From 5ebd2467cb6e388eb606e56f9ccc3c8a4a5a8709 Mon Sep 17 00:00:00 2001
From: Stuart McHattie <sm49@sanger.ac.uk>
Date: Fri, 13 Sep 2024 11:35:16 +0100
Subject: [PATCH 1/9] Switch SpecificTubeCreation requests to go through API v2

---
 .../labware_creators/plate_split_to_tube_racks.rb     | 11 +++++------
 app/models/labware_creators/pooled_tubes_base.rb      | 11 +++++------
 app/models/labware_creators/pooled_tubes_by_sample.rb | 11 +++++------
 .../pooled_tubes_by_submission_with_phi_x.rb          |  9 ++++-----
 .../pooled_tubes_from_whole_plates.rb                 | 11 +++++------
 .../sequencescape/api/v2/specific_tube_creation.rb    |  8 ++++++++
 6 files changed, 32 insertions(+), 29 deletions(-)
 create mode 100644 app/sequencescape/sequencescape/api/v2/specific_tube_creation.rb

diff --git a/app/models/labware_creators/plate_split_to_tube_racks.rb b/app/models/labware_creators/plate_split_to_tube_racks.rb
index da3e2098d..f869083cd 100644
--- a/app/models/labware_creators/plate_split_to_tube_racks.rb
+++ b/app/models/labware_creators/plate_split_to_tube_racks.rb
@@ -405,13 +405,12 @@ def parent_wells_for_contingency
     # @param tube_attributes [Hash] A hash of attributes to use for the created tubes.
     # @return [Hash<String, Tube>] A hash of the created tubes indexed by name.
     def create_tubes(tube_purpose_uuid, number_of_tubes, tube_attributes)
-      api
-        .specific_tube_creation
+      Sequencescape::Api::V2::SpecificTubeCreation
         .create!(
-          user: user_uuid,
-          parent: parent_uuid,
-          child_purposes: [tube_purpose_uuid] * number_of_tubes,
-          tube_attributes: tube_attributes
+          child_purpose_uuids: [tube_purpose_uuid] * number_of_tubes,
+          parent_uuids: [parent_uuid],
+          tube_attributes: tube_attributes,
+          user_uuid: user_uuid
         )
         .children
         .index_by(&:name)
diff --git a/app/models/labware_creators/pooled_tubes_base.rb b/app/models/labware_creators/pooled_tubes_base.rb
index f55e8bc3a..e8ae7a7e2 100644
--- a/app/models/labware_creators/pooled_tubes_base.rb
+++ b/app/models/labware_creators/pooled_tubes_base.rb
@@ -20,13 +20,12 @@ def create_labware!
     end
 
     def create_child_stock_tubes
-      api
-        .specific_tube_creation
+      Sequencescape::Api::V2::SpecificTubeCreation
         .create!(
-          user: user_uuid,
-          parent: parent_uuid,
-          child_purposes: [purpose_uuid] * pool_uuids.length,
-          tube_attributes: tube_attributes
+          child_purpose_uuids: [purpose_uuid] * pool_uuids.length,
+          parent_uuids: [parent_uuid],
+          tube_attributes: tube_attributes,
+          user_uuid: user_uuid
         )
         .children
         .index_by(&:name)
diff --git a/app/models/labware_creators/pooled_tubes_by_sample.rb b/app/models/labware_creators/pooled_tubes_by_sample.rb
index 29121318a..6504e0c76 100644
--- a/app/models/labware_creators/pooled_tubes_by_sample.rb
+++ b/app/models/labware_creators/pooled_tubes_by_sample.rb
@@ -47,13 +47,12 @@ def parent_v1
     # Have we made this class so cardinal-specific (e.g. lookup of ancestor vac tubes) that it cannot be re-used?
 
     def create_child_stock_tubes
-      api
-        .specific_tube_creation
+      Sequencescape::Api::V2::SpecificTubeCreation
         .create!(
-          user: user_uuid,
-          parent: parent_uuid,
-          child_purposes: [purpose_uuid] * pool_uuids.length,
-          tube_attributes: tube_attributes
+          child_purpose_uuids: [purpose_uuid] * pool_uuids.length,
+          parent_uuids: [parent_uuid],
+          tube_attributes: tube_attributes,
+          user_uuid: user_uuid
         )
         .children
         .index_by(&:name)
diff --git a/app/models/labware_creators/pooled_tubes_by_submission_with_phi_x.rb b/app/models/labware_creators/pooled_tubes_by_submission_with_phi_x.rb
index f0d6103f0..50d7a916d 100644
--- a/app/models/labware_creators/pooled_tubes_by_submission_with_phi_x.rb
+++ b/app/models/labware_creators/pooled_tubes_by_submission_with_phi_x.rb
@@ -15,13 +15,12 @@ class PooledTubesBySubmissionWithPhiX < PooledTubesBySubmission
     attr_accessor :spikedbuffer_tube_barcode
 
     def create_child_stock_tubes
-      api
-        .specific_tube_creation
+      Sequencescape::Api::V2::SpecificTubeCreation
         .create!(
-          user: user_uuid,
-          parents: parents,
           child_purposes: [purpose_uuid] * pool_uuids.length,
-          tube_attributes: tube_attributes
+          parent_uuids: parents,
+          tube_attributes: tube_attributes,
+          user_uuid: user_uuid
         )
         .children
         .index_by(&:name)
diff --git a/app/models/labware_creators/pooled_tubes_from_whole_plates.rb b/app/models/labware_creators/pooled_tubes_from_whole_plates.rb
index 41a09f490..33f9034ca 100644
--- a/app/models/labware_creators/pooled_tubes_from_whole_plates.rb
+++ b/app/models/labware_creators/pooled_tubes_from_whole_plates.rb
@@ -17,13 +17,12 @@ def create_labware!
       # Create a single tube
       # TODO: This should link to multiple parents in production
       @child =
-        api
-          .specific_tube_creation
+        Sequencescape::Api::V2::SpecificTubeCreation
           .create!(
-            user: user_uuid,
-            parent: parents.first.uuid,
-            child_purposes: [purpose_uuid],
-            tube_attributes: [{ name: "#{stock_plate_barcode}+" }]
+            child_purpose_uuids: [purpose_uuid],
+            parent_uuids: [parents.first.uuid],
+            tube_attributes: [{ name: "#{stock_plate_barcode}+" }],
+            user_uuid: user_uuid
           )
           .children
           .first
diff --git a/app/sequencescape/sequencescape/api/v2/specific_tube_creation.rb b/app/sequencescape/sequencescape/api/v2/specific_tube_creation.rb
new file mode 100644
index 000000000..035a70c5a
--- /dev/null
+++ b/app/sequencescape/sequencescape/api/v2/specific_tube_creation.rb
@@ -0,0 +1,8 @@
+# frozen_string_literal: true
+
+# Represents a specific tube creation in Limber via the Sequencescape API
+class Sequencescape::Api::V2::SpecificTubeCreation < Sequencescape::Api::V2::Base
+  has_many :children, class_name: 'Sequencescape::Api::V2::Tube'
+  has_many :parents, class_name: 'Sequencescape::Api::V2::Asset'
+  has_one :user, class_name: 'Sequencescape::Api::V2::User'
+end

