Master merge: DPL-1063 As a developer I need to create a table to store aliquots to track library volumes and enable top-up management

.gitignore

@@ -22,3 +22,5 @@ coverage
 
 # Ignore .talismanrc
 .talismanrc
+
+.idea

.release-version

@@ -1 +1 @@
-1.17.5
+1.17.6

Gemfile.lock

@@ -7,25 +7,25 @@ GIT
 GEM
   remote: https://rubygems.org/
   specs:
-    actionpack (7.0.8)
-      actionview (= 7.0.8)
-      activesupport (= 7.0.8)
+    actionpack (7.0.8.1)
+      actionview (= 7.0.8.1)
+      activesupport (= 7.0.8.1)
       rack (~> 2.0, >= 2.2.4)
       rack-test (>= 0.6.3)
       rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.0, >= 1.2.0)
-    actionview (7.0.8)
-      activesupport (= 7.0.8)
+    actionview (7.0.8.1)
+      activesupport (= 7.0.8.1)
       builder (~> 3.1)
       erubi (~> 1.4)
       rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.1, >= 1.2.0)
-    activemodel (7.0.8)
-      activesupport (= 7.0.8)
-    activerecord (7.0.8)
-      activemodel (= 7.0.8)
-      activesupport (= 7.0.8)
-    activesupport (7.0.8)
+    activemodel (7.0.8.1)
+      activesupport (= 7.0.8.1)
+    activerecord (7.0.8.1)
+      activemodel (= 7.0.8.1)
+      activesupport (= 7.0.8.1)
+    activesupport (7.0.8.1)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 1.6, < 2)
       minitest (>= 5.1)
@@ -42,7 +42,7 @@ GEM
     concurrent-ruby (1.2.3)
     connection_pool (2.2.5)
     crass (1.0.6)
-    diff-lcs (1.5.0)
+    diff-lcs (1.5.1)
     docile (1.4.0)
     erubi (1.12.0)
     factory_bot (6.4.5)
@@ -71,9 +71,9 @@ GEM
       guard-compat (~> 1.1)
       rspec (>= 2.99.0, < 4.0)
     hashie (5.0.0)
-    i18n (1.14.1)
+    i18n (1.14.4)
       concurrent-ruby (~> 1.0)
-    json (2.7.1)
+    json (2.7.2)
     language_server-protocol (3.17.0.3)
     listen (3.8.0)
       rb-fsevent (~> 0.10, >= 0.10.3)
@@ -84,12 +84,12 @@ GEM
     lumberjack (1.2.9)
     method_source (1.0.0)
     mini_portile2 (2.8.5)
-    minitest (5.21.2)
+    minitest (5.22.3)
     msgpack (1.7.2)
     multi_json (1.15.0)
     mysql2 (0.5.6)
     nenv (0.3.0)
-    nokogiri (1.16.2)
+    nokogiri (1.16.3)
       mini_portile2 (~> 2.8.2)
       racc (~> 1.4)
     notiffany (0.1.3)
@@ -103,7 +103,7 @@ GEM
       coderay (~> 1.1)
       method_source (~> 1.0)
     racc (1.7.3)
-    rack (2.2.8)
+    rack (2.2.9)
     rack-test (2.1.0)
       rack (>= 1.3)
     rails-dom-testing (2.2.0)
@@ -113,9 +113,9 @@ GEM
     rails-html-sanitizer (1.6.0)
       loofah (~> 2.21)
       nokogiri (~> 1.14)
-    railties (7.0.8)
-      actionpack (= 7.0.8)
-      activesupport (= 7.0.8)
+    railties (7.0.8.1)
+      actionpack (= 7.0.8.1)
+      activesupport (= 7.0.8.1)
       method_source
       rake (>= 12.2)
       thor (~> 1.0)
@@ -128,56 +128,59 @@ GEM
     rbtree (0.4.4)
     regexp_parser (2.9.0)
     rexml (3.2.6)
-    rspec (3.12.0)
-      rspec-core (~> 3.12.0)
-      rspec-expectations (~> 3.12.0)
-      rspec-mocks (~> 3.12.0)
-    rspec-core (3.12.2)
-      rspec-support (~> 3.12.0)
-    rspec-expectations (3.12.3)
+    rspec (3.13.0)
+      rspec-core (~> 3.13.0)
+      rspec-expectations (~> 3.13.0)
+      rspec-mocks (~> 3.13.0)
+    rspec-core (3.13.0)
+      rspec-support (~> 3.13.0)
+    rspec-expectations (3.13.0)
       diff-lcs (>= 1.2.0, < 2.0)
-      rspec-support (~> 3.12.0)
-    rspec-mocks (3.12.6)
+      rspec-support (~> 3.13.0)
+    rspec-mocks (3.13.0)
       diff-lcs (>= 1.2.0, < 2.0)
-      rspec-support (~> 3.12.0)
-    rspec-rails (6.1.1)
+      rspec-support (~> 3.13.0)
+    rspec-rails (6.1.2)
       actionpack (>= 6.1)
       activesupport (>= 6.1)
       railties (>= 6.1)
-      rspec-core (~> 3.12)
-      rspec-expectations (~> 3.12)
-      rspec-mocks (~> 3.12)
-      rspec-support (~> 3.12)
-    rspec-support (3.12.1)
-    rubocop (1.60.2)
+      rspec-core (~> 3.13)
+      rspec-expectations (~> 3.13)
+      rspec-mocks (~> 3.13)
+      rspec-support (~> 3.13)
+    rspec-support (3.13.1)
+    rubocop (1.63.0)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
       parser (>= 3.3.0.2)
       rainbow (>= 2.2.2, < 4.0)
       regexp_parser (>= 1.8, < 3.0)
       rexml (>= 3.2.5, < 4.0)
-      rubocop-ast (>= 1.30.0, < 2.0)
+      rubocop-ast (>= 1.31.1, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 2.4.0, < 3.0)
-    rubocop-ast (1.30.0)
-      parser (>= 3.2.1.0)
+    rubocop-ast (1.31.2)
+      parser (>= 3.3.0.4)
     rubocop-capybara (2.20.0)
       rubocop (~> 1.41)
-    rubocop-factory_bot (2.25.0)
-      rubocop (~> 1.33)
-    rubocop-performance (1.20.2)
+    rubocop-factory_bot (2.25.1)
+      rubocop (~> 1.41)
+    rubocop-performance (1.21.0)
       rubocop (>= 1.48.1, < 2.0)
-      rubocop-ast (>= 1.30.0, < 2.0)
-    rubocop-rails (2.23.1)
+      rubocop-ast (>= 1.31.1, < 2.0)
+    rubocop-rails (2.24.1)
       activesupport (>= 4.2.0)
       rack (>= 1.1)
       rubocop (>= 1.33.0, < 2.0)
-      rubocop-ast (>= 1.30.0, < 2.0)
-    rubocop-rspec (2.26.1)
+      rubocop-ast (>= 1.31.1, < 2.0)
+    rubocop-rspec (2.29.1)
       rubocop (~> 1.40)
       rubocop-capybara (~> 2.17)
       rubocop-factory_bot (~> 2.22)
+      rubocop-rspec_rails (~> 2.28)
+    rubocop-rspec_rails (2.28.2)
+      rubocop (~> 1.40)
     ruby-progressbar (1.13.0)
     sanger_warren (0.4.1)
       bunny (~> 2.17)
@@ -195,11 +198,11 @@ GEM
     sorted_set (1.0.3)
       rbtree
       set (~> 1.0)
-    thor (1.3.0)
+    thor (1.3.1)
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
     unicode-display_width (2.5.0)
-    zeitwerk (2.6.12)
+    zeitwerk (2.6.13)
 
