[release] Merge Develop into Master for 14.53.0

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

Gemfile

@@ -6,6 +6,11 @@ group :default do
   gem 'bootsnap'
   gem 'rails', '~> 7.0.8'
 
+  # Previously part of ruby or rails, now separate gems
+  gem 'drb', '~> 2.2'
+  gem 'mutex_m', '~> 0.3.0'
+  gem 'syslog', '~> 0.2.0'
+
   # Fix incompatibility with between Ruby 3.1 and Psych 4 (used for yaml)
   # see https://stackoverflow.com/a/71192990
   gem 'psych', '< 4'
@@ -79,6 +84,8 @@ group :default do
   # - Load the gem from the branch
   gem 'jsonapi-resources', github: 'sanger/jsonapi-resources', branch: 'develop'
 
+  gem 'csv', '~> 3.3' # Required by jsonapi-resources, previously part of ruby
+
   # Wraps bunny with connection pooling and consumer process handling
   gem 'sanger_warren'
 

Gemfile.lock

@@ -159,6 +159,7 @@ GEM
       bigdecimal
       rexml
     crass (1.0.6)
+    csv (3.3.2)
     cucumber (9.1.2)
       builder (~> 3.2, >= 3.2.4)
       cucumber-ci-environment (~> 9.2, >= 9.2.0)
@@ -205,6 +206,7 @@ GEM
     diff-lcs (1.5.1)
     docile (1.4.0)
     domain_name (0.6.20240107)
+    drb (2.2.1)
     dry-cli (1.0.0)
     erubi (1.13.1)
     exception_notification (4.5.0)
@@ -284,6 +286,7 @@ GEM
     multi_test (1.1.0)
     mustermann (3.0.0)
       ruby2_keywords (~> 0.0.1)
+    mutex_m (0.3.0)
     mysql2 (0.5.6)
     net-imap (0.5.5)
       date
@@ -510,6 +513,7 @@ GEM
       syntax_tree (>= 2.0.1)
     sys-uname (1.2.3)
       ffi (~> 1.1)
+    syslog (0.2.0)
     temple (0.10.3)
     test-prof (1.4.2)
     thor (1.3.2)
@@ -578,11 +582,13 @@ DEPENDENCIES
   carrierwave
   caxlsx
   configatron
+  csv (~> 3.3)
   cucumber-rails
   cucumber_github_formatter
   daemons
   database_cleaner
   delayed_job_active_record
+  drb (~> 2.2)
   exception_notification
   factory_bot_rails
   flipper (~> 0.25.0)
@@ -599,6 +605,7 @@ DEPENDENCIES
   minitest-profiler
   mocha
   multi_json
+  mutex_m (~> 0.3.0)
   mysql2
   net-ldap
   nokogiri
@@ -643,6 +650,7 @@ DEPENDENCIES
   syntax_tree
   syntax_tree-haml
   syntax_tree-rbs
+  syslog (~> 0.2.0)
   test-prof
   timecop
   traceroute

app/api/io/study.rb

@@ -26,7 +26,7 @@ class Io::Study < Core::Io::Base
           study_metadata.commercially_available     => commercially_available
     study_metadata.data_release_study_type.name     => data_release_sort_of_study
            study_metadata.data_release_strategy     => data_release_strategy
-study_metadata.contaminated_human_data_access_group     => contaminated_human_data_access_group
+study_metadata.contaminated_human_data_access_group => contaminated_human_data_access_group
   '
   )
 end

app/frontend/plate-picks/components/HelpToggle.test.js

@@ -1,5 +1,4 @@
 import { shallowMount } from "@vue/test-utils";
-import "@testing-library/jest-dom";
 import HelpToggle from "./HelpToggle.vue";
 
 describe("HelpToggle.vue", () => {

app/frontend/plate-picks/components/PicksSection.test.js

@@ -1,5 +1,4 @@
 import { shallowMount } from "@vue/test-utils";
-import "@testing-library/jest-dom";
 import PicksSection from "./PicksSection.vue";
 import PicksSectionBatch from "./PicksSectionBatch.vue";
 import defaultState from "../store/state";