From 1860cce4e0dcc49e02bf84dc8b67c6a11ac3355e Mon Sep 17 00:00:00 2001
From: Stuart McHattie <sm49@sanger.ac.uk>
Date: Mon, 16 Sep 2024 16:58:38 +0100
Subject: [PATCH 2/9] Fix tests for pooling multiple plates into one tube

---
 .../pooled_tubes_from_whole_plates.rb         |  6 ++-
 ...ling_multiple_plates_into_one_tube_spec.rb | 51 +++++++------------
 2 files changed, 24 insertions(+), 33 deletions(-)

diff --git a/app/models/labware_creators/pooled_tubes_from_whole_plates.rb b/app/models/labware_creators/pooled_tubes_from_whole_plates.rb
index 33f9034ca..937e23569 100644
--- a/app/models/labware_creators/pooled_tubes_from_whole_plates.rb
+++ b/app/models/labware_creators/pooled_tubes_from_whole_plates.rb
@@ -15,7 +15,7 @@ class PooledTubesFromWholePlates < Base
 
     def create_labware!
       # Create a single tube
-      # TODO: This should link to multiple parents in production
+      # TODO: {Y24-190} See if we can do all the transfers as part of the SpecificTubeCreation instead of separately.
       @child =
         Sequencescape::Api::V2::SpecificTubeCreation
           .create!(
@@ -39,6 +39,10 @@ def stock_plate_barcode
       "#{parents.first.stock_plate.barcode.prefix}#{parents.first.stock_plate.barcode.number}"
     end
 
+    def redirection_target
+      TubeProxy.new(@child.uuid)
+    end
+
     # TODO: This should probably be asynchronous
     def available_plates
       @search_options = OngoingPlate.new(purposes: [parent.plate_purpose.uuid], include_used: false, states: ['passed'])
diff --git a/spec/features/pooling_multiple_plates_into_one_tube_spec.rb b/spec/features/pooling_multiple_plates_into_one_tube_spec.rb
index 73937a3d7..1e2487b1a 100644
--- a/spec/features/pooling_multiple_plates_into_one_tube_spec.rb
+++ b/spec/features/pooling_multiple_plates_into_one_tube_spec.rb
@@ -57,32 +57,13 @@
   end
   let(:example_plate_3_listed) { associated(*example_plate3_args) }
 
-  let(:child_tube_uuid) { 'tube-0' }
-  let(:child_tube) do
-    create :v2_tube, purpose_uuid: 'child-purpose-0', purpose_name: 'Pool tube', uuid: child_tube_uuid
-  end
+  let(:child_tube) { create :v2_tube, purpose_uuid: 'child-purpose-0', purpose_name: 'Pool tube' }
 
-  let(:tube_creation_request_uuid) { SecureRandom.uuid }
-
-  let!(:tube_creation_request) do
-    # TODO: In reality we want to link in all four parents.
-    stub_api_post(
-      'specific_tube_creations',
-      payload: {
-        specific_tube_creation: {
-          user: user_uuid,
-          parent: plate_uuid,
-          child_purposes: ['child-purpose-0'],
-          tube_attributes: [{ name: 'DN2+' }]
-        }
-      },
-      body: json(:specific_tube_creation, uuid: tube_creation_request_uuid, children_count: 1)
-    )
-  end
+  let(:specific_tube_creation) do
+    response = double
+    allow(response).to receive(:children).and_return([child_tube])
 
-  # Find out what tubes we've just made!
-  let!(:tube_creation_children_request) do
-    stub_api_get(tube_creation_request_uuid, 'children', body: json(:tube_collection, names: ['DN1+']))
+    response
   end
 
   # Used to fetch the pools. This is the kind of thing we could pass through from a custom form
@@ -119,8 +100,6 @@
 
     stub_v2_plate(example_plate_new_api)
 
-    stub_v2_plate(example_plate_new_api)
-
     stub_api_get(plate_uuid, body: example_plate)
     stub_api_get(plate_uuid, 'wells', body: well_set_a)
 
@@ -132,13 +111,25 @@
   scenario 'creates multiple plates' do
     stub_v2_plate(example_plate_2)
 
+    expect_api_v2_posts(
+      'SpecificTubeCreation',
+      [
+        {
+          child_purpose_uuids: ['child-purpose-0'],
+          parent_uuids: [plate_uuid],
+          tube_attributes: [{ name: 'DN2+' }],
+          user_uuid: user_uuid
+        }
+      ],
+      [specific_tube_creation]
+    )
     expect_api_v2_posts(
       'Transfer',
       [plate_uuid, plate_uuid_2].map do |source_uuid|
         {
           user_uuid: user_uuid,
           source_uuid: source_uuid,
-          destination_uuid: 'tube-0',
+          destination_uuid: child_tube.uuid,
           transfer_template_uuid: 'whole-plate-to-tube'
         }
       end
@@ -156,15 +147,11 @@
     click_on('Make Pool')
     expect(page).to have_text('New empty labware added to the system')
     expect(page).to have_text('Pool tube')
-
-    # This isn't strictly speaking correct to test. But there isn't a great way
-    # of confirming that the right information got passed to the back end otherwise.
-    # (Although you expect it to fail on an incorrect request)
-    expect(tube_creation_request).to have_been_made
   end
 
   scenario 'detects tag clash' do
     stub_v2_plate(example_plate_3)
+
     fill_in_swipecard_and_barcode(user_swipecard, plate_barcode_1)
     plate_title = find('#plate-title')
     expect(plate_title).to have_text('example-purpose')

