Fixes for 4270 y24 245 remove fake cherry picks

Gemfile.lock

@@ -258,7 +258,7 @@ GEM
     listen (3.9.0)
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
-    logger (1.6.0)
+    logger (1.6.1)
     loofah (2.22.0)
       crass (~> 1.0.2)
       nokogiri (>= 1.12.0)
@@ -320,7 +320,7 @@ GEM
       pry (>= 0.13.0)
     psych (3.3.4)
     public_suffix (6.0.0)
-    puma (6.4.2)
+    puma (6.4.3)
       nio4r (~> 2.0)
     racc (1.8.1)
     rack (2.2.9)
@@ -389,8 +389,7 @@ GEM
       http-cookie (>= 1.0.2, < 2.0)
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
-    rexml (3.3.6)
-      strscan
+    rexml (3.3.7)
     roo (2.10.1)
       nokogiri (~> 1)
       rubyzip (>= 1.3.0, < 3.0.0)
@@ -471,7 +470,7 @@ GEM
     sanitize (6.1.0)
       crass (~> 1.0.2)
       nokogiri (>= 1.12.0)
-    selenium-webdriver (4.22.0)
+    selenium-webdriver (4.25.0)
       base64 (~> 0.2)
       logger (~> 1.4)
       rexml (~> 3.2, >= 3.2.5)
@@ -507,7 +506,6 @@ GEM
       activesupport (>= 6.1)
       sprockets (>= 3.0.0)
     ssrf_filter (1.1.2)
-    strscan (3.1.0)
     syntax_tree (6.2.0)
       prettier_print (>= 1.2.0)
     syntax_tree-haml (4.0.3)
@@ -544,7 +542,7 @@ GEM
       addressable (>= 2.8.0)
       crack (>= 0.3.2)
       hashdiff (>= 0.4.0, < 2.0.0)
-    websocket (1.2.10)
+    websocket (1.2.11)
     websocket-driver (0.7.6)
       websocket-extensions (>= 0.1.0)
     websocket-extensions (0.1.5)

app/frontend/.eslintrc.js

@@ -11,6 +11,7 @@ module.exports = {
   parserOptions: {
     parser: "babel-eslint",
     sourceType: "module",
+    ecmaVersion: 2018,
   },
   rules: {
     "no-unused-vars": [

features/api/tag_layout_templates.feature

@@ -40,7 +40,7 @@
       And the UUID for the plate "Testing the API" is "11111111-2222-3333-4444-000000000002"
       And all wells on the plate "Testing the API" have unique samples
 
-    Given a "Stock plate" plate called "Testing the tagging" exists
+    Given a "Stock plate" input plate called "Testing the tagging" exists
       And the UUID for the plate "Testing the tagging" is "11111111-2222-3333-4444-000000000001"
       And the wells for the plate "Testing the API" have been pooled in columns to the plate "Testing the tagging"
 
@@ -290,7 +290,7 @@
       And the UUID for the plate "Testing the API" is "11111111-2222-3333-4444-000000000002"
       And all wells on the plate "Testing the API" have unique samples
 
-    Given a "Stock plate" plate called "Testing the tagging" exists
+    Given a "Stock plate" input plate called "Testing the tagging" exists
       And the UUID for the plate "Testing the tagging" is "11111111-2222-3333-4444-000000000001"
       And the wells for the plate "Testing the API" have been pooled to the plate "Testing the tagging" according to the pooling strategy 96
       And "F11-F12" of the plate "Testing the tagging" have been failed
@@ -460,7 +460,7 @@
       And the UUID for the plate "Testing the API" is "11111111-2222-3333-4444-000000000002"
       And all wells on the plate "Testing the API" have unique samples
 
-    Given a "Stock plate" plate called "Testing the tagging" exists
+    Given a "Stock plate" input plate called "Testing the tagging" exists
       And the UUID for the plate "Testing the tagging" is "11111111-2222-3333-4444-000000000001"
       And the wells for the plate "Testing the API" have been pooled in columns to the plate "Testing the tagging"
 
