Merge branch 'develop' into fix-well-library-delegate-error

.release-version

@@ -1 +1 @@
-3.6.4
+3.6.4

app/controllers/application_controller.rb

@@ -5,6 +5,14 @@ class ApplicationController < ActionController::Base
   include JSONAPI::ActsAsResourceController
   skip_before_action :verify_authenticity_token
 
+  on_server_error :send_exception_notification
+
+  def self.send_exception_notification(exception)
+    ExceptionNotifier.notify_exception(exception)
+  end
+
+  private
+
   # Caution: Using this approach for a 'create' action is not strictly JSON API
   # compliant.
   def serialize_array(array)

app/resources/v1/pacbio/run_resource.rb

@@ -13,6 +13,16 @@ class RunResource < JSONAPI::Resource
       has_one :plate, foreign_key_on: :related, foreign_key: 'pacbio_run_id',
                       class_name: 'Runs::Plate'
 
+      def self.records_for_populate(*_args)
+        super.preload(plate: {
+                        wells: {
+                          libraries: {
+                            request_libraries: { request: :sample }
+                          }
+                        }
+                      })
+      end
+
       def created_at
         @model.created_at.to_s(:us)
       end

config/environments/development.rb

@@ -1,5 +1,4 @@
 # frozen_string_literal: true
-
 Rails.application.configure do
   # Settings specified here will take precedence over those in config/application.rb.
 
@@ -60,4 +59,10 @@
     end
   end
 
+  config.middleware.use ExceptionNotification::Rack
+
+  # We don't want to send emails in development mode, but its useful to see
+  # when the notifier has been triggered.
+  ExceptionNotifier.add_notifier :console_notifier,
+    ->(exception, _) { puts "📧 Exception logged: #{exception.message}"}
 end

lefthook.yml

@@ -0,0 +1,51 @@
+# https://github.com/Arkweid/lefthook
+# Rubocop globs built based on https://github.com/rubocop-hq/rubocop/blob/master/config/default.yml With globbing support povided by
+# https://pkg.go.dev/github.com/gobwas/glob#section-documentation
+# Has the advantage of quicker commits when no rubocop files
+pre-commit:
+  parallel: true
+  commands:
+    rubocop:
+      glob: "{*.{rb,arb,axlsx,builder,fcgi,gemfile,gemspec,god,jb,jbuilder,mspec,opal,pluginspec,podspec,rabl,rake,rbuild,rbw,rbx,ru,ruby,spec,thor,watchr},.irbrc,.pryrc,.simplecov,buildfile,Appraisals,Berksfile,Brewfile,Buildfile,Capfile,Cheffile,Dangerfile,Deliverfile,Fastfile,*Fastfile,Gemfile,Guardfile,Jarfile,Mavenfile,Podfile,Puppetfile,Rakefile,rakefile,Snapfile,Steepfile,Thorfile,Vagabondfile,Vagrantfile}"
+      run: rubocop --display-style-guide --extra-details --force-exclusion --parallel {staged_files} || (echo 'Run `lefthook run fix` to run autocorrect on staged files only'; exit 1)
+
+fix:
+  parallel: true
+  commands:
+    rubocop:
+      glob: "{*.{rb,arb,axlsx,builder,fcgi,gemfile,gemspec,god,jb,jbuilder,mspec,opal,pluginspec,podspec,rabl,rake,rbuild,rbw,rbx,ru,ruby,spec,thor,watchr},.irbrc,.pryrc,.simplecov,buildfile,Appraisals,Berksfile,Brewfile,Buildfile,Capfile,Cheffile,Dangerfile,Deliverfile,Fastfile,*Fastfile,Gemfile,Guardfile,Jarfile,Mavenfile,Podfile,Puppetfile,Rakefile,rakefile,Snapfile,Steepfile,Thorfile,Vagabondfile,Vagrantfile}"
+      run: rubocop --display-style-guide --extra-details --auto-correct --force-exclusion {staged_files}
+# EXAMPLE USAGE
+# Refer for explanation to following link:
+# https://github.com/Arkweid/lefthook/blob/master/docs/full_guide.md
+#
+# pre-push:
+#   commands:
+#     packages-audit:
+#       tags: frontend security
+#       run: yarn audit
+#     gems-audit:
+#       tags: backend security
+#       run: bundle audit
+#
+# pre-commit:
+#   parallel: true
+#   commands:
+#     eslint:
+#       glob: "*.{js,ts}"
+#       run: yarn eslint {staged_files}
+#     rubocop:
+#       tags: backend style
+#       glob: "*.rb"
+#       exclude: "application.rb|routes.rb"
+#       run: bundle exec rubocop --force-exclusion {all_files}
+#     govet:
+#       tags: backend style
+#       files: git ls-files -m
+#       glob: "*.go"
+#       run: go vet {files}
+#   scripts:
+#     "hello.js":
+#       runner: node
+#     "any.go":
+#       runner: go run

lib/tasks/ont_data.rake

@@ -3,6 +3,7 @@
 require_relative '../traction_graphql'
 
 namespace :ont_data do
+  desc 'Populate the database with ont plates and runs'
   task :create, [:num] => :environment do |_t, args|
     puts '-> Creating ONT data using GraphQL'
 

lib/tasks/pacbio_data.rake

@@ -1,6 +1,7 @@
 # frozen_string_literal: true
 
 namespace :pacbio_data do
+  desc 'Populate the database with pacbio plates and runs'
   task create: :environment do
     require 'factory_bot'
 

lib/tasks/saphyr_runs.rake

@@ -1,6 +1,7 @@
 # frozen_string_literal: true
 
 namespace :saphyr_runs do
+  desc 'Populate the database with saphyr tubes and runs'
   task create: :environment do
     attributes = (1..5).collect { |i| { name: "Sample#{i}", external_id: i, external_study_id: i, species: "Species#{i}" } }