 PLATFORMS
   ruby

app/models/aliquot.rb

@@ -0,0 +1,18 @@
+# frozen_string_literal: true
+
+# Aliquot model
+# This model is used to store aliquot data
+class Aliquot < ApplicationRecord
+  include ResourceTools
+  include SingularResourceTools
+
+  def self.base_resource_key
+    'lims_uuid'
+  end
+
+  json do
+    translate(
+      uuid: :lims_uuid
+    )
+  end
+end

db/migrate/20240404142248_create_aliquots.rb

@@ -0,0 +1,24 @@
+class CreateAliquots < ActiveRecord::Migration[7.0]
+  def up
+    create_table :aliquot, primary_key: :id, options: 'CHARSET=utf8 COLLATE=utf8_unicode_ci' do |t|
+      t.string :id_lims, null: false, comment: 'The LIMS system that the aliquot was created in'
+      t.string :lims_uuid, null: false, comment: 'The UUID of the aliquot in the LIMS system'
+      t.string :aliquot_type, null: false, comment: 'The type of the aliquot'
+      t.string :source_type, null: false, comment: 'The type of the source of the aliquot'
+      t.string :source_barcode, null: false, comment: 'The barcode of the source of the aliquot'
+      t.string :sample_name, null: false, comment: 'The name of the sample that the aliquot was created from'
+      t.string :used_by_type, null: false, comment: 'The type of the entity that the aliquot is used by'
+      t.string :used_by_barcode, null: false, comment: 'The barcode of the entity that the aliquot is used by'
+      t.decimal :volume, precision: 10, scale: 2, null: false, comment: 'The volume of the aliquot (uL)'
+      t.decimal :concentration, precision: 10, scale: 2, comment: 'The concentration of the aliquot (ng/ul)'
+      t.datetime :created, null: false, comment: 'The date and time that the aliquot was created'
+      t.datetime :last_updated, null: false, comment: 'The date and time that the aliquot was last updated'
+      t.datetime :deleted_at, comment: 'The date and time that the aliquot was deleted'
+      t.datetime :recorded_at, comment: 'The date and time that the aliquot was recorded'
+    end
+  end
+
+  def down
+    drop_table :aliquot
+  end
+end