@@ -550,7 +550,7 @@
       And the UUID for the plate "Testing the API" is "11111111-2222-3333-4444-000000000002"
       And all wells on the plate "Testing the API" have unique samples
 
-    Given a "Stock plate" plate called "Testing the tagging" exists
+    Given a "Stock plate" input plate called "Testing the tagging" exists
       And the UUID for the plate "Testing the tagging" is "11111111-2222-3333-4444-000000000001"
       And the wells for the plate "Testing the API" have been pooled to the plate "Testing the tagging" according to the pooling strategy 8, 4, 8, 4, 8, 4, 8, 4, 8, 4, 8, 4, 8, 4, 8, 4
 
@@ -597,7 +597,7 @@
       }
       """
 
     Then the tag layout on the plate "Testing the tagging" should be:
       | AAAA | AAAA | AAAA | AAAA | AAAA | AAAA | AAAA | AAAA | AAAA | AAAA | AAAA | AAAA |
       | CCCC | CCCC | CCCC | CCCC | CCCC | CCCC | CCCC | CCCC | CCCC | CCCC | CCCC | CCCC |
       | TTTT | TTTT | TTTT | TTTT | TTTT | TTTT | TTTT | TTTT | TTTT | TTTT | TTTT | TTTT |
@@ -633,7 +633,7 @@
       And the UUID for the plate "Testing the API" is "11111111-2222-3333-4444-000000000002"
       And all wells on the plate "Testing the API" have unique samples
 
-    Given a "Stock plate" plate called "Testing the tagging" exists
+    Given a "Stock plate" input plate called "Testing the tagging" exists
       And the UUID for the plate "Testing the tagging" is "11111111-2222-3333-4444-000000000001"
       And the wells for the plate "Testing the API" have been pooled to the plate "Testing the tagging" according to the pooling strategy 8, 2, 10, 4, 8, 2, 10, 4, 8, 2, 10, 4, 8, 8, 8
 
@@ -681,7 +681,7 @@
       }
       """
 
     Then the tag layout on the plate "Testing the tagging" should be:
       | AAAA | AAAA | AAAA | AAAA | AAAA | AAAA | AAAA | AAAA | AAAA | AAAA | AAAA | AAAA |
       | CCCC | CCCC | CCCC | CCCC | CCCC | CCCC | CCCC | CCCC | CCCC | CCCC | CCCC | CCCC |
       | TTTT | TTTT | GAGA | TTTT | TTTT | GAGA | TTTT | TTTT | GAGA | TTTT | TTTT | TTTT |
@@ -706,7 +706,7 @@
       And the UUID for the plate "Testing the API" is "11111111-2222-3333-4444-000000000002"
       And all wells on the plate "Testing the API" have unique samples
 
-    Given a "Stock plate" plate called "Testing the tagging" exists
+    Given a "Stock plate" input plate called "Testing the tagging" exists
       And the UUID for the plate "Testing the tagging" is "11111111-2222-3333-4444-000000000001"
       And the wells for the plate "Testing the API" have been pooled to the plate "Testing the tagging" according to the pooling strategy 96
 
@@ -747,7 +747,7 @@
       And all wells on the plate "Testing the API" have unique samples
       And H12 on the plate "Testing the API" is empty
 
-    Given a "Stock plate" plate called "Testing the tagging" exists
+    Given a "Stock plate" input plate called "Testing the tagging" exists
       And the UUID for the plate "Testing the tagging" is "11111111-2222-3333-4444-000000000001"
       And the wells for the plate "Testing the API" have been pooled to the plate "Testing the tagging" according to the pooling strategy 95
 

features/api/tag_layouts.feature

@@ -55,6 +55,46 @@
       }
       """
 
