Merge pull request #2875 from sanger/develop

Develop into master

Gemfile.lock

@@ -104,7 +104,7 @@ GEM
     backports (3.18.1)
     binding_of_caller (0.8.0)
       debug_inspector (>= 0.0.1)
-    bootsnap (1.4.6)
+    bootsnap (1.4.7)
       msgpack (~> 1.0)
     bootstrap (4.5.0)
       autoprefixer-rails (>= 9.1.0)
@@ -163,11 +163,11 @@ GEM
       cucumber-messages (~> 12.2, >= 12.2.0)
       sys-uname (~> 1.2, >= 1.2.1)
     cucumber-cucumber-expressions (10.2.1)
-    cucumber-gherkin (14.0.1)
-      cucumber-messages (~> 12.2, >= 12.2.0)
+    cucumber-gherkin (14.1.0)
+      cucumber-messages (~> 12.3, >= 12.3.2)
     cucumber-html-formatter (7.0.0)
       cucumber-messages (~> 12.2, >= 12.2.0)
-    cucumber-messages (12.2.0)
+    cucumber-messages (12.3.2)
       protobuf-cucumber (~> 3.10, >= 3.10.8)
     cucumber-rails (2.1.0)
       capybara (>= 2.12, < 4)
@@ -240,7 +240,7 @@ GEM
     http-accept (1.7.0)
     http-cookie (1.0.3)
       domain_name (~> 0.5)
-    i18n (1.8.3)
+    i18n (1.8.5)
       concurrent-ruby (~> 1.0)
     jquery-rails (4.4.0)
       rails-dom-testing (>= 1, < 3)
@@ -259,7 +259,7 @@ GEM
       rake
     launchy (2.5.0)
       addressable (~> 2.7)
-    libv8 (7.3.492.27.1)
+    libv8 (8.4.255.0)
     loofah (2.6.0)
       crass (~> 1.0.2)
       nokogiri (>= 1.5.9)
@@ -275,8 +275,8 @@ GEM
     mimemagic (0.3.5)
     mini_mime (1.0.2)
     mini_portile2 (2.4.0)
-    mini_racer (0.2.15)
-      libv8 (> 7.3)
+    mini_racer (0.3.1)
+      libv8 (~> 8.4.255)
     minitest (5.10.3)
     minitest-profiler (0.0.2)
       activesupport (>= 4.1.0)
@@ -327,7 +327,7 @@ GEM
       rack (>= 1.1.0)
     rack-cors (1.1.1)
       rack (>= 2.0.0)
-    rack-mini-profiler (2.0.2)
+    rack-mini-profiler (2.0.3)
       rack (>= 1.2.0)
     rack-protection (2.0.8.1)
       rack
@@ -422,14 +422,14 @@ GEM
       rubocop-ast (>= 0.1.0, < 1.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 1.4.0, < 2.0)
-    rubocop-ast (0.1.0)
+    rubocop-ast (0.2.0)
       parser (>= 2.7.0.1)
     rubocop-performance (1.7.1)
       rubocop (>= 0.82.0)
-    rubocop-rails (2.6.0)
+    rubocop-rails (2.7.1)
       activesupport (>= 4.2.0)
       rack (>= 1.1)
-      rubocop (>= 0.82.0)
+      rubocop (>= 0.87.0)
     rubocop-rspec (1.42.0)
       rubocop (>= 0.87.0)
     ruby-graphviz (1.2.5)

app/uat_actions/uat_actions.rb

@@ -14,10 +14,22 @@ class UatActions
   self.message = 'Completed successfully'
 
   class << self
+    #
+    # Returns a list of all registered UatActions
+    #
+    # @return [Array<UatAction>] All registered UatActions
+    #
     def all
       uat_actions.values
     end
 
+    #
+    # Find the UatAction identified by the id (Usually the class name parameterized)
+    #
+    # @param [String] id The id of the UatAction to find.
+    #
+    # @return [Class] A UatAction class
+    #
     def find(id)
       uat_actions[id]
     end
@@ -27,7 +39,9 @@ def uat_actions
       @uat_actions ||= {}
     end
 
-    # Called by UatActions classes to register themselves
+    # Automatically called by UatActions classes to register themselves
+    #
+    # @param [Class] other Automatically called when inherited. Receives the descendant class
     def inherited(other)
       # Register the form_fields of the parent class
       other.form_fields.concat(form_fields)
@@ -42,6 +56,21 @@ def id
       name.demodulize.parameterize
     end
 