db/schema.rb

@@ -10,7 +10,24 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema[7.0].define(version: 2024_02_28_140011) do
+ActiveRecord::Schema[7.0].define(version: 2024_04_04_142248) do
+  create_table "aliquot", charset: "utf8mb3", collation: "utf8mb3_unicode_ci", force: :cascade do |t|
+    t.string "id_lims", null: false, comment: "The LIMS system that the aliquot was created in"
+    t.string "lims_uuid", null: false, comment: "The UUID of the aliquot in the LIMS system"
+    t.string "aliquot_type", null: false, comment: "The type of the aliquot"
+    t.string "source_type", null: false, comment: "The type of the source of the aliquot"
+    t.string "source_barcode", null: false, comment: "The barcode of the source of the aliquot"
+    t.string "sample_name", null: false, comment: "The name of the sample that the aliquot was created from"
+    t.string "used_by_type", null: false, comment: "The type of the entity that the aliquot is used by"
+    t.string "used_by_barcode", null: false, comment: "The barcode of the entity that the aliquot is used by"
+    t.decimal "volume", precision: 10, scale: 2, null: false, comment: "The volume of the aliquot (uL)"
+    t.decimal "concentration", precision: 10, scale: 2, comment: "The concentration of the aliquot (ng/ul)"
+    t.datetime "created", null: false, comment: "The date and time that the aliquot was created"
+    t.datetime "last_updated", null: false, comment: "The date and time that the aliquot was last updated"
+    t.datetime "deleted_at", comment: "The date and time that the aliquot was deleted"
+    t.datetime "recorded_at", comment: "The date and time that the aliquot was recorded"
+  end
+
   create_table "bmap_flowcell", primary_key: "id_bmap_flowcell_tmp", id: :integer, charset: "utf8mb3", collation: "utf8mb3_unicode_ci", force: :cascade do |t|
     t.datetime "last_updated", precision: nil, null: false, comment: "Timestamp of last update"
     t.datetime "recorded_at", precision: nil, null: false, comment: "Timestamp of warehouse update"

lib/resource_tools/json.rb

@@ -146,7 +146,6 @@ def custom_value(name, &block)
       end
     end
 
-    # rubocop:disable Style/ArgumentsForwarding
     def initialize(*args, &block)
       super
       if self.class.custom_values.present?
@@ -157,7 +156,6 @@ def initialize(*args, &block)
       convert_booleans
       delete_if { |k, _| ignoreable.include?(k) }
     end
-    # rubocop:enable Style/ArgumentsForwarding
 
     def convert_booleans
       self.stored_as_boolean.each do |key|

spec/factories.rb

@@ -82,4 +82,20 @@
     created_at { Time.new(2020, 4, 2, 1, 0, 0, '+00:00') }
     updated_at { Time.new(2020, 4, 2, 1, 0, 0, '+00:00') }
   end
+
+  factory :aliquot do
+    sequence(:id) { |n| n }
+    id_lims { 'example' }
+    lims_uuid { '000000-0000-0000-0000-0000000002' }
+    aliquot_type { 'derivative' }
+    source_type { 'library' }
+    source_barcode { 'PR-rna-00000001_H12' }
+    sample_name { 'aliquot-sample' }
+    used_by_type { 'pool' }
+    used_by_barcode { 'pool-barcode' }
+    volume { 24.98589115 }
+    concentration { 12.46979445 }
+    created { Time.new(2012, 3, 11, 10, 20, 8, '+00:00') }
+    last_updated { Time.new(2012, 3, 11, 10, 20, 8, '+00:00') }
+  end
 end

spec/models/aliquots_spec.rb

@@ -0,0 +1,23 @@
+# frozen_string_literal: true
+
+require 'spec_helper'
+
+describe Aliquot do
+  context 'aliquots' do
+    let(:json) do
+      { 'id_lims' => 'example',
+        'aliquot_type' => 'DNA',
+        'volume' => 5.43,
+        'concentration' => 2.34,
+        'lims_uuid' => '000000-0000-0000-0000-0000000002',
+        'source_type' => 'library',
+        'source_barcode' => 'PR-rna-00000001_H12',
+        'sample_name' => 'aliquot-sample',
+        'used_by_type' => 'pool',
+        'used_by_barcode' => 'pool-barcode',
+        'last_updated' => '2012-03-11 10:20:08',
+        'created' => '2012-03-11 10:20:08' }
+    end
+    it_behaves_like 'a singular resource'
+  end
+end