Merge branch 'develop' into allow_submission_from_stock_plate_test_br…

…anch

.gitignore

@@ -53,3 +53,6 @@ release.tar.gz
 
 # Bye-bug history
 .byebug_history
+
+# RubyMine
+.idea

.release-version

@@ -1 +1 @@
-3.57.0
+3.60.0

Gemfile.lock

@@ -28,71 +28,71 @@ GIT
 GEM
   remote: https://rubygems.org/
   specs:
-    actioncable (7.1.3.4)
-      actionpack (= 7.1.3.4)
-      activesupport (= 7.1.3.4)
+    actioncable (7.1.4)
+      actionpack (= 7.1.4)
+      activesupport (= 7.1.4)
       nio4r (~> 2.0)
       websocket-driver (>= 0.6.1)
       zeitwerk (~> 2.6)
-    actionmailbox (7.1.3.4)
-      actionpack (= 7.1.3.4)
-      activejob (= 7.1.3.4)
-      activerecord (= 7.1.3.4)
-      activestorage (= 7.1.3.4)
-      activesupport (= 7.1.3.4)
+    actionmailbox (7.1.4)
+      actionpack (= 7.1.4)
+      activejob (= 7.1.4)
+      activerecord (= 7.1.4)
+      activestorage (= 7.1.4)
+      activesupport (= 7.1.4)
       mail (>= 2.7.1)
       net-imap
       net-pop
       net-smtp
-    actionmailer (7.1.3.4)
-      actionpack (= 7.1.3.4)
-      actionview (= 7.1.3.4)
-      activejob (= 7.1.3.4)
-      activesupport (= 7.1.3.4)
+    actionmailer (7.1.4)
+      actionpack (= 7.1.4)
+      actionview (= 7.1.4)
+      activejob (= 7.1.4)
+      activesupport (= 7.1.4)
       mail (~> 2.5, >= 2.5.4)
       net-imap
       net-pop
       net-smtp
       rails-dom-testing (~> 2.2)
-    actionpack (7.1.3.4)
-      actionview (= 7.1.3.4)
-      activesupport (= 7.1.3.4)
+    actionpack (7.1.4)
+      actionview (= 7.1.4)
+      activesupport (= 7.1.4)
       nokogiri (>= 1.8.5)
       racc
       rack (>= 2.2.4)
       rack-session (>= 1.0.1)
       rack-test (>= 0.6.3)
       rails-dom-testing (~> 2.2)
       rails-html-sanitizer (~> 1.6)
-    actiontext (7.1.3.4)
-      actionpack (= 7.1.3.4)
-      activerecord (= 7.1.3.4)
-      activestorage (= 7.1.3.4)
-      activesupport (= 7.1.3.4)
+    actiontext (7.1.4)
+      actionpack (= 7.1.4)
+      activerecord (= 7.1.4)
+      activestorage (= 7.1.4)
+      activesupport (= 7.1.4)
       globalid (>= 0.6.0)
       nokogiri (>= 1.8.5)
-    actionview (7.1.3.4)
-      activesupport (= 7.1.3.4)
+    actionview (7.1.4)
+      activesupport (= 7.1.4)
       builder (~> 3.1)
       erubi (~> 1.11)
       rails-dom-testing (~> 2.2)
       rails-html-sanitizer (~> 1.6)
-    activejob (7.1.3.4)
-      activesupport (= 7.1.3.4)
+    activejob (7.1.4)
+      activesupport (= 7.1.4)
       globalid (>= 0.3.6)
-    activemodel (7.1.3.4)
-      activesupport (= 7.1.3.4)
-    activerecord (7.1.3.4)
-      activemodel (= 7.1.3.4)
-      activesupport (= 7.1.3.4)
+    activemodel (7.1.4)
+      activesupport (= 7.1.4)
+    activerecord (7.1.4)
+      activemodel (= 7.1.4)
