applied some updates suggested by rails app:update

left the more complex initializers for now

bin/rails

@@ -1,4 +1,4 @@
 #!/usr/bin/env ruby
-APP_PATH = File.expand_path('../config/application', __dir__)
+APP_PATH = File.expand_path("../config/application", __dir__)
 require_relative "../config/boot"
 require "rails/commands"

bin/setup

@@ -2,32 +2,32 @@
 require "fileutils"
 
 # path to your application root.
-APP_ROOT = File.expand_path('..', __dir__)
+APP_ROOT = File.expand_path("..", __dir__)
 
 def system!(*args)
-  system(*args) || abort("\n== Command #{args} failed ==")
+  system(*args, exception: true)
 end
 
 FileUtils.chdir APP_ROOT do
   # This script is a way to set up or update your development environment automatically.
   # This script is idempotent, so that you can run it at any time and get an expectable outcome.
   # Add necessary setup steps to this file.
 
-  puts '== Installing dependencies =='
-  system! 'gem install bundler --conservative'
-  system('bundle check') || system!('bundle install')
+  puts "== Installing dependencies =="
+  system! "gem install bundler --conservative"
+  system("bundle check") || system!("bundle install")
 
   # puts "\n== Copying sample files =="
-  # unless File.exist?('config/database.yml')
-  #   FileUtils.cp 'config/database.yml.sample', 'config/database.yml'
+  # unless File.exist?("config/database.yml")
+  #   FileUtils.cp "config/database.yml.sample", "config/database.yml"
   # end
 
   puts "\n== Preparing database =="
-  system! 'bin/rails db:prepare'
+  system! "bin/rails db:prepare"
 
   puts "\n== Removing old logs and tempfiles =="
-  system! 'bin/rails log:clear tmp:clear'
+  system! "bin/rails log:clear tmp:clear"
 
   puts "\n== Restarting application server =="
-  system! 'bin/rails restart'
+  system! "bin/rails restart"
 end

config/boot.rb

@@ -1,3 +1,3 @@
-ENV['BUNDLE_GEMFILE'] ||= File.expand_path('../Gemfile', __dir__)
+ENV["BUNDLE_GEMFILE"] ||= File.expand_path("../Gemfile", __dir__)
 
 require "bundler/setup" # Set up gems listed in the Gemfile.

config/initializers/content_security_policy.rb

@@ -1,28 +1,25 @@
 # Be sure to restart your server when you modify this file.
 
-# Define an application-wide content security policy
-# For further information see the following documentation
-# https://developer.mozilla.org/en-US/docs/Web/HTTP/Headers/Content-Security-Policy
+# Define an application-wide content security policy.
+# See the Securing Rails Applications Guide for more information:
+# https://guides.rubyonrails.org/security.html#content-security-policy-header
 
-# Rails.application.config.content_security_policy do |policy|
-#   policy.default_src :self, :https
-#   policy.font_src    :self, :https, :data
-#   policy.img_src     :self, :https, :data
-#   policy.object_src  :none
-#   policy.script_src  :self, :https
-#   policy.style_src   :self, :https
-
-#   # Specify URI for violation reports
-#   # policy.report_uri "/csp-violation-report-endpoint"
+# Rails.application.configure do
+#   config.content_security_policy do |policy|
+#     policy.default_src :self, :https
+#     policy.font_src    :self, :https, :data
+#     policy.img_src     :self, :https, :data
+#     policy.object_src  :none
+#     policy.script_src  :self, :https
+#     policy.style_src   :self, :https
+#     # Specify URI for violation reports
+#     # policy.report_uri "/csp-violation-report-endpoint"
+#   end
+#
+#   # Generate session nonces for permitted importmap, inline scripts, and inline styles.
+#   config.content_security_policy_nonce_generator = ->(request) { request.session.id.to_s }
+#   config.content_security_policy_nonce_directives = %w(script-src style-src)
+#
+#   # Report violations without enforcing the policy.
+#   # config.content_security_policy_report_only = true
 # end
-
-# If you are using UJS then enable automatic nonce generation
-# Rails.application.config.content_security_policy_nonce_generator = -> request { SecureRandom.base64(16) }
-
-# Set the nonce only to specific directives
-# Rails.application.config.content_security_policy_nonce_directives = %w(script-src)
-
-# Report CSP violations to a specified URI
-# For further information see the following documentation:
-# https://developer.mozilla.org/en-US/docs/Web/HTTP/Headers/Content-Security-Policy-Report-Only
-# Rails.application.config.content_security_policy_report_only = true

config/initializers/cors.rb

@@ -1,6 +1,14 @@
-Rails.application.config.middleware.insert_before 0, Rack::Cors do
-  allow do
-    origins '*'
-    resource '/ga4gh/trs/v2/*', headers: :any, methods: [:get, :head, :options]
-  end
-end
+# Be sure to restart your server when you modify this file.
+
+# Avoid CORS issues when API is called from the frontend app.
+# Handle Cross-Origin Resource Sharing (CORS) in order to accept cross-origin Ajax requests.
+
+# Read more: https://github.com/cyu/rack-cors
+
+
+ Rails.application.config.middleware.insert_before 0, Rack::Cors do
+    allow do
+      origins '*'
+      resource '/ga4gh/trs/v2/*', headers: :any, methods: [:get, :head, :options]
+    end
+ end

config/initializers/filter_parameter_logging.rb

@@ -1,6 +1,8 @@
 # Be sure to restart your server when you modify this file.
 
-# Configure sensitive parameters which will be filtered from the log file.
+# Configure parameters to be partially matched (e.g. passw matches password) and filtered from the log file.
+# Use this to limit dissemination of sensitive information.
+# See the ActiveSupport::ParameterFilter documentation for supported notations and behaviors.
 Rails.application.config.filter_parameters += [
   :passw, :secret, :token, :_key, :crypt, :salt, :certificate, :otp, :ssn
 ]

config/initializers/inflections.rb

@@ -1,4 +1,21 @@
   # Be sure to restart your server when you modify this file.
+
+# Add new inflection rules using the following format. Inflections
+# are locale specific, and you may define rules for as many different
+# locales as you wish. All of these examples are active by default:
+# ActiveSupport::Inflector.inflections(:en) do |inflect|
+#   inflect.plural /^(ox)$/i, "\\1en"
+#   inflect.singular /^(ox)en/i, "\\1"
+#   inflect.irregular "person", "people"
+#   inflect.uncountable %w( fish sheep )
+# end
+
+# These inflection rules are supported but not enabled by default:
+# ActiveSupport::Inflector.inflections(:en) do |inflect|
+#   inflect.acronym "RESTful"
+# end
+
+
 SEEK::Application.configure do
 
   ActiveSupport::Inflector.inflections do |inflect|