Master merge from develop

.release-version

@@ -1 +1 @@
-1.18.1
+1.19.0

.ruby-version

@@ -1 +1 @@
-3.1.2
+3.3.4

Dockerfile

@@ -1,4 +1,4 @@
-FROM ruby:3.1.2
+FROM ruby:3.3.4
 
 RUN gem install bundler
 

Gemfile

@@ -19,7 +19,9 @@ gem 'bundler', '>= 1.3.0'
 gem 'railties', '~> 7.0.4'
 # # RAILS DEPENDENCIES
 
-gem 'sanger_warren'
+gem 'bunny', '>= 2.22.0'
+gem 'rbtree', '~> 0.4.5'
+gem 'sanger_warren', '~> 0.4.1'
 
 gem 'bootsnap', '~> 1.7', '>= 1.7.3', require: false
 gem 'hashie', '~> 5.0'

Gemfile.lock

@@ -35,7 +35,7 @@ GEM
     bootsnap (1.18.3)
       msgpack (~> 1.2)
     builder (3.3.0)
-    bunny (2.19.0)
+    bunny (2.23.0)
       amq-protocol (~> 2.3, >= 2.3.1)
       sorted_set (~> 1, >= 1.0.2)
     coderay (1.1.3)
@@ -96,7 +96,7 @@ GEM
       nenv (~> 0.1)
       shellany (~> 0.0)
     parallel (1.25.1)
-    parser (3.3.3.0)
+    parser (3.3.4.0)
       ast (~> 2.4.1)
       racc
     pry (0.14.2)
@@ -125,9 +125,9 @@ GEM
     rb-fsevent (0.11.2)
     rb-inotify (0.10.1)
       ffi (~> 1.0)
-    rbtree (0.4.4)
+    rbtree (0.4.6)
     regexp_parser (2.9.2)
-    rexml (3.3.1)
+    rexml (3.3.2)
       strscan
     rspec (3.13.0)
       rspec-core (~> 3.13.0)
@@ -150,13 +150,13 @@ GEM
       rspec-mocks (~> 3.13)
       rspec-support (~> 3.13)
     rspec-support (3.13.1)
-    rubocop (1.64.1)
+    rubocop (1.65.0)
       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)
+      regexp_parser (>= 2.4, < 3.0)
       rexml (>= 3.2.5, < 4.0)
       rubocop-ast (>= 1.31.1, < 2.0)
       ruby-progressbar (~> 1.7)
@@ -171,15 +171,15 @@ GEM
       rack (>= 1.1)
       rubocop (>= 1.33.0, < 2.0)
       rubocop-ast (>= 1.31.1, < 2.0)
-    rubocop-rspec (3.0.1)
+    rubocop-rspec (3.0.3)
       rubocop (~> 1.61)
     ruby-progressbar (1.13.0)
     sanger_warren (0.4.1)
       bunny (~> 2.17)
       connection_pool (~> 2.2)
       multi_json (~> 1.0)
       thor (~> 1.1)
-    set (1.0.2)
+    set (1.1.0)
     shellany (0.0.1)
     simplecov (0.22.0)
       docile (~> 1.1)
@@ -206,6 +206,7 @@ DEPENDENCIES
   activesupport (~> 7.0.4)
   bootsnap (~> 1.7, >= 1.7.3)
   bundler (>= 1.3.0)
+  bunny (>= 2.22.0)
   factory_bot_rails
   guard
   guard-bundler
@@ -214,12 +215,13 @@ DEPENDENCIES
   mysql2 (~> 0.5.3)
   pry
   railties (~> 7.0.4)
+  rbtree (~> 0.4.5)
   rspec-rails
   rubocop
   rubocop-performance
   rubocop-rails
   rubocop-rspec
-  sanger_warren
+  sanger_warren (~> 0.4.1)
   simplecov
   views_schema!
 