From 1d5fc5f29be24452fdfa28cc7da04732a5fac702 Mon Sep 17 00:00:00 2001
From: Stuart McHattie <sm49@sanger.ac.uk>
Date: Mon, 16 Sep 2024 17:02:21 +0100
Subject: [PATCH 3/9] Fix test for pooled tubes from whole plates

---
 .../pooled_tubes_from_whole_plates_spec.rb    | 49 +++++++------------
 1 file changed, 19 insertions(+), 30 deletions(-)

diff --git a/spec/models/labware_creators/pooled_tubes_from_whole_plates_spec.rb b/spec/models/labware_creators/pooled_tubes_from_whole_plates_spec.rb
index e5ce80273..993edb48b 100644
--- a/spec/models/labware_creators/pooled_tubes_from_whole_plates_spec.rb
+++ b/spec/models/labware_creators/pooled_tubes_from_whole_plates_spec.rb
@@ -53,54 +53,43 @@
       { user_uuid: user_uuid, purpose_uuid: purpose_uuid, parent_uuid: parent_uuid, barcodes: barcodes }
     end
 
-    let(:tube_creation_request_uuid) { SecureRandom.uuid }
+    let(:child_tube) { create :v2_tube }
+    let(:specific_tube_creation) do
+      response = double
+      allow(response).to receive(:children).and_return([child_tube])
 
-    let(:tube_creation_request) do
-      # TODO: In reality we want to link in all four parents.
-      stub_api_post(
-        'specific_tube_creations',
-        payload: {
-          specific_tube_creation: {
-            user: user_uuid,
-            parent: parent_uuid,
-            child_purposes: [purpose_uuid],
-            tube_attributes: [{ name: 'DN2+' }]
-          }
-        },
-        body: json(:specific_tube_creation, uuid: tube_creation_request_uuid, children_count: 1)
-      )
+      response
     end
 
-    # Find out what tubes we've just made!
-    let(:tube_creation_children_request) do
-      stub_api_get(tube_creation_request_uuid, 'children', body: json(:tube_collection, names: ['DN2+']))
-    end
-
-    # Used to fetch the pools. This is the kind of thing we could pass through from a custom form
-    let(:stub_barcode_searches) { stub_asset_search(barcodes, [parent, parent2, parent3, parent4]) }
-
-    before do
-      stub_barcode_searches
-      tube_creation_children_request
-      tube_creation_request
-    end
+    before { stub_asset_search(barcodes, [parent, parent2, parent3, parent4]) }
 
     context 'with compatible plates' do
       it 'pools from all the plates' do
+        expect_api_v2_posts(
+          'SpecificTubeCreation',
+          [
+            {
+              child_purpose_uuids: [purpose_uuid],
+              parent_uuids: [parent_uuid],
+              tube_attributes: [{ name: 'DN2+' }],
+              user_uuid: user_uuid
+            }
+          ],
+          [specific_tube_creation]
+        )
         expect_api_v2_posts(
           'Transfer',
           [parent_uuid, parent2_uuid, parent3_uuid, parent4_uuid].map do |source_uuid|
             {
               user_uuid: user_uuid,
               source_uuid: source_uuid,
-              destination_uuid: 'tube-0',
+              destination_uuid: child_tube.uuid,
               transfer_template_uuid: 'whole-plate-to-tube'
             }
           end
         )
 
         expect(subject.save!).to be_truthy
-        expect(tube_creation_request).to have_been_made.once
       end
     end
   end

From a4a38082c09ab4cc636603e0e0b3460bc96503b7 Mon Sep 17 00:00:00 2001
From: Stuart McHattie <sm49@sanger.ac.uk>
Date: Tue, 17 Sep 2024 13:24:13 +0100
Subject: [PATCH 4/9] Fix tests for plate_split_to_tube_racks

---
 .../plate_split_to_tube_racks_spec.rb         | 380 +++++++-----------
 1 file changed, 144 insertions(+), 236 deletions(-)

diff --git a/spec/models/labware_creators/plate_split_to_tube_racks_spec.rb b/spec/models/labware_creators/plate_split_to_tube_racks_spec.rb
index 4ab8c6154..040feb362 100644
--- a/spec/models/labware_creators/plate_split_to_tube_racks_spec.rb
+++ b/spec/models/labware_creators/plate_split_to_tube_racks_spec.rb
@@ -201,6 +201,56 @@
     )
   end
 
+  def prepare_created_child_tubes(tube_attributes)
+    # Prepare child tubes and stub their lookups.
+    child_tubes =
+      tube_attributes.map { |attrs| create(:v2_tube, name: attrs[:name], foreign_barcode: attrs[:foreign_barcode]) }
+    child_tubes.each { |child_tube| stub_v2_labware(child_tube) }
+
+    child_tubes
+  end
+
+  def expect_specific_tube_creation(child_purpose_uuid, child_tubes)
+    # Create a mock for the specific tube creation.
+    specific_tube_creation = double
+    allow(specific_tube_creation).to receive(:children).and_return(child_tubes)
+
+    # Expect the post request and return the mock.
+    expect_api_v2_posts(
+      'SpecificTubeCreation',
+      [
+        {
+          child_purpose_uuids: [child_purpose_uuid] * child_tubes.size,
+          parent_uuids: [parent_uuid],
+          tube_attributes: child_tubes.map { |tube| { name: tube.name, foreign_barcode: tube.foreign_barcode } },
+          user_uuid: user_uuid
+        }
+      ],
+      [specific_tube_creation]
+    )
+  end
+
+  # tubes_hash should be a hash with tube rack barcodes as keys and arrays of tubes as values.
+  def expect_custom_metadatum_collection_posts(tubes_hash)
+    # Prepare the expected call arguments.
+    expected_call_args =
+      tubes_hash.flat_map do |tube_rack_barcode, tubes|
+        tubes.map do |tube|
+          metadata = {
+            user_id: user.id,
+            asset_id: tube.id,
+            metadata: {
+              tube_rack_barcode: tube_rack_barcode,
+              tube_rack_position: tube.name.split(':').last
+            }
+          }
+        end
+      end
+
+    # Expect the post requests.
+    expect_api_v2_posts('CustomMetadatumCollection', expected_call_args)
+  end
+
   before do
     # need both child tubes to have a purpose config here
     create(
@@ -661,48 +711,16 @@
         )
     end
 