app/frontend/plate-picks/components/PicksSectionBatch.test.js

@@ -1,5 +1,4 @@
 import { shallowMount } from "@vue/test-utils";
-import "@testing-library/jest-dom";
 import PicksSectionBatch from "./PicksSectionBatch.vue";
 import PicksSectionBatchPick from "./PicksSectionBatchPick.vue";
 

app/frontend/plate-picks/components/PicksSectionBatchPick.test.js

@@ -1,5 +1,4 @@
 import { shallowMount } from "@vue/test-utils";
-import "@testing-library/jest-dom";
 import PicksSectionBatchPick from "./PicksSectionBatchPick.vue";
 import defaultState from "../store/state";
 import { storePlateWithPicks } from "../_test_examples_";
@@ -81,7 +80,7 @@ describe("PicksSectionBatchPick.vue", () => {
   });
 
   it("includes an editable short name", async () => {
-    const commit = jest.fn();
+    const commit = vi.fn();
     const wrapper = shallowMount(PicksSectionBatchPick, {
       propsData: {
         name,

app/frontend/plate-picks/components/PlatesSection.test.js

@@ -1,5 +1,4 @@
 import { shallowMount } from "@vue/test-utils";
-import "@testing-library/jest-dom";
 import PlatesSection from "./PlatesSection.vue";
 import PlatesSectionPlate from "./PlatesSectionPlate.vue";
 import defaultState from "../store/state";
@@ -33,7 +32,7 @@ describe("PlatesSection.vue", () => {
   it("triggers plate lookup", async () => {
     const mockStore = {
       state: defaultState(),
-      dispatch: jest.fn(),
+      dispatch: vi.fn(),
       getters: { sortedScannedPlates: [] },
     };
     const wrapper = shallowMount(PlatesSection, {
@@ -52,7 +51,7 @@ describe("PlatesSection.vue", () => {
   it("ignores empty input", async () => {
     const mockStore = {
       state: defaultState(),
-      dispatch: jest.fn(),
+      dispatch: vi.fn(),
       getters: { sortedScannedPlates: [] },
     };
     const wrapper = shallowMount(PlatesSection, {

app/frontend/plate-picks/components/PlatesSectionPlate.test.js

@@ -1,5 +1,4 @@
 import { shallowMount } from "@vue/test-utils";
-import "@testing-library/jest-dom";
 import PlatesSectionPlate from "./PlatesSectionPlate.vue";
 import defaultState from "../store/state";
 

