Merge pull request #284 from ncbo/251-ruby-v3-support

Refactor: upgrade Ruby from 2.7 to 3.0.6

.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
 

.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

.gitignore

@@ -25,8 +25,6 @@ config/deploy/*
 /public/assets/
 nohup.out
 
-.ruby-version
-
 # Ignore editor files
 .idea
 *.swp

.ruby-version

@@ -0,0 +1 @@
+3.0.6

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 }

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

Gemfile.lock

@@ -79,17 +79,18 @@ GEM
       zeitwerk (~> 2.3)
     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)
@@ -105,6 +106,9 @@ GEM
     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 (2.0.25)
+    graphql (2.0.26)
     graphql-client (0.18.0)
       activesupport (>= 3.0)
       graphql
@@ -188,14 +192,14 @@ GEM
     marcel (1.0.2)
     matrix (0.4.2)
     method_source (1.0.0)
-    mime-types (3.5.0)
+    mime-types (3.5.1)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2023.0218.1)
-    mini_mime (1.1.2)
+    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)
+    mysql2 (0.5.5)
     net-imap (0.3.7)
       date
       net-protocol
@@ -209,13 +213,15 @@ GEM
       net-protocol
     net-ssh (7.2.0)
     netrc (0.11.0)
-    newrelic_rpm (9.3.1)
+    newrelic_rpm (9.4.2)
     nio4r (2.5.9)
-    nokogiri (1.15.3-x86_64-darwin)
+    nokogiri (1.15.4-arm64-darwin)
+      racc (~> 1.4)
+    nokogiri (1.15.4-x86_64-darwin)
       racc (~> 1.4)
-    nokogiri (1.15.3-x86_64-linux)
+    nokogiri (1.15.4-x86_64-linux)
       racc (~> 1.4)
-    oj (3.15.1)
+    oj (3.16.0)
     open_uri_redirections (0.2.1)
     parallel (1.23.0)
     parser (3.2.2.3)
@@ -297,7 +303,8 @@ GEM
       rspec-mocks (~> 3.12)
       rspec-support (~> 3.12)
     rspec-support (3.12.1)
-    rubocop (1.55.1)
+    rubocop (1.56.2)
+      base64 (~> 0.1.1)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
@@ -364,18 +371,20 @@ GEM
     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
@@ -392,7 +401,7 @@ DEPENDENCIES
   jquery-ui-rails
   listen
   multi_json
-  mysql2 (= 0.5.2)
+  mysql2 (= 0.5.5)
   newrelic_rpm
   oj
   ontologies_api_client!
@@ -405,6 +414,7 @@ DEPENDENCIES
   rdoc
   recaptcha (~> 5.9.0)
   rest-client
+  rexml (~> 3)
   rspec-rails
   rubocop
   sass-rails (~> 5.0)
@@ -415,4 +425,4 @@ DEPENDENCIES
   will_paginate (~> 3.0)
 
 BUNDLED WITH
-   2.3.22
+   2.4.18

app/controllers/application_controller.rb

@@ -1,5 +1,4 @@
 require 'uri'
-require 'open-uri'
 require 'net/http'
 require 'net/https'
 require 'net/ftp'
@@ -29,6 +28,8 @@ class ApplicationController < ActionController::Base
   EXPIRY_RECENT_MAPPINGS = 60 * 60     #  1:00 hours
   EXPIRY_ONTOLOGY_SIMPLIFIED = 60 * 1  #  0:01 minute
 
+  RETRY_LIMIT = 1
+
   $trial_license_initialized = false
 
   if !$EMAIL_EXCEPTIONS.nil? && $EMAIL_EXCEPTIONS == true
@@ -579,22 +580,18 @@ def get_apikey()
   end
 
   def parse_json(uri)
-    uri = URI.parse(uri)
     begin
-      response = open(uri, "Authorization" => "apikey token=#{get_apikey}").read
-    rescue Exception => error
+      response = Net::HTTP.get(URI(uri), { 'Authorization' => "apikey token=#{get_apikey}" })
+    rescue StandardError => e
       @retries ||= 0
-      if @retries < 1  # retry once only
-        @retries += 1
-        retry
-      else
-        raise error
-      end
+      raise e unless @retries < RETRY_LIMIT
+
+      @retries += 1
+      retry
     end
     JSON.parse(response)
   end
 
-
   def get_batch_results(params)
     begin
       response = RestClient.post REST_URI_BATCH, params.to_json, :content_type => :json, :accept => :json, :authorization => "apikey token=#{get_apikey}"

app/controllers/submissions_controller.rb

@@ -1,11 +1,19 @@
-class SubmissionsController < ApplicationController
+# frozen_string_literal: true
 
