem 'haml', '~> 5.1'
 gem 'i18n'
 gem 'iconv'
 gem 'multi_json'
 gem 'mysql2', '0.5.2'
 gem 'oj'
 gem 'open_uri_redirections'
-gem 'psych', '< 4'
 gem 'pry'
+gem 'psych', '< 4'
 gem 'rack-mini-profiler'
 gem 'rails_autolink'
 gem 'rdoc'
@@ -45,7 +48,7 @@ gem 'stackprof', require: false
 gem 'thin'
 gem 'will_paginate', '~> 3.0'
 
-gem 'ontologies_api_client', github: 'ncbo/ontologies_api_ruby_client', tag: 'v2.1.0'
+gem 'ontologies_api_client', github: 'ncbo/ontologies_api_ruby_client', tag: 'v2.2.1'
 
 group :staging, :production do
   # application monitoring
@@ -56,7 +59,7 @@ group :staging, :production do
 end
 
 group :development do
-   # Capistrano Deployment
+  # 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-bundler', require: false