app/frontend/plate-picks/store/actions.test.js

@@ -20,8 +20,8 @@ describe("actions.js", () => {
       // mock commit
       const plates = { 1: plateWithPicks() };
       const state = { ...defaultState(), plates };
-      const dispatch = jest.fn();
-      const commit = jest.fn((_) => (state.scanStore[`_${exampleBarcode}`] = { barcode: exampleBarcode, id: 1 }));
+      const dispatch = vi.fn();
+      const commit = vi.fn((_) => (state.scanStore[`_${exampleBarcode}`] = { barcode: exampleBarcode, id: 1 }));
       // apply action
       await plateBarcodeScan({ commit, state, dispatch }, exampleBarcode);
       // assert result
@@ -36,8 +36,8 @@ describe("actions.js", () => {
       mirageServer.create("plate", plateWithoutPicks({ id: "1" }));
       // mock commit
       const state = defaultState();
-      const commit = jest.fn((_) => (state.scanStore[`_${exampleBarcode}`] = { barcode: exampleBarcode }));
-      const dispatch = jest.fn();
+      const commit = vi.fn((_) => (state.scanStore[`_${exampleBarcode}`] = { barcode: exampleBarcode }));
+      const dispatch = vi.fn();
       // apply action
       await plateBarcodeScan({ commit, state, dispatch }, exampleBarcode);
       // assert result
@@ -53,8 +53,8 @@ describe("actions.js", () => {
       mirageServer.create("plate", plateWithoutPicks({ id: "1", control: true }));
       // mock commit
       const state = defaultState();
-      const commit = jest.fn((_) => (state.scanStore[`_${exampleBarcode}`] = { barcode: exampleBarcode }));
-      const dispatch = jest.fn();
+      const commit = vi.fn((_) => (state.scanStore[`_${exampleBarcode}`] = { barcode: exampleBarcode }));
+      const dispatch = vi.fn();
       // apply action
       await plateBarcodeScan({ commit, state, dispatch }, exampleBarcode);
       // assert result
@@ -73,10 +73,10 @@ describe("actions.js", () => {
       // mock the console
       // We don't *need* to do this, but it clutters the output and confuses
       // actual failing tests
-      console.error = jest.fn();
+      console.error = vi.fn();
       // mock commit
       const state = defaultState();
-      const commit = jest.fn((_) => (state.scanStore["_BadPlate"] = { barcode: "BadPlate" }));
+      const commit = vi.fn((_) => (state.scanStore["_BadPlate"] = { barcode: "BadPlate" }));
       // mock dependencies
       // apply action
       await plateBarcodeScan({ commit, state }, "BadPlate");
@@ -93,8 +93,8 @@ describe("actions.js", () => {
   describe("fetchBatches", () => {
     it("fetches each batch`", () => {
       // mock commit
-      const commit = jest.fn();
-      const dispatch = jest.fn();
+      const commit = vi.fn();
+      const dispatch = vi.fn();
       const state = defaultState();
       // apply action
       fetchBatches({ commit, dispatch, state }, { ids: [1, 2] });
@@ -132,8 +132,8 @@ describe("actions.js", () => {
 
       // mock commit
       const state = defaultState();
-      const commit = jest.fn().mockImplementationOnce((_) => (state.batches["b1"] = { id: "1" }));
-      const dispatch = jest.fn((_) => (state.pickCount += 1));
+      const commit = vi.fn().mockImplementationOnce((_) => (state.batches["b1"] = { id: "1" }));
+      const dispatch = vi.fn((_) => (state.pickCount += 1));
 
       // apply action
       await fetchBatch({ commit, dispatch, state }, { id: "1" });
@@ -170,7 +170,7 @@ describe("actions.js", () => {
       // Set up initial state
       const state = defaultState();
       // apply action
-      const commit = jest.fn((_) => (state.pickCount += 1));
+      const commit = vi.fn((_) => (state.pickCount += 1));
       const returned = nextPickId({ commit, state });
       expect(commit).toHaveBeenCalledWith("incrementPick");
       expect(returned).toBe(1);

app/frontend/plate-picks/store/mutations.test.js

@@ -38,7 +38,7 @@ describe("mutations.js", () => {
     it("updates plates when they exist already", () => {
       // Provided by the browser. We mock it. Currently just mock a string as we're not doing anything fancy
       global.SpeechSynthesisUtterance = class extends String {};
-      global.speechSynthesis = { speak: jest.fn() };
+      global.speechSynthesis = { speak: vi.fn() };
       // mock state
       const state = defaultState();
       state.plates = { 1: plateWithoutPicks({ id: 1 }) };
@@ -64,7 +64,7 @@ describe("mutations.js", () => {
     it("updates picks when they exist already", () => {
       // Provided by the browser. We mock it. Currently just mock a string as we're not doing anything fancy
       global.SpeechSynthesisUtterance = class extends String {};
-      global.speechSynthesis = { speak: jest.fn() };
+      global.speechSynthesis = { speak: vi.fn() };
       // mock state
       const state = {
         ...defaultState(),

app/frontend/shared/components/BaseRadio.test.js

@@ -1,5 +1,4 @@
 import { shallowMount } from "@vue/test-utils";
-import "@testing-library/jest-dom";
 import BaseRadio from "./BaseRadio.vue";
 
 describe("BaseRadio.vue", () => {

app/frontend/shared/components/BaseRadio.vue

@@ -56,6 +56,7 @@ export default {
     name: { type: String, required: true },
     id: { type: String, required: true }, // Unique id essential for generating labels
   },
+  emits: ["change"],
   data: function () {
     return {
       value: this.selected,