-    # stub the contingency tube creation
-    let!(:stub_contingency_tube_creation_request_uuid) { SecureRandom.uuid }
-    let!(:stub_contingency_tube_creation_request) do
-      stub_api_post(
-        'specific_tube_creations',
-        payload: {
-          specific_tube_creation: {
-            child_purposes: [
-              child_contingency_tube_purpose_uuid,
-              child_contingency_tube_purpose_uuid,
-              child_contingency_tube_purpose_uuid
-            ],
-            tube_attributes: [
-              # sample 1 from well A2 to contingency tube 1 in A1
-              { name: 'SPR:NT1O:A1', foreign_barcode: 'FX00000011' },
-              # sample 2 from well B2 to contingency tube 2 in B1
-              { name: 'SPR:NT2P:B1', foreign_barcode: 'FX00000012' },
-              # sample 1 from well A3 to contingency tube 3 in C1
-              { name: 'SPR:NT1O:C1', foreign_barcode: 'FX00000013' }
-            ],
-            user: user_uuid,
-            parent: parent_uuid
-          }
-        },
-        body: json(:specific_tube_creation, uuid: stub_contingency_tube_creation_request_uuid, children_count: 3)
-      )
-    end
-
-    # stub what contingency tubes were just made
-    let!(:stub_contingency_tube_creation_children_request) do
-      stub_api_get(
-        stub_contingency_tube_creation_request_uuid,
-        'children',
-        body:
-          json(
-            :tube_collection_with_barcodes_specified,
-            size: 3,
-            names: %w[SPR:NT1O:A1 SPR:NT2P:B1 SPR:NT1O:C1],
-            barcode_prefix: 'FX',
-            barcode_numbers: [11, 12, 13],
-            uuid_index_offset: 2
-          )
+    let(:contingency_tubes) do
+      prepare_created_child_tubes(
+        [
+          # sample 1 from well A2 to contingency tube 1 in A1
+          { name: 'SPR:NT1O:A1', foreign_barcode: 'FX00000011' },
+          # sample 2 from well B2 to contingency tube 2 in B1
+          { name: 'SPR:NT2P:B1', foreign_barcode: 'FX00000012' },
+          # sample 1 from well A3 to contingency tube 3 in C1
+          { name: 'SPR:NT1O:C1', foreign_barcode: 'FX00000013' }
+        ]
       )
     end
 
@@ -742,6 +760,17 @@
         content
       end
 
+      let(:sequencing_tubes) do
+        prepare_created_child_tubes(
+          [
+            # sample 1 in well A1 to seq tube 1 in A1
+            { name: 'SEQ:NT1O:A1', foreign_barcode: 'FX00000001' },
+            # sample 2 in well B1 to seq tube 2 in B1
+            { name: 'SEQ:NT2P:B1', foreign_barcode: 'FX00000002' }
+          ]
+        )
+      end
+
       # stub the sequencing file upload
       let!(:stub_sequencing_file_upload) do
         stub_request(:post, api_url_for(parent_uuid, 'qc_files'))
@@ -761,58 +790,20 @@
           )
       end
 
-      # stub the sequencing tube creation
-      let!(:stub_sequencing_tube_creation_request_uuid) { SecureRandom.uuid }
-      let!(:stub_sequencing_tube_creation_request) do
-        stub_api_post(
-          'specific_tube_creations',
-          payload: {
-            specific_tube_creation: {
-              child_purposes: [child_sequencing_tube_purpose_uuid, child_sequencing_tube_purpose_uuid],
-              tube_attributes: [
-                # sample 1 in well A1 to seq tube 1 in A1
-                { name: 'SEQ:NT1O:A1', foreign_barcode: 'FX00000001' },
-                # sample 2 in well B1 to seq tube 2 in B1
-                { name: 'SEQ:NT2P:B1', foreign_barcode: 'FX00000002' }
-              ],
-              user: user_uuid,
-              parent: parent_uuid
-            }
-          },
-          body: json(:specific_tube_creation, uuid: stub_sequencing_tube_creation_request_uuid, children_count: 2)
-        )
-      end
-
-      # stub what sequencing tubes were just made
-      let!(:stub_sequencing_tube_creation_children_request) do
-        stub_api_get(
-          stub_sequencing_tube_creation_request_uuid,
-          'children',
-          body:
-            json(
-              :tube_collection_with_barcodes_specified,
-              size: 2,
-              names: %w[SEQ:NT1O:A1 SEQ:NT2P:B1],
-              barcode_prefix: 'FX',
-              barcode_numbers: [1, 2]
-            )
-        )
-      end
-
       # stub the transfer creation
       let!(:stub_transfer_creation_request) do
+        parent_wells = [parent_well_a1, parent_well_b1, parent_well_a2, parent_well_b2, parent_well_a3]
+        target_tubes = sequencing_tubes + contingency_tubes
+        transfer_requests =
+          parent_wells.map.with_index do |parent_well, index|
+            { 'submission_id' => '2', 'source_asset' => parent_well.uuid, 'target_asset' => target_tubes[index].uuid }
+          end
         stub_api_post(
           'transfer_request_collections',
           payload: {
             transfer_request_collection: {
               user: user_uuid,
-              transfer_requests: [
-                { 'submission_id' => '2', 'source_asset' => parent_well_a1.uuid, 'target_asset' => 'tube-0' },
-                { 'submission_id' => '2', 'source_asset' => parent_well_b1.uuid, 'target_asset' => 'tube-1' },
-                { 'submission_id' => '2', 'source_asset' => parent_well_a2.uuid, 'target_asset' => 'tube-2' },
-                { 'submission_id' => '2', 'source_asset' => parent_well_b2.uuid, 'target_asset' => 'tube-3' },
-                { 'submission_id' => '2', 'source_asset' => parent_well_a3.uuid, 'target_asset' => 'tube-4' }
-              ]
+              transfer_requests: transfer_requests
             }
           },
           body: '{}'
@@ -860,17 +851,17 @@
       end
 
