Merge pull request #683 from sanger/develop

Develop into Master

.release-version

@@ -1 +1 @@
-1.20.0
+1.21.0

.ruby-version

@@ -1 +1 @@
-3.3.4
+3.3.5

Dockerfile

@@ -1,4 +1,4 @@
-FROM ruby:3.3.4
+FROM ruby:3.3.5
 
 RUN gem install bundler
 

Gemfile.lock

@@ -39,7 +39,7 @@ GEM
       amq-protocol (~> 2.3, >= 2.3.1)
       sorted_set (~> 1, >= 1.0.2)
     coderay (1.1.3)
-    concurrent-ruby (1.3.3)
+    concurrent-ruby (1.3.4)
     connection_pool (2.2.5)
     crass (1.0.6)
     diff-lcs (1.5.1)
@@ -50,7 +50,7 @@ GEM
     factory_bot_rails (6.4.3)
       factory_bot (~> 6.4)
       railties (>= 5.0.0)
-    ffi (1.15.5)
+    ffi (1.17.0)
     formatador (1.1.0)
     guard (2.18.1)
       formatador (>= 0.2.4)
@@ -84,19 +84,19 @@ GEM
     lumberjack (1.2.9)
     method_source (1.1.0)
     mini_portile2 (2.8.7)
-    minitest (5.24.1)
+    minitest (5.25.1)
     msgpack (1.7.2)
     multi_json (1.15.0)
     mysql2 (0.5.6)
     nenv (0.3.0)
-    nokogiri (1.16.6)
+    nokogiri (1.16.7)
       mini_portile2 (~> 2.8.2)
       racc (~> 1.4)
     notiffany (0.1.3)
       nenv (~> 0.1)
       shellany (~> 0.0)
-    parallel (1.25.1)
-    parser (3.3.4.0)
+    parallel (1.26.3)
+    parser (3.3.5.0)
       ast (~> 2.4.1)
       racc
     pry (0.14.2)
@@ -127,51 +127,48 @@ GEM
       ffi (~> 1.0)
     rbtree (0.4.6)
     regexp_parser (2.9.2)
-    rexml (3.3.4)
-      strscan
     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-core (3.13.1)
       rspec-support (~> 3.13.0)
-    rspec-expectations (3.13.1)
+    rspec-expectations (3.13.3)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.13.0)
     rspec-mocks (3.13.1)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.13.0)
-    rspec-rails (6.1.3)
-      actionpack (>= 6.1)
-      activesupport (>= 6.1)
-      railties (>= 6.1)
+    rspec-rails (7.0.1)
+      actionpack (>= 7.0)
+      activesupport (>= 7.0)
+      railties (>= 7.0)
       rspec-core (~> 3.13)
       rspec-expectations (~> 3.13)
       rspec-mocks (~> 3.13)
       rspec-support (~> 3.13)
     rspec-support (3.13.1)
-    rubocop (1.65.1)
+    rubocop (1.66.1)
       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 (>= 2.4, < 3.0)
-      rexml (>= 3.2.5, < 4.0)
-      rubocop-ast (>= 1.31.1, < 2.0)
+      rubocop-ast (>= 1.32.2, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 2.4.0, < 3.0)
-    rubocop-ast (1.32.0)
+    rubocop-ast (1.32.3)
       parser (>= 3.3.1.0)
     rubocop-performance (1.21.1)
       rubocop (>= 1.48.1, < 2.0)
       rubocop-ast (>= 1.31.1, < 2.0)
-    rubocop-rails (2.25.1)
+    rubocop-rails (2.26.1)
       activesupport (>= 4.2.0)
       rack (>= 1.1)
-      rubocop (>= 1.33.0, < 2.0)
+      rubocop (>= 1.52.0, < 2.0)
       rubocop-ast (>= 1.31.1, < 2.0)
-    rubocop-rspec (3.0.4)
+    rubocop-rspec (3.0.5)
       rubocop (~> 1.61)
     ruby-progressbar (1.13.0)
     sanger_warren (0.4.1)
@@ -190,12 +187,11 @@ GEM
     sorted_set (1.0.3)
       rbtree
       set (~> 1.0)
-    strscan (3.1.0)
-    thor (1.3.1)
+    thor (1.3.2)
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
-    unicode-display_width (2.5.0)
-    zeitwerk (2.6.16)
+    unicode-display_width (2.6.0)
+    zeitwerk (2.6.18)
 
 PLATFORMS
   ruby

db/migrate/20240919134424_increase_size_of_id_sample_lims_column_in_sample.rb

@@ -0,0 +1,9 @@
+class IncreaseSizeOfIdSampleLimsColumnInSample < ActiveRecord::Migration[7.0]
+  def up
+    change_column :sample, :id_sample_lims, :string, limit: 255
+  end
+
+  def down
+    change_column :sample, :id_sample_lims, :string, limit: 20
+  end
+end

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: 2024_08_14_125331) do
+ActiveRecord::Schema[7.0].define(version: 2024_09_19_134424) 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 "aliquot_uuid", null: false, comment: "The UUID of the aliquot in the LIMS system"
@@ -305,7 +305,7 @@
   create_table "sample", primary_key: "id_sample_tmp", id: { type: :integer, unsigned: true }, charset: "utf8mb3", collation: "utf8mb3_unicode_ci", force: :cascade do |t|
     t.string "id_lims", limit: 10, null: false, comment: "LIM system identifier, e.g. CLARITY-GCLP, SEQSCAPE"
     t.string "uuid_sample_lims", limit: 36, comment: "LIMS-specific sample uuid"
-    t.string "id_sample_lims", limit: 20, null: false, comment: "LIMS-specific sample identifier"
+    t.string "id_sample_lims", null: false, comment: "LIMS-specific sample identifier"
     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"
     t.datetime "deleted_at", precision: nil, comment: "Timestamp of sample deletion"
@@ -463,7 +463,7 @@
     t.string "programme"
     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 ["id_study_lims"], name: "index_study_on_id_study_lims", unique: false
+    t.index ["id_study_lims"], name: "index_study_on_id_study_lims"
     t.index ["name"], name: "study_name_index"
     t.index ["uuid_study_lims"], name: "study_uuid_study_lims_index", unique: true
   end

db/views_schema.rb

@@ -29,4 +29,4 @@
       'lh_biosero_cp_error_recovered_destination_plate_completed','lh_biosero_cp_error_recovered_destination_plate_partial_completed'
     )
 SQL
-)
+)

spec/models/sample_spec.rb

@@ -28,7 +28,7 @@
 
     let(:json) do
       {
-        'id' => 1,
+        'id' => '1' * 255.to_i,
         'name' => 'name',
         'reference_genome' => 'reference genome',
         'organism' => 'organism',

spec/spec_helper.rb

@@ -12,7 +12,7 @@
 
 # Requires supporting ruby files with custom matchers and macros, etc,
 # in spec/support/ and its subdirectories.
-Dir[Rails.root.join('spec/support/**/*.rb')].each { |f| require f }
+Rails.root.glob('spec/support/**/*.rb').each { |f| require f }
 
 RSpec.configure do |config|
   config.use_transactional_fixtures = true