+  @tag_layout @create @barcode-service
+  Scenario: Creating a tag layout of an entire plate using 96 tags by pools
+    Given the Baracoda barcode service returns "SQPD-1000001"
+    Given the Baracoda barcode service returns "SQPD-1000002"
+    Given the tag group "Example Tag Group" exists
+      And the UUID for the tag group "Example Tag Group" is "00000000-1111-2222-3333-444444444444"
+      And the tag group "Example Tag Group" has 20 tags
+
+    Given a "Stock plate" plate called "Testing the API" exists
+      And the UUID for the plate "Testing the API" is "11111111-2222-3333-4444-000000000002"
+      And all wells on the plate "Testing the API" have unique samples
+
+    Given a "Stock plate" plate called "Testing the tagging" exists
+      And the UUID for the plate "Testing the tagging" is "11111111-2222-3333-4444-000000000001"
+      And the wells for the plate "Testing the API" have been pooled to the plate "Testing the tagging" according to the pooling strategy 12, 8, 20, 12, 8, 20, 16
+
+    When I make an authorised POST with the following JSON to the API path "/tag_layouts":
+      """
+      {
+        "tag_layout": {
+          "plate": "11111111-2222-3333-4444-000000000001",
+          "user": "99999999-8888-7777-6666-555555555555",
+          "tag_group": "00000000-1111-2222-3333-444444444444",
+          "direction": "column",
+          "walking_by": "manual by pool",
+          "initial_tag": 0
+        }
+      }
+      """
+    Then the HTTP response should be "201 Created"
+
+    Then the tag layout on the plate "Testing the tagging" should be:
+      | TAG1 | TAG9  | TAG5 | TAG5  | TAG13 | TAG1 | TAG9  | TAG5 | TAG5  | TAG13 | TAG1 | TAG9  |
+      | TAG2 | TAG10 | TAG6 | TAG6  | TAG14 | TAG2 | TAG10 | TAG6 | TAG6  | TAG14 | TAG2 | TAG10 |
+      | TAG3 | TAG11 | TAG7 | TAG7  | TAG15 | TAG3 | TAG11 | TAG7 | TAG7  | TAG15 | TAG3 | TAG11 |
+      | TAG4 | TAG12 | TAG8 | TAG8  | TAG16 | TAG4 | TAG12 | TAG8 | TAG8  | TAG16 | TAG4 | TAG12 |
+      | TAG5 | TAG1  | TAG1 | TAG9  | TAG17 | TAG5 | TAG1  | TAG1 | TAG9  | TAG17 | TAG5 | TAG13 |
+      | TAG6 | TAG2  | TAG2 | TAG10 | TAG18 | TAG6 | TAG2  | TAG2 | TAG10 | TAG18 | TAG6 | TAG14 |
+      | TAG7 | TAG3  | TAG3 | TAG11 | TAG19 | TAG7 | TAG3  | TAG3 | TAG11 | TAG19 | TAG7 | TAG15 |
+      | TAG8 | TAG4  | TAG4 | TAG12 | TAG20 | TAG8 | TAG4  | TAG4 | TAG12 | TAG20 | TAG8 | TAG16 |
 
   @tag_layout @create @barcode-service
   Scenario: Creating a tag layout of an entire plate using 96 tags by pools
@@ -139,6 +179,47 @@
       | TAG8 | TAG16  | TAG24 | TAG32  | TAG40 | TAG47 | TAG55 | TAG63 | TAG71 | TAG79 | TAG87 | TAG95 |
 