+      activesupport (= 7.1.4)
       timeout (>= 0.4.0)
-    activestorage (7.1.3.4)
-      actionpack (= 7.1.3.4)
-      activejob (= 7.1.3.4)
-      activerecord (= 7.1.3.4)
-      activesupport (= 7.1.3.4)
+    activestorage (7.1.4)
+      actionpack (= 7.1.4)
+      activejob (= 7.1.4)
+      activerecord (= 7.1.4)
+      activesupport (= 7.1.4)
       marcel (~> 1.0)
-    activesupport (7.1.3.4)
+    activesupport (7.1.4)
       base64
       bigdecimal
       concurrent-ruby (~> 1.0, >= 1.0.2)
@@ -126,7 +126,7 @@ GEM
       selenium-webdriver
     childprocess (5.0.0)
     coderay (1.1.3)
-    concurrent-ruby (1.3.3)
+    concurrent-ruby (1.3.4)
     connection_pool (2.4.1)
     crack (1.0.0)
       bigdecimal
@@ -191,7 +191,7 @@ GEM
     i18n (1.14.5)
       concurrent-ruby (~> 1.0)
     io-console (0.7.2)
-    irb (1.13.2)
+    irb (1.14.0)
       rdoc (>= 4.0.0)
       reline (>= 0.4.2)
     json (2.7.2)
@@ -217,7 +217,7 @@ GEM
     method_source (1.0.0)
     mini_mime (1.1.5)
     mini_portile2 (2.8.7)
-    minitest (5.24.1)
+    minitest (5.25.1)
     msgpack (1.7.2)
     multi_json (1.15.0)
     multipart-post (2.4.0)
@@ -256,7 +256,7 @@ GEM
     psych (5.1.2)
       stringio
     public_suffix (6.0.0)
-    puma (6.4.2)
+    puma (6.4.3)
       nio4r (~> 2.0)
     racc (1.8.1)
     rack (3.1.7)
@@ -271,20 +271,20 @@ GEM
     rackup (2.1.0)
       rack (>= 3)
       webrick (~> 1.8)
-    rails (7.1.3.4)
-      actioncable (= 7.1.3.4)
-      actionmailbox (= 7.1.3.4)
-      actionmailer (= 7.1.3.4)
-      actionpack (= 7.1.3.4)
-      actiontext (= 7.1.3.4)
-      actionview (= 7.1.3.4)
-      activejob (= 7.1.3.4)
-      activemodel (= 7.1.3.4)
-      activerecord (= 7.1.3.4)
-      activestorage (= 7.1.3.4)
-      activesupport (= 7.1.3.4)
+    rails (7.1.4)
+      actioncable (= 7.1.4)
+      actionmailbox (= 7.1.4)
+      actionmailer (= 7.1.4)
+      actionpack (= 7.1.4)
+      actiontext (= 7.1.4)
+      actionview (= 7.1.4)
+      activejob (= 7.1.4)
+      activemodel (= 7.1.4)
+      activerecord (= 7.1.4)
+      activestorage (= 7.1.4)
+      activesupport (= 7.1.4)
       bundler (>= 1.15.0)
-      railties (= 7.1.3.4)
+      railties (= 7.1.4)
     rails-controller-testing (1.0.5)
       actionpack (>= 5.0.1.rc1)
       actionview (>= 5.0.1.rc1)
@@ -296,9 +296,9 @@ GEM
     rails-html-sanitizer (1.6.0)
       loofah (~> 2.21)
       nokogiri (~> 1.14)
-    railties (7.1.3.4)
-      actionpack (= 7.1.3.4)
-      activesupport (= 7.1.3.4)
+    railties (7.1.4)
+      actionpack (= 7.1.4)
+      activesupport (= 7.1.4)
       irb
       rackup (>= 1.0.0)
       rake (>= 12.2)
@@ -415,7 +415,7 @@ GEM
     xpath (3.2.0)
       nokogiri (~> 1.8)
     yard (0.9.36)
-    zeitwerk (2.6.16)
+    zeitwerk (2.6.17)
 