app/models/api/study_io.rb

@@ -101,5 +101,8 @@ def render_class
     map_attribute_to_json_attribute(:data_deletion_period)
     map_attribute_to_json_attribute(:contaminated_human_data_access_group)
     with_association(:program, lookup_by: :id) { map_attribute_to_json_attribute(:name, 'programme') }
+    map_attribute_to_json_attribute(:ebi_library_strategy)
+    map_attribute_to_json_attribute(:ebi_library_source)
+    map_attribute_to_json_attribute(:ebi_library_selection)
   end
 end

app/models/study.rb

@@ -107,6 +107,10 @@ class Study < ApplicationRecord # rubocop:todo Metrics/ClassLength
 
   DATA_RELEASE_DELAY_PERIODS = ['3 months', '6 months', '9 months', '12 months', '18 months'].freeze
 
+  EBI_LIBRARY_STRATEGY_OPTIONS = Rails.configuration.ena_requirement_fields['EBI_Library_strategy']
+  EBI_LIBRARY_SOURCE_OPTIONS = Rails.configuration.ena_requirement_fields['EBI_Library_source']
+  EBI_LIBRARY_SELECTION_OPTIONS = Rails.configuration.ena_requirement_fields['EBI_Library_selection']
+
   # Class variables
   self.per_page = 500
 
@@ -214,6 +218,11 @@ class Study < ApplicationRecord # rubocop:todo Metrics/ClassLength
     custom_attribute(:commercially_available, required: true, in: YES_OR_NO)
     custom_attribute(:study_name_abbreviation)
 
+    # add ebi library strategy
+    custom_attribute(:ebi_library_strategy, required: true, in: EBI_LIBRARY_STRATEGY_OPTIONS)
+    custom_attribute(:ebi_library_source, required: true, in: EBI_LIBRARY_SOURCE_OPTIONS)
+    custom_attribute(:ebi_library_selection, required: true, in: EBI_LIBRARY_SELECTION_OPTIONS)
+
     custom_attribute(
       :data_release_strategy,
       required: true,
@@ -309,6 +318,10 @@ class Study < ApplicationRecord # rubocop:todo Metrics/ClassLength
                 allow_blank: true
               }
 
+    validates :ebi_library_strategy, inclusion: { in: EBI_LIBRARY_STRATEGY_OPTIONS }
+    validates :ebi_library_source, inclusion: { in: EBI_LIBRARY_SOURCE_OPTIONS }
+    validates :ebi_library_selection, inclusion: { in: EBI_LIBRARY_SELECTION_OPTIONS }
+
     before_validation do |record|
       record.reference_genome_id = 1 if record.reference_genome_id.blank?
 

app/models/submission/flexible_request_graph.rb

@@ -110,6 +110,8 @@ def build! # rubocop:todo Metrics/AbcSize
             .order
             .create_request_of_type!(request_type, asset: source_asset, target_asset: target_asset)
             .tap do |request|
+              # Removed from linear_request_graph module as it caused unnecessary links in pipelines where
+              # a limber_multiplexing request is the first step.
               if source_asset&.labware.present? && target_asset&.labware.present?
                 AssetLink.create_edge(source_asset.labware, target_asset.labware)
               end

app/models/submission/linear_request_graph.rb

@@ -88,14 +88,6 @@ def create_request_chain!(request_type_and_multiplier_pairs, source_data_set, mu
         target_asset = target_assets[index]
 
         create_request_of_type!(request_type, asset: source_asset, target_asset: target_asset).tap do |request|
-          # TODO: AssetLink is supposed to disappear at some point in the future because it makes no real sense
-          # given that the request graph describes this relationship.
-          # JG: Its removal only really makes sense if we can walk the request graph in a timely manner.
-          # We use save not save! as AssetLink throws validation errors when the link already exists
-          if source_asset&.labware.present? && target_asset&.labware.present?
-            AssetLink.create_edge(source_asset.labware, target_asset.labware)
-          end
-
           request.qc_metrics = qc_metrics.compact.uniq
           request.update_responsibilities!