[OSU-114] Service sanger admin tab

app/views/shared/nav/_manage_product.html.haml

@@ -0,0 +1,6 @@
+= content_for :h1 do
+  = current_facility
+= content_for :sidebar do
+  = render "admin/shared/sidenav_product", sidenav_tab: @product.class.name.pluralize.underscore
+= content_for :tabnav do
+  = render "admin/shared/tabnav_product", secondary_tab: local_assigns[:secondary_tab]

db/schema.rb

@@ -10,7 +10,7 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema[7.0].define(version: 2025_01_10_132703) do
+ActiveRecord::Schema[7.0].define(version: 2025_01_13_205804) do
   create_table "account_facility_joins", id: :integer, charset: "utf8mb3", force: :cascade do |t|
     t.integer "facility_id", null: false
     t.integer "account_id", null: false
@@ -735,6 +735,7 @@
     t.string "group", null: false
     t.datetime "created_at", precision: nil
     t.datetime "updated_at", precision: nil
+    t.boolean "needs_primer", default: false, null: false
     t.index ["product_id"], name: "index_sanger_seq_product_groups_on_product_id", unique: true
   end
 

vendor/engines/sanger_sequencing/app/controllers/sanger_sequencing/admin/batches_controller.rb

@@ -82,7 +82,7 @@ class UploadError < StandardError
 
       def validate_product_group
         @product_group = params[:group].presence
-        raise ActiveRecord::RecordNotFound unless @product_group.blank? || ProductGroup::GROUPS.include?(@product_group)
+        raise ActiveRecord::RecordNotFound unless @product_group.blank? || SangerProduct::GROUPS.include?(@product_group)
       end
 
       def load_batch

vendor/engines/sanger_sequencing/app/controllers/sanger_sequencing/sanger_products_controller.rb

@@ -0,0 +1,52 @@
+# frozen_string_literal: true
+
+module SangerSequencing
+
+  class SangerProductsController < BaseController
+    before_action :set_resources
+    before_action { @active_tab = "admin_products" }
+    before_action { authorize! :manage, current_facility }
+
+    layout "two_column"
+    admin_tab :all
+
+    def show
+    end
+
+    def edit
+    end
+
+    def update
+      if @sanger_product.update(sanger_product_params)
+        redirect_to [current_facility, @product, :sanger_sequencing, :sanger_product], notice: text(".update.success")
+      else
+        render :edit
+      end
+    end
+
+    private
+
+    def sanger_product_groups
+      SangerProduct::GROUPS.map do |group|
+        [SangerProduct.human_attribute_name("group.#{group}"), group]
+      end
+    end
+
+    helper_method :sanger_product_groups
+
+    def sanger_product_params
+      params.require(:sanger_sequencing_sanger_product).permit(
+        :needs_primer,
+        :group
+      )
+    end
+
+    def set_resources
+      @product = current_facility.products.find_by!(
+        url_name: params[:service_id]
+      )
+      @sanger_product = @product.sanger_product || @product.create_sanger_product
+    end
+  end
+
+end

vendor/engines/sanger_sequencing/app/models/concerns/sanger_sequencing/sanger_enabled_product.rb

@@ -0,0 +1,15 @@
+# frozen_string_literal: true
+
+module SangerSequencing
+
+  module SangerEnabledProduct
+
+    extend ActiveSupport::Concern
+
+    included do
+      has_one :sanger_product, class_name: "SangerSequencing::SangerProduct", foreign_key: :product_id
+    end
+
+  end
+
+end

vendor/engines/sanger_sequencing/app/models/sanger_sequencing/product_group.rb → vendor/engines/sanger_sequencing/app/models/sanger_sequencing/sanger_product.rb

@@ -2,14 +2,19 @@
 
 module SangerSequencing
 
-  class ProductGroup < ApplicationRecord
+  ##
+  # Model that holds Sanger module configuration
+  # for a product
+  class SangerProduct < ApplicationRecord
 