       it 'creates the child tubes' do
-        expect_api_v2_posts(
-          'CustomMetadatumCollection',
-          [tube_1_create_args, tube_2_create_args, tube_3_create_args, tube_4_create_args, tube_5_create_args]
+        expect_specific_tube_creation(child_sequencing_tube_purpose_uuid, sequencing_tubes)
+        expect_specific_tube_creation(child_contingency_tube_purpose_uuid, contingency_tubes)
+
+        expect_custom_metadatum_collection_posts(
+          { 'TR00000001' => sequencing_tubes, 'TR00000002' => contingency_tubes }
         )
 
         expect(subject.valid?).to be_truthy
         expect(subject.save).to be_truthy
         expect(stub_sequencing_file_upload).to have_been_made.once
-        expect(stub_sequencing_tube_creation_request).to have_been_made.once
         expect(stub_contingency_file_upload).to have_been_made.once
-        expect(stub_contingency_tube_creation_request).to have_been_made.once
         expect(stub_transfer_creation_request).to have_been_made.once
       end
 
@@ -880,94 +871,20 @@
           create(:v2_well, location: 'A1', aliquots: [parent_aliquot_sample1_aliquot1], state: 'failed')
         end
 
-        # as A1 is failed order of samples is changed
-        let!(:stub_sequencing_tube_creation_request) do
-          stub_api_post(
-            'specific_tube_creations',
-            payload: {
-              specific_tube_creation: {
-                child_purposes: [child_sequencing_tube_purpose_uuid, child_sequencing_tube_purpose_uuid],
-                tube_attributes: [
-                  # sample 2 in well B1 to seq tube 1 in A1
-                  { name: 'SEQ:NT2P:A1', foreign_barcode: 'FX00000001' },
-                  # sample 1 in well A2 to seq tube 2 in B1
-                  { name: 'SEQ:NT1O:B1', foreign_barcode: 'FX00000002' }
-                ],
-                user: user_uuid,
-                parent: parent_uuid
-              }
-            },
-            body: json(:specific_tube_creation, uuid: stub_sequencing_tube_creation_request_uuid, children_count: 2)
-          )
-        end
-
-        # stub what sequencing tubes were just made (order changed)
-        let!(:stub_sequencing_tube_creation_children_request) do
-          stub_api_get(
-            stub_sequencing_tube_creation_request_uuid,
-            'children',
-            body:
-              json(
-                :tube_collection_with_barcodes_specified,
-                size: 2,
-                names: %w[SEQ:NT2P:A1 SEQ:NT1O:B1],
-                barcode_prefix: 'FX',
-                barcode_numbers: [1, 2]
-              )
-          )
-        end
-
-        # only 2 contingency tubes will be needed
-        let!(:stub_contingency_tube_creation_request) do
-          stub_api_post(
-            'specific_tube_creations',
-            payload: {
-              specific_tube_creation: {
-                child_purposes: [child_contingency_tube_purpose_uuid, child_contingency_tube_purpose_uuid],
-                tube_attributes: [
-                  # sample 2 from well B2 to contingency tube 1 in A1
-                  { name: 'SPR:NT2P:A1', foreign_barcode: 'FX00000011' },
-                  # sample 1 from well A3 to contingency tube 2 in B1
-                  { name: 'SPR:NT1O:B1', foreign_barcode: 'FX00000012' }
-                ],
-                user: user_uuid,
-                parent: parent_uuid
-              }
-            },
-            body: json(:specific_tube_creation, uuid: stub_contingency_tube_creation_request_uuid, children_count: 3)
-          )
-        end
-
-        # stub what contingency tubes were just made (just 2)
-        let!(:stub_contingency_tube_creation_children_request) do
-          stub_api_get(
-            stub_contingency_tube_creation_request_uuid,
-            'children',
-            body:
-              json(
-                :tube_collection_with_barcodes_specified,
-                size: 2,
-                names: %w[SPR:NT2P:A1 SPR:NT1O:B1],
-                barcode_prefix: 'FX',
-                barcode_numbers: [11, 12],
-                uuid_index_offset: 2
-              )
-          )
-        end
-
         # one fewer transfer request
         let!(:stub_transfer_creation_request) do
+          parent_wells = [parent_well_b1, parent_well_a2, parent_well_b2, parent_well_a3]
+          target_tubes = sequencing_tubes + contingency_tubes
+          transfer_requests =
+            parent_wells.map.with_index do |parent_well, index|
+              { 'submission_id' => '2', 'source_asset' => parent_well.uuid, 'target_asset' => target_tubes[index].uuid }
+            end
           stub_api_post(
             'transfer_request_collections',
             payload: {
               transfer_request_collection: {
                 user: user_uuid,
-                transfer_requests: [
-                  { 'submission_id' => '2', 'source_asset' => parent_well_b1.uuid, 'target_asset' => 'tube-0' },
-                  { 'submission_id' => '2', 'source_asset' => parent_well_a2.uuid, 'target_asset' => 'tube-1' },
-                  { 'submission_id' => '2', 'source_asset' => parent_well_b2.uuid, 'target_asset' => 'tube-2' },
-                  { 'submission_id' => '2', 'source_asset' => parent_well_a3.uuid, 'target_asset' => 'tube-3' }
-                ]
+                transfer_requests: transfer_requests
               }
             },
             body: '{}'
@@ -981,6 +898,28 @@
           )
         end
 