 
+  @tag_layout @create @barcode-service
+  Scenario: Creating a tag layout of an entire plate using 96 tags by pools with an offset
+    Given the Baracoda barcode service returns "SQPD-1000001"
+    Given the Baracoda barcode service returns "SQPD-1000002"
+    Given the tag group "Example Tag Group" exists
+      And the UUID for the tag group "Example Tag Group" is "00000000-1111-2222-3333-444444444444"
+      And the tag group "Example Tag Group" has 30 tags
+
+    Given a "Stock plate" plate called "Testing the API" exists
+      And the UUID for the plate "Testing the API" is "11111111-2222-3333-4444-000000000002"
+      And all wells on the plate "Testing the API" have unique samples
+
+    Given a "Stock plate" plate called "Testing the tagging" exists
+      And the UUID for the plate "Testing the tagging" is "11111111-2222-3333-4444-000000000001"
+      And the wells for the plate "Testing the API" have been pooled to the plate "Testing the tagging" according to the pooling strategy 12, 8, 20, 12, 8, 20, 16
+
+    When I make an authorised POST with the following JSON to the API path "/tag_layouts":
+      """
+      {
+        "tag_layout": {
+          "plate": "11111111-2222-3333-4444-000000000001",
+          "user": "99999999-8888-7777-6666-555555555555",
+          "tag_group": "00000000-1111-2222-3333-444444444444",
+          "direction": "column",
+          "walking_by": "manual by pool",
+          "initial_tag": 10
+        }
+      }
+      """
+    Then the HTTP response should be "201 Created"
+
+    Then the tag layout on the plate "Testing the tagging" should be:
+      | TAG11 | TAG19  | TAG15 | TAG15 | TAG23 | TAG11 | TAG19 | TAG15 | TAG15  | TAG23 | TAG11 | TAG19 |
+      | TAG12 | TAG20  | TAG16 | TAG16 | TAG24 | TAG12 | TAG20 | TAG16 | TAG16  | TAG24 | TAG12 | TAG20 |
+      | TAG13 | TAG21  | TAG17 | TAG17 | TAG25 | TAG13 | TAG21 | TAG17 | TAG17  | TAG25 | TAG13 | TAG21 |
+      | TAG14 | TAG22  | TAG18 | TAG18 | TAG26 | TAG14 | TAG22 | TAG18 | TAG18  | TAG26 | TAG14 | TAG22 |
+      | TAG15 | TAG11  | TAG11 | TAG19 | TAG27 | TAG15 | TAG11 | TAG11 | TAG19  | TAG27 | TAG15 | TAG23 |
+      | TAG16 | TAG12  | TAG12 | TAG20 | TAG28 | TAG16 | TAG12 | TAG12 | TAG20  | TAG28 | TAG16 | TAG24 |
+      | TAG17 | TAG13  | TAG13 | TAG21 | TAG29 | TAG17 | TAG13 | TAG13 | TAG21  | TAG29 | TAG17 | TAG25 |
+      | TAG18 | TAG14  | TAG14 | TAG22 | TAG30 | TAG18 | TAG14 | TAG14 | TAG22  | TAG30 | TAG18 | TAG26 |
+
   @tag_layout @create @barcode-service
   Scenario: Creating a tag layout of an entire plate using 96 tags by pools with an offset
     Given the Baracoda barcode service returns "SQPD-1000001"

features/support/step_definitions/plate_steps.rb

@@ -125,6 +125,12 @@
   plate_purpose.create!(name: plate_name)
 end
 
+Given /^a "([^"]+)" input plate called "([^"]+)" exists$/ do |name, plate_name|
+  plate_purpose = PlatePurpose.find_by!(name: name)
+  # binding.pry
+  plate_purpose.create!(name: plate_name)
+end
+
 Given(/^a plate called "([^"]*)" exists with purpose "([^"]*)"$/) do |name, purpose_name|
   purpose = Purpose.find_by(name: purpose_name) || FactoryBot.create(:plate_purpose, name: purpose_name)
   FactoryBot.create(:plate, name: name, purpose: purpose, well_count: 8)

features/support/step_definitions/tag_layout_steps.rb

@@ -112,27 +112,53 @@ def check_tag2_layout(name, well_range, expected_wells_to_oligos) # rubocop:todo
   set_uuid_for(TagLayout.find(id).plate, uuid_value)
 end
 
+# Pooling from source plate ("Testing the API") to destination plate ("Testing the tagging") with a specified pooling
+# strategy
+#
 # rubocop:todo Metrics/MethodLength
 def pool_by_strategy(source, destination, pooling_strategy) # rubocop:todo Metrics/AbcSize
   unless pooling_strategy.sum == source.size
     Rails.logger.info("Pooling strategy does not fit plate size #{source.size}: #{pooling_strategy.inspect}")
   end
+
+  # Column major: reads columns from left to right, top to bottom
+  # Row major: reads rows from top to bottom, left to right
+  # For example, a 96-well plate would be read as: A1, B1, C1, D1, E1, F1, G1, H1, A2, B2, C2, D2, E2, F2, G2, H2, ...
   source_wells = source.wells.in_column_major_order.to_a
   destination_wells = destination.wells.in_column_major_order.to_a
 