     # sanger_sequencing_product_groups is too long of a table name for Oracle
     self.table_name = "sanger_seq_product_groups"
     GROUPS = WellPlateConfiguration::CONFIGS.keys
 
     belongs_to :product
 
+    attribute :group, default: 'default'
+
     validates :group, presence: true, inclusion: { in: GROUPS }
     validates :product, presence: true, uniqueness: { case_sensitive: false }
 

vendor/engines/sanger_sequencing/app/models/sanger_sequencing/submission.rb

@@ -33,9 +33,9 @@ class Submission < ApplicationRecord
 
     def self.for_product_group(product_group)
       if product_group.present?
-        where(order_details: { product_id: ProductGroup.where(group: product_group).pluck(:product_id) })
+        where(order_details: { product_id: SangerProduct.where(group: product_group).pluck(:product_id) })
       else
-        where.not(order_details: { product_id: ProductGroup.pluck(:product_id) })
+        where.not(order_details: { product_id: SangerProduct.pluck(:product_id) })
       end
     end
 

vendor/engines/sanger_sequencing/app/views/sanger_sequencing/admin/shared/tabnav_product/_sanger.html.haml

@@ -0,0 +1,4 @@
+- if @product.sanger_sequencing_enabled? && can?(:manage, current_facility)
+  = tab t("sanger_sequencing.tabnav_product"),
+    facility_service_sanger_sequencing_sanger_product_path(current_facility, @product),
+    (secondary_tab == "sanger")

vendor/engines/sanger_sequencing/app/views/sanger_sequencing/sanger_products/edit.html.haml

@@ -0,0 +1,17 @@
+= render "shared/nav/manage_product", secondary_tab: "sanger"
+
+%h2= text("title")
+
+= simple_form_for @sanger_product, url: facility_service_sanger_sequencing_sanger_product_path(current_facility, @product) do |f|
+  = f.input :needs_primer,
+    as: :boolean,
+    label: false,
+    inline_label: SangerSequencing::SangerProduct.human_attribute_name(:needs_primer),
+    include_blank: false,
+    hint: text("needs_primer")
+
+  = f.input :group,
+    collection: sanger_product_groups,
+    hint: text("group")
+
+  = f.submit text("shared.save"), class: "btn btn-primary"

vendor/engines/sanger_sequencing/app/views/sanger_sequencing/sanger_products/show.html.haml

@@ -0,0 +1,13 @@
+= render "shared/nav/manage_product", secondary_tab: "sanger"
+
+%h2= text("title")
+
+= readonly_form_for @sanger_product.class.name.underscore, @sanger_product do |f|
+  = f.input :needs_primer, as: :boolean
+  = f.input :group,
+    input_html: { value: SangerSequencing::SangerProduct.human_attribute_name("group.#{@sanger_product.group}") }
+
+- if can? :edit, @product
+  %ul.inline
+    %li= link_to "Edit", edit_facility_service_sanger_sequencing_sanger_product_path(current_facility, @product), class: "btn"
+

vendor/engines/sanger_sequencing/config/locales/en.yml

@@ -5,16 +5,27 @@ en:
     product_groups:
       default: Sanger Sequencing
       fragment: Fragment Analysis
+    tabnav_product: Sanger
 
   controllers:
     sanger_sequencing/admin/batches:
       create:
         success: "We have saved your batch"
       destroy:
         success: "Batch was successfully deleted"
+    sanger_sequencing/sanger_products:
+      update:
+        success: Sanger Configuration updated successfully
 
   views:
     sanger_sequencing:
+      sanger_products:
+        show:
+          title: Sanger Configuration
+        edit:
+          title: Sanger Configuration
+          needs_primer: Require submissions to include a primer
+          group: Submissions of the same type can be batched together
       submissions:
         form:
           submit: "Save Submission"
@@ -52,6 +63,12 @@ en:
       sanger_sequencing/batch:
         created_at: Created
         created_by: Created By
+      sanger_sequencing/sanger_product:
+        needs_primer: Needs a Primer
+        group: Plated Service Type
+      sanger_sequencing/sanger_product/group:
+          default: Sanger Sequencing
+          fragment: Fragment Analysis
 
     models:
       sanger_sequencing/submission:

vendor/engines/sanger_sequencing/config/routes.rb

@@ -10,6 +10,11 @@
   end
 
   resources :facilities, only: [] do
+    resources :services, only: [] do
+      namespace :sanger_sequencing do
+        resource :sanger_product, only: [:show, :edit, :update]
+      end
+    end
     namespace :sanger_sequencing do
       namespace :admin do
         resources :submissions, only: [:index, :show]

vendor/engines/sanger_sequencing/db/migrate/20250113205804_add_product_group_primer.rb