+        let(:sequencing_tubes) do
+          prepare_created_child_tubes(
+            [
+              # sample 2 in well B1 to seq tube 1 in A1
+              { name: 'SEQ:NT2P:A1', foreign_barcode: 'FX00000001' },
+              # sample 1 in well A2 to seq tube 2 in B1
+              { name: 'SEQ:NT1O:B1', foreign_barcode: 'FX00000002' }
+            ]
+          )
+        end
+
+        let(:contingency_tubes) do
+          prepare_created_child_tubes(
+            [
+              # sample 2 from well B2 to contingency tube 1 in A1
+              { name: 'SPR:NT2P:A1', foreign_barcode: 'FX00000011' },
+              # sample 1 from well A3 to contingency tube 2 in B1
+              { name: 'SPR:NT1O:B1', foreign_barcode: 'FX00000012' }
+            ]
+          )
+        end
+
         before do
           stub_get_labware_metadata(child_tube_1_v2.barcode.machine, child_tube_1_v1)
           stub_get_labware_metadata(child_tube_2_v2.barcode.machine, child_tube_2_v1)
@@ -994,17 +933,17 @@
         end
 
         it 'does not create a tube for the failed well' do
-          expect_api_v2_posts(
-            'CustomMetadatumCollection',
-            [tube_1_create_args, tube_2_create_args, tube_3_create_args, tube_4_create_args] # no tube 5
+          expect_specific_tube_creation(child_sequencing_tube_purpose_uuid, sequencing_tubes)
+          expect_specific_tube_creation(child_contingency_tube_purpose_uuid, contingency_tubes)
+
+          expect_custom_metadatum_collection_posts(
+            { 'TR00000001' => sequencing_tubes, 'TR00000002' => contingency_tubes }
           )
 
           expect(subject.valid?).to be_truthy
           expect(subject.save).to be_truthy
           expect(stub_sequencing_file_upload).to have_been_made.once
-          expect(stub_sequencing_tube_creation_request).to have_been_made.once
           expect(stub_contingency_file_upload).to have_been_made.once
-          expect(stub_contingency_tube_creation_request).to have_been_made.once
           expect(stub_transfer_creation_request).to have_been_made.once
         end
       end
@@ -1090,69 +1029,40 @@
         )
       end
 
-      # stub the contingency tube creation
-      let!(:stub_contingency_tube_creation_request) do
-        stub_api_post(
-          'specific_tube_creations',
-          payload: {
-            specific_tube_creation: {
-              child_purposes: [
-                child_contingency_tube_purpose_uuid,
-                child_contingency_tube_purpose_uuid,
-                child_contingency_tube_purpose_uuid,
-                child_contingency_tube_purpose_uuid,
-                child_contingency_tube_purpose_uuid
-              ],
-              tube_attributes: [
-                # sample 1 from well A1 to contingency tube 1 in A1
-                { name: 'SPR:NT1O:A1', foreign_barcode: 'FX00000011' },
-                # sample 2 from well B1 to contingency tube 2 in B1
-                { name: 'SPR:NT2P:B1', foreign_barcode: 'FX00000012' },
-                # sample 1 from well A2 to contingency tube 3 in C1
-                { name: 'SPR:NT1O:C1', foreign_barcode: 'FX00000013' },
-                # sample 2 from well B2 to contingency tube 4 in E1  (D1 set as NO READ)
-                { name: 'SPR:NT2P:E1', foreign_barcode: 'FX00000014' },
-                # sample 1 from well A3 to contingency tube 5 in F1
-                { name: 'SPR:NT1O:F1', foreign_barcode: 'FX00000015' }
-              ],
-              user: user_uuid,
-              parent: parent_uuid
-            }
-          },
-          body: json(:specific_tube_creation, uuid: stub_contingency_tube_creation_request_uuid, children_count: 5)
-        )
-      end
-
-      # stub what contingency tubes were just made
-      let!(:stub_contingency_tube_creation_children_request) do
-        stub_api_get(
-          stub_contingency_tube_creation_request_uuid,
-          'children',
-          body:
-            json(
-              :tube_collection_with_barcodes_specified,
-              size: 5,
-              names: %w[SPR:NT1O:A1 SPR:NT2P:B1 SPR:NT1O:C1 SPR:NT2P:E1 SPR:NT1O:F1],
-              barcode_prefix: 'FX',
-              barcode_numbers: [11, 12, 13, 14, 15]
-            )
+      let(:contingency_tubes) do
+        prepare_created_child_tubes(
+          [
+            # sample 1 from well A1 to contingency tube 1 in A1
+            { name: 'SPR:NT1O:A1', foreign_barcode: 'FX00000011' },
+            # sample 2 from well B1 to contingency tube 2 in B1
+            { name: 'SPR:NT2P:B1', foreign_barcode: 'FX00000012' },
+            # sample 1 from well A2 to contingency tube 3 in C1
+            { name: 'SPR:NT1O:C1', foreign_barcode: 'FX00000013' },
+            # sample 2 from well B2 to contingency tube 4 in E1  (D1 set as NO READ)
+            { name: 'SPR:NT2P:E1', foreign_barcode: 'FX00000014' },
+            # sample 1 from well A3 to contingency tube 5 in F1
+            { name: 'SPR:NT1O:F1', foreign_barcode: 'FX00000015' }
+          ]
         )
       end
 