   pooling_strategy.each_with_index do |pool, _old_submission_id|
-    submission_id = Submission.create!(user: User.first || User.create!(login: 'a')).id
+    # This will generate a new submission for each pool. So the number of submissions will be equal to the number of
+    # pools. For example, for a pooling strategy of [8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8], there will be 12 submissions.
+    submission = Submission.create!(user: User.first || User.create!(login: 'a'))
+    submission_id = submission.id
+    # Slice operation cuts the array in place (i.e., removes the elements cut from the well array),
+    # so we need to assign the result to a new variable
     wells_for_source, wells_for_destination = source_wells.slice!(0, pool), destination_wells.slice!(0, pool)
     wells_for_source
       .zip(wells_for_destination)
       .each do |w|
+        # Because of the way we use zip w.first would be the source, w.last would be the destination
+        # This is the transfer request that would be created by the API.
+        # Note that transfer request behavior not used for input plates. For input plates, it is overridden
+        # to use requests (see app/models/well.rb:120).
+        # Creating TransferRequests invokes a callback that transfers aliquots from source to destination wells.
         TransferRequest.create!(asset: w.first, target_asset: w.last, submission_id: submission_id)
+        # This request is for the source plate.
         FactoryBot.create :request_without_submission,
                           asset: w.first,
                           target_asset: w.last,
                           submission_id: submission_id
       end
   end
+
+  # Create a request for each well in the destination plate
+  # This is required for input plates
+  if destination.purpose.is_a?(PlatePurpose::Input)
+    destination.wells.each do |well|
+      FactoryBot.create(:customer_request, asset: well, sti_type: 'Request::LibraryCreation', state: 'pending')
+    end
+  end
 end
 # rubocop:enable Metrics/MethodLength
 # This fakes out the transfers so that they look like they came from different submissions, effectively meaning

package.json

@@ -47,7 +47,7 @@
     "jest": "^26.6.3",
     "miragejs": "^0.1.48",
     "prettier": "^3.3.2",
-    "vite": "^5.3.2",
+    "vite": "^5.3.6",
     "vite-plugin-ruby": "^5.0.0",
     "vite-plugin-vue2": "^1.9.3",
     "vue-jest": "^3.0.7"

vite.config.ts

@@ -5,7 +5,10 @@ import { createVuePlugin } from "vite-plugin-vue2";
 import legacy from "@vitejs/plugin-legacy";
 
 export default defineConfig({
-  build: { emptyOutDir: true },
+  build: {
+    emptyOutDir: true,
+    target: ["chrome65", "es2019"],
+  },
   plugins: [RubyPlugin(), createVuePlugin(), legacy({ targets: ["defaults"] })],
   resolve: {
     alias: {

yarn.lock

@@ -7281,10 +7281,10 @@ vite-plugin-vue2@^1.9.3:
     source-map "^0.7.3"
     vue-template-es2015-compiler "^1.9.1"
 
-vite@^5.3.2:
-  version "5.3.3"
-  resolved "https://registry.yarnpkg.com/vite/-/vite-5.3.3.tgz#5265b1f0a825b3b6564c2d07524777c83e3c04c2"
-  integrity sha512-NPQdeCU0Dv2z5fu+ULotpuq5yfCS1BzKUIPhNbP3YBfAMGJXbt2nS+sbTFu+qchaqWTD+H3JK++nRwr6XIcp6A==
+vite@^5.3.6:
+  version "5.3.6"
+  resolved "https://registry.yarnpkg.com/vite/-/vite-5.3.6.tgz#e097c0a7b79adb2e60bec9ef7907354f09d027bd"
+  integrity sha512-es78AlrylO8mTVBygC0gTC0FENv0C6T496vvd33ydbjF/mIi9q3XQ9A3NWo5qLGFKywvz10J26813OkLvcQleA==
   dependencies:
     esbuild "^0.21.3"
     postcss "^8.4.39"