@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+class AddProductGroupPrimer < ActiveRecord::Migration[4.2]
+  def change
+    add_column(
+      :sanger_seq_product_groups,
+      :needs_primer,
+      :boolean,
+      default: false,
+      null: false
+    )
+  end
+end

vendor/engines/sanger_sequencing/lib/sanger_sequencing/engine.rb

@@ -9,6 +9,13 @@ class Engine < ::Rails::Engine
 
       ViewHook.add_hook "orders.receipt", "after_note", "sanger_sequencing/orders/samples_on_receipt"
       ViewHook.add_hook "purchase_notifier.order_receipt", "after_note", "sanger_sequencing/orders/samples_on_receipt"
+      ViewHook.add_hook(
+        "admin.shared.tabnav_product",
+        "additional_tabs",
+        "sanger_sequencing/admin/shared/tabnav_product/sanger"
+      )
+
+      Service.include SangerSequencing::SangerEnabledProduct
     end
 
     config.generators do |g|

vendor/engines/sanger_sequencing/sanger_sequencing.gemspec

@@ -19,6 +19,4 @@ Gem::Specification.new do |s|
 
   s.add_dependency "rails", ">= 4.0"
   # s.add_dependency "jquery-rails"
-
-  s.add_development_dependency "rails-rspec"
 end

vendor/engines/sanger_sequencing/spec/controllers/sanger_sequencing/sanger_products_spec.rb

@@ -0,0 +1,73 @@
+# frozen_string_literal: true
+
+require "rails_helper"
+require "controller_spec_helper"
+
+RSpec.describe SangerSequencing::SangerProductsController do
+  let(:facility) { create(:setup_facility, sanger_sequencing_enabled: true) }
+  let(:service) { create(:setup_service, facility:, sanger_sequencing_enabled: true) }
+  let(:user) { create(:user, :facility_administrator, facility:) }
+
+  before do
+    sign_in user
+
+    @params = { facility_id: facility.url_name, service_id: service.url_name }
+  end
+
+  shared_examples "creates a sanger product if needed" do
+    it "creates a sanger product if needed" do
+      expect { do_request }.to(
+        change do
+          service.reload.sanger_product
+        end.from(nil).to(SangerSequencing::SangerProduct)
+      )
+    end
+  end
+
+  describe "show" do
+    before do
+      @method = :get
+      @action = :show
+    end
+
+    include_examples "creates a sanger product if needed"
+  end
+
+  describe "edit" do
+    before do
+      @method = :get
+      @action = :edit
+    end
+
+    include_examples "creates a sanger product if needed"
+  end
+
+  describe "update" do
+    before do
+      @method = :put
+      @action = :update
+      @params[:sanger_sequencing_sanger_product] = { group: "default" }
+    end
+
+    include_examples "creates a sanger product if needed"
+
+    it "updates the sanger product" do
+      sanger_product_json = {
+        "needs_primer" => true, "group" => "fragment"
+      }
+      @params[:sanger_sequencing_sanger_product] = sanger_product_json
+
+      service.create_sanger_product
+
+      expect { do_request }.to(
+        change do
+          service.reload.sanger_product.as_json(only: %i[needs_primer group])
+        end.from(
+          { "needs_primer" => false, "group" => "default" }
+        ).to(
+          sanger_product_json
+        )
+      )
+    end
+  end
+end

vendor/engines/sanger_sequencing/spec/factories/product_groups.rb → vendor/engines/sanger_sequencing/spec/factories/sanger_products.rb

@@ -1,7 +1,7 @@
 # frozen_string_literal: true
 
 FactoryBot.define do
-  factory :product_group, class: SangerSequencing::ProductGroup do
+  factory :product_group, class: SangerSequencing::SangerProduct do
     product factory: :setup_service
 
     trait :default do

vendor/engines/sanger_sequencing/spec/system/batches/creating_a_batch_spec.rb

@@ -83,7 +83,7 @@ def click_add(submission_id)
 
     describe "when the service is mapped to the fragment group" do
       before do
-        SangerSequencing::ProductGroup.create!(product: service, group: "fragment")
+        SangerSequencing::SangerProduct.create!(product: service, group: "fragment")
         visit facility_sanger_sequencing_admin_batches_path(facility, group: "fragment")
         click_link "Create New Batch"
       end