Merge branch 'develop' into Y24-051-hide-pools-tab-if-not-relevant

Dockerfile

@@ -1,9 +1,11 @@
 ARG CHIPSET=default
+ARG RUBY_VERSION=3.3.6
+ARG APPLE_PLATFORM=linux/amd64
 
 # Use the correct base image depending on the architecture
 # For Apple M1 Chip, run: docker build --build-arg CHIPSET=m1 .
-FROM ruby:3.3.6-slim AS base_default
-FROM --platform=linux/amd64 ruby:3.2.5-slim AS base_m1
+FROM ruby:${RUBY_VERSION}-slim AS base_default
+FROM --platform=${APPLE_PLATFORM} ruby:${RUBY_VERSION}-slim AS base_m1
 FROM base_${CHIPSET} AS base
 
 COPY .nvmrc /.nvmrc

db/migrate/20250123105050_migrate_sample_metadata_for_invalid_insdc_country_of_origin.rb

@@ -0,0 +1,17 @@
+# frozen_string_literal: true
+# Migrates the data related to invalid INSDC countries of origin to their current equivalent
+# See DisableInvalidInsdcCountries migration for more details
+class MigrateSampleMetadataForInvalidInsdcCountryOfOrigin < ActiveRecord::Migration[7.0]
+  def change
+    sample_metadata =
+      Sample::Metadata.where(country_of_origin: ['not applicable: control sample', 'not applicable: sample group'])
+
+    sample_metadata.each do |sm|
+      if sm.country_of_origin == 'not applicable: control sample'
+        sm.update!(country_of_origin: 'missing: control sample')
+      elsif sm.country_of_origin == 'not applicable: sample group'
+        sm.update!(country_of_origin: 'missing: sample group')
+      end
+    end
+  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: 2025_01_14_135342) do
+ActiveRecord::Schema[7.0].define(version: 2025_01_23_105050) do
   create_table "aliquot_indices", id: :integer, charset: "utf8mb4", collation: "utf8mb4_unicode_ci", options: "ENGINE=InnoDB ROW_FORMAT=DYNAMIC", force: :cascade do |t|
     t.integer "aliquot_id", null: false
     t.integer "lane_id", null: false

features/support/capybara.rb

@@ -12,7 +12,7 @@
 
   options.add_argument('--window-size=1600,3200')
   options.add_preference('download.default_directory', DownloadHelpers::PATH.to_s)
-  options.add_argument('--headless=old')
+  options.add_argument('--headless')
   options.add_argument('--disable-gpu')
   options.add_argument('--disable-search-engine-choice-screen')
   Capybara::Selenium::Driver.new(app, browser: :chrome, options: options)

features/support/step_definitions/robot_verification_steps.rb

@@ -13,7 +13,7 @@
   step('I follow "Select Plate Template"')
   step('I select "testtemplate" from "Plate Template"')
   step('I select "Infinium 670k" from "Output plate purpose"')
-  step('I fill in "nano_grams_per_micro_litre_volume_required" with "13"')
+  fill_in('nano_grams_per_micro_litre_volume_required', with: '13', fill_options: { clear: :backspace })
   step('I fill in "nano_grams_per_micro_litre_concentration_required" with "50"')
   fill_in('nano_grams_per_micro_litre_robot_minimum_picking_volume', with: minimum_robot_pick)
   step('I press "Next step"')

spec/spec_helper.rb

@@ -52,7 +52,7 @@
   options = Selenium::WebDriver::Chrome::Options.new
 
   options.add_preference('download.default_directory', DownloadHelpers::PATH.to_s)
-  options.add_argument('--headless=old')
+  options.add_argument('--headless')
   options.add_argument('--disable-gpu')
   options.add_argument('--disable-search-engine-choice-screen')
   Capybara::Selenium::Driver.new(app, browser: :chrome, options: options)