 PLATFORMS
   ruby

README.md

@@ -228,12 +228,68 @@ There are a few tools available to assist with writing specs:
 
 - Helpers: `with_has_many_associations` and `with_belongs_to_associations` can be used in factories to set up the relevant json. They won't actually mock up the relevant requests, but ensure that things like actions are defined so that the api knows where to find them.
 
-#### Request stubbing
+#### Request stubbing for the Sequencescape v1 API
 
 Request stubs are provided by webmock. Two helper methods will assist with the majority of mocking requests to the api, `stub_api_get` and `stub_api_post`. See `spec/support/api_url_helper.rb` for details.
 
 **Note**: Due to the way the api functions, the factories don't yet support nested associations.
 
+#### Request stubbing for the Sequencescape v2 API
+
+The V2 API uses `JsonApiClient::Resource` sub-classes to represent the records in memory.
+Generally these are quite dynamic so you don't need to explicitly specify every property the API will respond with.
+The base class also provides us with methods that are familiar to Rails for finding one or more records that match criteria.
+So to stub the API, the easiest thing to do is to get FactoryBot to make up resources using the specific resource sub-class for the V2 API, and then mock the calls to those lookup methods.
+Many of these have already been done for you in `spec/support/api_url_helper.rb` such as `stub_v2_study` and `stub_v2_tag_layout_templates` which sets up the `find` method for studies by name and the `all` method for tag layout templates, respectively.
+However there's also `stub_api_v2_post`, `stub_api_v2_patch` and `stub_api_v2_save` which ensures that any calls to the `create`, `update` and the `save` method for resources of a particular type are expected and give a return value.
+If none of the existing method suit your needs, you should add new ones.
+
+##### FactoryBot is not mocking my related resources correctly
+
+Nested relationships, such as Wells inside a Plate, the resource should indicate this with keywords like `has_one`, `has_many`, `belongs_to`, etc.
+See the [json_api_client repository](https://github.com/JsonApiClient/json_api_client) for this topic and more.
+However, FactoryBot does not get on well with some of these relationship methods and will not mock them properly using standard FactoryBot definitions.
+
+If you find that FactoryBot is not giving you the expected resource for a related record, you can inject the related resource directly into the `JsonApiClient::Resource`'s cache of relationships.
+To do that, define the related resource as a `transient` variable and use an `after(:build)` block to assign the resource to the `_cached_relationship` method.
+For example, where the Resource might be defined as the following class:
+
+```ruby
+class Sequencescape::Api::V2::RootRecord < JsonApiClient::Resource
+  has_one :related_thing
+end
+```
+
+You might expect to be able to use FactoryBot in the following way:
+
+```ruby
+FactoryBot.define do
+  factory :root_record, class: Sequencescape::Api::V2::RootRecord do
+    skip_create
+
+    related_thing { create :related_thing }
+  end
+end
+```
+
+But the related thing will not be the one you defined to be generated by another factory.
+It appears the `has_one` method in the resource over-rides the mocked value and you get an empty record back instead.
+So, instead, you should create the `related_thing` record as a transient and assign it to the `root_record` in an `after(:build)` block as shown here.
+
+```ruby
+FactoryBot.define do
+  factory :root_record, class: Sequencescape::Api::V2::RootRecord do
+    skip_create
+
+    transient { related_thing { create :v2_tag_group_with_tags } }
+
+    after(:build) do |record, factory|
+      record._cached_relationship(:related_thing) { factory.related_thing } if evaluator.related_thing
+    end
+  end
+end
+```
+
 #### Feature debugging
 
 To help with debugging feature specs, temporarily comment out the line `options.add_argument('--headless')` in `spec/spec_helper.rb`. This will allow you to see the browser as the tests run. To pause the execution at certain point, possibly before an expected failure, insert `binding.pry` at the appropriate place in the spec.

app/controllers/labware_controller.rb

@@ -81,14 +81,19 @@ def locate_labware
   end
 
   def find_printers
-    @printers = api.barcode_printer.all
+    @printers = Sequencescape::Api::V2::BarcodePrinter.all
   end
 
   def state_changer_for(purpose_uuid, labware_uuid)
     StateChangers.lookup_for(purpose_uuid).new(api, labware_uuid, current_user_uuid)
   end
 
   def presenter_for(labware)
-    Presenters.lookup_for(labware).new(api: api, labware: labware)
+    presenter = Presenters.lookup_for(labware).new(labware: labware)
+
+    # TODO: {Y24-190} - Remove this line when the API v1 is removed from Presenters::ExtendedCsv
+    presenter.api = api if presenter.respond_to?(:api=)
+
+    presenter
   end
 end

app/controllers/plates_controller.rb

@@ -14,13 +14,13 @@ def fail_wells # rubocop:todo Metrics/AbcSize
         notice: 'No wells were selected to fail' # rubocop:todo Rails/I18nLocaleTexts
       )
     else
-      api.state_change.create!(
-        user: current_user_uuid,
-        target: params[:id],
+      Sequencescape::Api::V2::StateChange.create!(
         contents: wells_to_fail,
-        target_state: 'failed',
+        customer_accepts_responsibility: params[:customer_accepts_responsibility],
         reason: 'Individual Well Failure',
-        customer_accepts_responsibility: params[:customer_accepts_responsibility]
+        target_state: 'failed',
+        target_uuid: params[:id],
+        user_uuid: current_user_uuid
       )
       redirect_to(
         limber_plate_path(params[:id]),

app/controllers/print_jobs_controller.rb

@@ -35,7 +35,7 @@ def print_job_params
   def find_printer_from_name
     # there's bound to be a better way of doing this, so we don't have to
     # requery all the printers here to find the right one
-    printers = api.barcode_printer.all
+    printers = Sequencescape::Api::V2::BarcodePrinter.all
     printers.find { |p| p.name == print_job_params[:printer_name] }
   end
 end

app/controllers/robots_controller.rb

@@ -74,7 +74,7 @@ def update_bed_labware_metadata(bed, robot_barcode)
   #
   def labware_created_with_robot(labware_barcode, robot_barcode)
     LabwareMetadata
-      .new(api: api, user: current_user_uuid, barcode: labware_barcode)
+      .new(user_uuid: current_user_uuid, barcode: labware_barcode)
       .update!(created_with_robot: robot_barcode)
   end
 

app/frontend/javascript/legacy_scripts_a.js

@@ -1,6 +1,10 @@
 import $ from 'jquery'
 import { ENTER_KEYCODE, TAB_KEYCODE } from '@/javascript/lib/keycodes.js'
 
+// The majority of the code below is for the data-plate-view data attribute used to
+// show differing colours based on the view selected, eg: pools, binning, etc.
+// The pattern is to have a data-plate-view attribute on all tab links, but only have the
+// required views defined below. This allows for easy extension of the views in the future.
 let PlateViewModel = function (plateElement) {
   this['pools-view'] = {
     activate: function () {