+    #
+    # Register a new {UatActions::FormField}. This will be automatically rendered by the UI
+    # and any attributes will be available and instance attributes.
+    #
+    # @param [Symbol] attribute The attribute the field is linked to.
+    # @param [Symbol] type The type of field to render. Should be something {ActionView::Helpers::FormBuilder}
+    #                  responds to. @see https://api.rubyonrails.org/classes/ActionView/Helpers/FormBuilder.html
+    # @param [Hash] options Configure the attributes
+    # @option options [String] :label The human readable label for the attribute, determines the field label
+    # @option options [String] :help More verbose help text to explain the field (shown to the user)
+    # @option options [Hash] :options Additional options passed through to the {ActionView::Helpers::FormBuilder} field
+    #                                 itself. Eg. required, max, min, include_blank
+    #
+    # @return [void]
+    #
     def form_field(attribute, type, options = {})
       @form_fields ||= []
       attr_accessor attribute

app/uat_actions/uat_actions/generate_tagged_plates.rb

@@ -2,7 +2,7 @@
 
 # Will construct plates with well_count wells filled with samples
 class UatActions::GenerateTaggedPlates < UatActions::GeneratePlates
-  # These walking algortihms have dependencies on submission and do
+  # These walking algorithms have dependencies on submission and do
   # not make sense here.
   EXCLUDED_WALKING = ['wells in pools', 'manual by pool'].freeze
 
@@ -23,7 +23,8 @@ class UatActions::GenerateTaggedPlates < UatActions::GeneratePlates
              label: 'i5 (tag2) Tag group',
              help: 'Select the tag group to use for the i7 tag. '\
                    'Set to \'Untagged\' for single indexed samples.',
-             select_options: -> { TagGroup.visible.alphabetical.pluck(:name) }
+             select_options: -> { TagGroup.visible.alphabetical.pluck(:name) },
+             options: { include_blank: 'Untagged' }
   form_field :direction,
              :select,
              label: 'Tag direction',
@@ -45,7 +46,7 @@ class UatActions::GenerateTaggedPlates < UatActions::GeneratePlates
   validates :walking_by, inclusion: { in: TagLayout::WALKING_ALGORITHMS.keys - EXCLUDED_WALKING }, presence: true
   validates :tag_group_name, presence: true
   validates :tag_group, presence: { message: 'could not be found' }, if: :tag_group_name
-  validates :tag2_group, presence: { message: 'could not be found' }, if: :tag2_group_name
+  validates :tag2_group, presence: { message: 'could not be found' }, if: :tag2_group_name?
 
   def self.default
     new(
@@ -74,6 +75,10 @@ def perform
 
   private
 
+  def tag2_group_name?
+    tag2_group_name.present?
+  end
+
   def user
     UatActions::StaticRecords.user
   end

lib/label_printer/label_printer/label/base_tube.rb

@@ -32,7 +32,7 @@ def round_label_bottom_line(tube)
       end
 
       def barcode(tube)
-        tube.ean13_barcode
+        tube.machine_barcode
       end
 
       def tubes

spec/lib/label_printer/asset_labels_spec.rb

@@ -73,7 +73,7 @@
           bottom_line: date,
           round_label_top_line: asset.prefix,
           round_label_bottom_line: asset.barcode_number,
-          barcode: asset.machine_barcode.to_s } }
+          barcode: asset.machine_barcode } }
       end
     end
 

test/lib/label_printer/batch_multiplex_test.rb

@@ -28,7 +28,7 @@ def setup
                bottom_line: (Date.today.strftime('%e-%^b-%Y')).to_s,
                round_label_top_line: prefix,
                round_label_bottom_line: barcode1,
-               barcode: tube1.ean13_barcode }
+               barcode: tube1.machine_barcode }
   end
 
   test 'should return correct tubes' do

test/lib/label_printer/plate_to_tube_test.rb

@@ -22,7 +22,7 @@ def setup
                bottom_line: (Date.today.strftime('%e-%^b-%Y')).to_s,
                round_label_top_line: prefix,
                round_label_bottom_line: barcode1,
-               barcode: tube1.ean13_barcode }
+               barcode: tube1.machine_barcode }
   end
 
   test 'should have tubes' do

test/lib/label_printer/sample_manifest_multiplex_test.rb

@@ -26,7 +26,7 @@ def setup
                bottom_line: (Date.today.strftime('%e-%^b-%Y')).to_s,
                round_label_top_line: prefix,
                round_label_bottom_line: barcode1,
-               barcode: tube1.ean13_barcode }
+               barcode: tube1.machine_barcode }
   end
 
   test 'should return correct tubes' do

test/lib/label_printer/sample_manifest_tube_test.rb

@@ -26,7 +26,7 @@ def setup
                bottom_line: (Date.today.strftime('%e-%^b-%Y')).to_s,
                round_label_top_line: prefix,
                round_label_bottom_line: barcode1,
-               barcode: tube1.ean13_barcode }
+               barcode: tube1.machine_barcode }
   end
 
   test 'should return the right list of tubes' do