       # stub the transfer creation
       let!(:stub_transfer_creation_request) do
+        parent_wells = [parent_well_a1, parent_well_b1, parent_well_a2, parent_well_b2, parent_well_a3]
+        transfer_requests =
+          parent_wells.map.with_index do |parent_well, index|
+            {
+              'submission_id' => '2',
+              'source_asset' => parent_well.uuid,
+              'target_asset' => contingency_tubes[index].uuid
+            }
+          end
         stub_api_post(
           'transfer_request_collections',
           payload: {
             transfer_request_collection: {
               user: user_uuid,
-              transfer_requests: [
-                { 'submission_id' => '2', 'source_asset' => parent_well_a1.uuid, 'target_asset' => 'tube-0' },
-                { 'submission_id' => '2', 'source_asset' => parent_well_b1.uuid, 'target_asset' => 'tube-1' },
-                { 'submission_id' => '2', 'source_asset' => parent_well_a2.uuid, 'target_asset' => 'tube-2' },
-                { 'submission_id' => '2', 'source_asset' => parent_well_b2.uuid, 'target_asset' => 'tube-3' },
-                { 'submission_id' => '2', 'source_asset' => parent_well_a3.uuid, 'target_asset' => 'tube-4' }
-              ]
+              transfer_requests: transfer_requests
             }
           },
           body: '{}'
@@ -1193,15 +1103,13 @@
       end
 
       it 'creates the child tubes' do
-        expect_api_v2_posts(
-          'CustomMetadatumCollection',
-          [tube_1_create_args, tube_2_create_args, tube_3_create_args, tube_4_create_args, tube_5_create_args]
-        )
+        # Contingency tubes creation
+        expect_specific_tube_creation(child_contingency_tube_purpose_uuid, contingency_tubes)
+        expect_custom_metadatum_collection_posts({ 'TR00000002' => contingency_tubes })
 
         expect(subject.valid?).to be_truthy
         expect(subject.save).to be_truthy
         expect(stub_contingency_file_upload).to have_been_made.once
-        expect(stub_contingency_tube_creation_request).to have_been_made.once
         expect(stub_transfer_creation_request).to have_been_made.once
       end
     end

From 9ebf0823a185b37be58def6aaaed80fe4b356632 Mon Sep 17 00:00:00 2001
From: Stuart McHattie <sm49@sanger.ac.uk>
Date: Tue, 17 Sep 2024 13:34:33 +0100
Subject: [PATCH 5/9] Remove unneeded fixtures for child tubes

---
 .../plate_split_to_tube_racks_spec.rb         | 245 +-----------------
 1 file changed, 10 insertions(+), 235 deletions(-)

diff --git a/spec/models/labware_creators/plate_split_to_tube_racks_spec.rb b/spec/models/labware_creators/plate_split_to_tube_racks_spec.rb
index 040feb362..6fd9a237b 100644
--- a/spec/models/labware_creators/plate_split_to_tube_racks_spec.rb
+++ b/spec/models/labware_creators/plate_split_to_tube_racks_spec.rb
@@ -116,77 +116,6 @@
     { user_uuid: user_uuid, purpose_uuid: child_sequencing_tube_purpose_uuid, parent_uuid: parent_uuid }
   end
 
-  # child tubes for lookup after creation
-  let(:child_tube_1_uuid) { SecureRandom.uuid }
-  let(:child_tube_1_aliquot) { create(:v2_aliquot, sample: sample1) }
-  let(:child_tube_1_v2) do
-    create(
-      :v2_stock_tube,
-      state: 'passed',
-      purpose_name: child_sequencing_tube_purpose_name,
-      aliquots: [child_tube_1_aliquot],
-      barcode_prefix: 'FX',
-      barcode_number: 1,
-      uuid: child_tube_1_uuid
-    )
-  end
-
-  let(:child_tube_2_uuid) { SecureRandom.uuid }
-  let(:child_tube_2_aliquot) { create(:v2_aliquot, sample: sample2) }
-  let(:child_tube_2_v2) do
-    create(
-      :v2_stock_tube,
-      state: 'passed',
-      purpose_name: child_sequencing_tube_purpose_name,
-      aliquots: [child_tube_2_aliquot],
-      barcode_prefix: 'FX',
-      barcode_number: 2,
-      uuid: child_tube_2_uuid
-    )
-  end
-
-  let(:child_tube_3_uuid) { SecureRandom.uuid }
-  let(:child_tube_3_aliquot) { create(:v2_aliquot, sample: sample1) }
-  let(:child_tube_3_v2) do
-    create(
-      :v2_stock_tube,
-      state: 'passed',
-      purpose_name: child_contingency_tube_purpose_name,
-      aliquots: [child_tube_3_aliquot],
-      barcode_prefix: 'FX',
-      barcode_number: 11,
-      uuid: child_tube_3_uuid
-    )
-  end
-
-  let(:child_tube_4_uuid) { SecureRandom.uuid }
-  let(:child_tube_4_aliquot) { create(:v2_aliquot, sample: sample1) }
-  let(:child_tube_4_v2) do
-    create(
-      :v2_stock_tube,
-      state: 'passed',
-      purpose_name: child_contingency_tube_purpose_name,
-      aliquots: [child_tube_4_aliquot],
-      barcode_prefix: 'FX',
-      barcode_number: 12,
-      uuid: child_tube_4_uuid
-    )
-  end
-
-  let(:child_tube_5_uuid) { SecureRandom.uuid }
-  let(:child_tube_5_aliquot) { create(:v2_aliquot, sample: sample2) }
-  let(:child_tube_5_v2) do
-    create(
-      :v2_stock_tube,
-      state: 'passed',
-      purpose_name: child_contingency_tube_purpose_name,
-      aliquots: [child_tube_5_aliquot],
-      barcode_prefix: 'FX',
-      barcode_number: 13,
-      uuid: child_tube_5_uuid
-    )
-  end
-
   let(:sequencing_file) do
     fixture_file_upload(
       'spec/fixtures/files/scrna_core/scrna_core_sequencing_tube_rack_scan.csv',
@@ -271,12 +200,14 @@ def expect_custom_metadatum_collection_posts(tubes_hash)
     stub_v2_tube(ancestor_tube_1_v2, stub_search: false)
     stub_v2_tube(ancestor_tube_2_v2, stub_search: false)
 