README.md

@@ -16,15 +16,13 @@ A denormalised warehouse for multiple LIMS.
 ### Installation
 
 1. Clone the git repository
-2. Install the relevant ruby from `.ruby-version`
+2. Install the relevant ruby from `.ruby-version`  
+    Rbenv will read .ruby-version automatically   
+   `rbenv install`
 
-    Rbenv will read .ruby-version automatically
-
-       rbenv install
-
-3. Run the setup process:
-
-       bin/setup
+3. Run the setup process:  
+    3.1. Set up your MySQL root password inside the file config/database.yml  
+    3.2. Run `bin/setup ` 
 
 **NB**: If getting an error while installing the `mysql2` gem, try:
 

app/models/aliquot.rb

@@ -7,12 +7,12 @@ class Aliquot < ApplicationRecord
   include SingularResourceTools
 
   def self.base_resource_key
-    'lims_uuid'
+    'aliquot_uuid'
   end
 
   json do
     translate(
-      uuid: :lims_uuid
+      uuid: :aliquot_uuid
     )
 
     ignore :created

db/migrate/20240723152109_rename_lims_uuid_colum_to_aliquot_uu_id_in_aliquot_table.rb

@@ -0,0 +1,9 @@
+class RenameLimsUuidColumToAliquotUuIdInAliquotTable < ActiveRecord::Migration[7.0]
+  def up
+    rename_column :aliquot, :lims_uuid, :aliquot_uuid
+  end
+
+  def down
+    rename_column :aliquot, :aliquot_uuid, :lims_uuid
+  end
+end

db/migrate/20240726144332_add_contaminated_human_data_to_study.rb

@@ -0,0 +1,5 @@
+class AddContaminatedHumanDataToStudy < ActiveRecord::Migration[7.0]
+  def change
+    add_column :study, :contaminated_human_data_access_group, :string, default: nil
+  end
+end

db/schema.rb

@@ -10,10 +10,10 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema[7.0].define(version: 2024_07_08_081135) do
+ActiveRecord::Schema[7.0].define(version: 2024_07_26_144332) 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_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"
@@ -459,6 +459,7 @@
     t.string "data_destination", comment: "The data destination type(s) for the study. It could be 'standard', '14mg' or 'gseq'. This may be extended, if Sanger gains more external customers. It can contain multiply destinations separated by a space."
     t.string "s3_email_list"
     t.string "data_deletion_period"
+    t.string "contaminated_human_data_access_group"
     t.index ["accession_number"], name: "study_accession_number_index"
     t.index ["id_lims", "id_study_lims"], name: "study_id_lims_id_study_lims_index", unique: true
     t.index ["name"], name: "study_name_index"

spec/factories.rb

@@ -86,7 +86,7 @@
   factory :aliquot do
     sequence(:id) { |n| n }
     id_lims { 'example' }
-    lims_uuid { '000000-0000-0000-0000-0000000002' }
+    aliquot_uuid { '000000-0000-0000-0000-0000000002' }
     aliquot_type { 'derivative' }
     source_type { 'library' }
     source_barcode { 'PR-rna-00000001_H12' }

spec/models/aliquot_spec.rb

@@ -12,7 +12,7 @@
         'volume' => 5.43,
         'concentration' => 2.34,
         'insert_size' => 100,
-        'lims_uuid' => '000000-0000-0000-0000-0000000002',
+        'aliquot_uuid' => '000000-0000-0000-0000-0000000002',
         'source_type' => 'library',
         'source_barcode' => 'PR-rna-00000001_H12',
         'sample_name' => 'aliquot-sample',

spec/models/study_spec.rb

@@ -65,7 +65,8 @@
         'hmdmc_number' => 'H12345; H67890; And then a comment',
         'data_destination' => 'standard',
         's3_email_list' => '[email protected];[email protected]',
-        'data_deletion_period' => '3 months'
+        'data_deletion_period' => '3 months',
+        'contaminated_human_data_access_group' => 'contaminated human data'
       }
     end