+class SubmissionsController < ApplicationController
   layout :determine_layout
-  before_action :authorize_and_redirect, :only=>[:edit,:update,:create,:new]
+  before_action :authorize_and_redirect, only: [:edit, :update, :create, :new]
 
   def new
-    @ontology = LinkedData::Client::Models::Ontology.get(CGI.unescape(params[:ontology_id])) rescue nil
-    @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology_id]).first unless @ontology
+    begin
+      # REVIEW: do we really need this double attempt to locate an ontology? I think find_by_acronym (below) should
+      #    be sufficient. It's not evident that we call the new method with a full URI anymore.
+      @ontology = LinkedData::Client::Models::Ontology.get(CGI.unescape(params[:ontology_id]))
+    rescue MultiJson::ParseError
+      nil
+    end
+
+    @ontology ||= LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology_id]).first
     @submission = @ontology.explore.latest_submission
     @submission ||= LinkedData::Client::Models::OntologySubmission.new
   end
@@ -16,21 +24,21 @@ def create
 
     @submission = LinkedData::Client::Models::OntologySubmission.new(values: submission_params)
     @ontology = LinkedData::Client::Models::Ontology.get(params[:submission][:ontology])
-    
+
     # Update summaryOnly on ontology object
-    @ontology.summaryOnly = @submission.isRemote.eql?("3")
+    @ontology.summaryOnly = @submission.isRemote.eql?('3')
     @ontology.update
-    
-    @submission_saved = @submission.save
+
+    @submission_saved = @submission.save(cache_refresh_all: false)
     if response_error?(@submission_saved)
       @errors = response_errors(@submission_saved) # see application_controller::response_errors
       if @errors && @errors[:uploadFilePath]
-        @errors = ["Please specify the location of your ontology"]
+        @errors = ['Please specify the location of your ontology']
       elsif @errors && @errors[:contact]
-        @errors = ["Please enter a contact"]
+        @errors = ['Please enter a contact']
       end
 
-      render "new"
+      render 'new'
     else
       redirect_to "/ontologies/success/#{@ontology.acronym}"
     end
@@ -39,7 +47,7 @@ def create
   def edit
     @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology_id]).first
     submissions = @ontology.explore.submissions
-    @submission = submissions.select {|o| o.submissionId == params["id"].to_i}.first
+    @submission = submissions.select { |o| o.submissionId == params['id'].to_i }.first
   end
 
   def update
@@ -50,13 +58,13 @@ def update
 
     @ontology = LinkedData::Client::Models::Ontology.get(params[:submission][:ontology])
     submissions = @ontology.explore.submissions
-    @submission = submissions.select {|o| o.submissionId == params["id"].to_i}.first
+    @submission = submissions.select { |o| o.submissionId == params['id'].to_i }.first
 
     @submission.update_from_params(submission_params)
     # Update summaryOnly on ontology object
-    @ontology.summaryOnly = @submission.isRemote.eql?("3")
+    @ontology.summaryOnly = @submission.isRemote.eql?('3')
     @ontology.update
-    error_response = @submission.update
+    error_response = @submission.update(cache_refresh_all: false)
     if response_error?(error_response)
       @errors = response_errors(error_response) # see application_controller::response_errors
       render 'edit'
@@ -71,9 +79,8 @@ def submission_params
     p = params.require(:submission).permit(:ontology, :description, :hasOntologyLanguage, :prefLabelProperty,
                                            :synonymProperty, :definitionProperty, :authorProperty, :obsoleteProperty,
                                            :obsoleteParent, :version, :status, :released, :isRemote, :pullLocation,
-                                           :filePath, { contact:[:name, :email] }, :homepage, :documentation,
+                                           :filePath, { contact: [:name, :email] }, :homepage, :documentation,
                                            :publication)
     p.to_h
   end
-
 end

config/deploy.rb

@@ -23,7 +23,7 @@
 # set :format, :pretty
 
 # Default value for :log_level is :debug
-set :log_level, :error
+# set :log_level, :error
 
 # Default value for :pty is false
 # set :pty, true
@@ -55,6 +55,10 @@
 # If you don't set `:passenger_restart_with_touch`, capistrano-passenger will check what version of passenger you are running
 # and use `passenger-config restart-app` if it is available in that version.
 
+# rbenv ruby version
+set :rbenv_type, :system
+set :rbenv_ruby, File.read('.ruby-version').strip
+
 desc "Check if agent forwarding is working"
 task :forwarding do
   on roles(:all) do |h|