-    # child tube lookups
-    stub_v2_tube(child_tube_1_v2, stub_search: false)
-    stub_v2_tube(child_tube_2_v2, stub_search: false)
-    stub_v2_tube(child_tube_3_v2, stub_search: false)
-    stub_v2_tube(child_tube_4_v2, stub_search: false)
-    stub_v2_tube(child_tube_5_v2, stub_search: false)
+    # Block finding tubes by given barcodes.
+    allow(Sequencescape::Api::V2::Tube).to receive(:find_by).with(barcode: 'FX00000001').and_return(nil)
+    allow(Sequencescape::Api::V2::Tube).to receive(:find_by).with(barcode: 'FX00000002').and_return(nil)
+    allow(Sequencescape::Api::V2::Tube).to receive(:find_by).with(barcode: 'FX00000011').and_return(nil)
+    allow(Sequencescape::Api::V2::Tube).to receive(:find_by).with(barcode: 'FX00000012').and_return(nil)
+    allow(Sequencescape::Api::V2::Tube).to receive(:find_by).with(barcode: 'FX00000013').and_return(nil)
+    allow(Sequencescape::Api::V2::Tube).to receive(:find_by).with(barcode: 'FX00000014').and_return(nil)
+    allow(Sequencescape::Api::V2::Tube).to receive(:find_by).with(barcode: 'FX00000015').and_return(nil)
   end
 
   context 'on new' do
@@ -423,13 +354,6 @@ def expect_custom_metadatum_collection_posts(tubes_hash)
           'wells.aliquots,wells.aliquots.sample,wells.downstream_tubes,' \
             'wells.downstream_tubes.custom_metadatum_collection'
       )
-      allow(Sequencescape::Api::V2::Tube).to receive(:find_by).with(barcode: 'FX00000001').and_return(nil)
-      allow(Sequencescape::Api::V2::Tube).to receive(:find_by).with(barcode: 'FX00000002').and_return(nil)
-      allow(Sequencescape::Api::V2::Tube).to receive(:find_by).with(barcode: 'FX00000011').and_return(nil)
-      allow(Sequencescape::Api::V2::Tube).to receive(:find_by).with(barcode: 'FX00000012').and_return(nil)
-      allow(Sequencescape::Api::V2::Tube).to receive(:find_by).with(barcode: 'FX00000013').and_return(nil)
-      allow(Sequencescape::Api::V2::Tube).to receive(:find_by).with(barcode: 'FX00000014').and_return(nil)
-      allow(Sequencescape::Api::V2::Tube).to receive(:find_by).with(barcode: 'FX00000015').and_return(nil)
     end
 
     context 'when files are not present' do
@@ -548,13 +472,6 @@ def expect_custom_metadatum_collection_posts(tubes_hash)
           'wells.aliquots,wells.aliquots.sample,wells.downstream_tubes,' \
             'wells.downstream_tubes.custom_metadatum_collection'
       )
-      allow(Sequencescape::Api::V2::Tube).to receive(:find_by).with(barcode: 'FX00000001').and_return(nil)
-      allow(Sequencescape::Api::V2::Tube).to receive(:find_by).with(barcode: 'FX00000002').and_return(nil)
-      allow(Sequencescape::Api::V2::Tube).to receive(:find_by).with(barcode: 'FX00000011').and_return(nil)
-      allow(Sequencescape::Api::V2::Tube).to receive(:find_by).with(barcode: 'FX00000012').and_return(nil)
-      allow(Sequencescape::Api::V2::Tube).to receive(:find_by).with(barcode: 'FX00000013').and_return(nil)
-      allow(Sequencescape::Api::V2::Tube).to receive(:find_by).with(barcode: 'FX00000014').and_return(nil)
-      allow(Sequencescape::Api::V2::Tube).to receive(:find_by).with(barcode: 'FX00000015').and_return(nil)
     end
 
     context 'when files are not present' do
@@ -733,13 +650,6 @@ def expect_custom_metadatum_collection_posts(tubes_hash)
             'wells.downstream_tubes.custom_metadatum_collection'
       )
       stub_api_get(parent_uuid, body: parent_v1)
-      allow(Sequencescape::Api::V2::Tube).to receive(:find_by).with(barcode: 'FX00000001').and_return(nil)
-      allow(Sequencescape::Api::V2::Tube).to receive(:find_by).with(barcode: 'FX00000002').and_return(nil)
-      allow(Sequencescape::Api::V2::Tube).to receive(:find_by).with(barcode: 'FX00000011').and_return(nil)
-      allow(Sequencescape::Api::V2::Tube).to receive(:find_by).with(barcode: 'FX00000012').and_return(nil)
-      allow(Sequencescape::Api::V2::Tube).to receive(:find_by).with(barcode: 'FX00000013').and_return(nil)
-      allow(Sequencescape::Api::V2::Tube).to receive(:find_by).with(barcode: 'FX00000014').and_return(nil)
-      allow(Sequencescape::Api::V2::Tube).to receive(:find_by).with(barcode: 'FX00000015').and_return(nil)
     end
 
     context 'with both sequencing and contingency files' do
@@ -810,29 +720,6 @@ def expect_custom_metadatum_collection_posts(tubes_hash)
         )
       end
 
-      # need api v1 versions of child tubes
-      let(:child_tube_1_v1) { json :tube, uuid: child_tube_1_uuid, barcode_prefix: 'FX', barcode_number: 1 }
-      let(:child_tube_2_v1) { json :tube, uuid: child_tube_2_uuid, barcode_prefix: 'FX', barcode_number: 2 }
-      let(:child_tube_3_v1) { json :tube, uuid: child_tube_3_uuid, barcode_prefix: 'FX', barcode_number: 11 }
-      let(:child_tube_4_v1) { json :tube, uuid: child_tube_4_uuid, barcode_prefix: 'FX', barcode_number: 12 }
-      let(:child_tube_5_v1) { json :tube, uuid: child_tube_5_uuid, barcode_prefix: 'FX', barcode_number: 13 }
-
-      # Metadata expected to be sent in POST requests
-      let!(:metadata_for_tube_1) { { tube_rack_barcode: 'TR00000001', tube_rack_position: 'A1' } }
-      let(:tube_1_create_args) { { user_id: user.id, asset_id: child_tube_1_v2.id, metadata: metadata_for_tube_1 } }
-
-      let!(:metadata_for_tube_2) { { tube_rack_barcode: 'TR00000001', tube_rack_position: 'B1' } }
-      let(:tube_2_create_args) { { user_id: user.id, asset_id: child_tube_2_v2.id, metadata: metadata_for_tube_2 } }
-
-      let!(:metadata_for_tube_3) { { tube_rack_barcode: 'TR00000002', tube_rack_position: 'A1' } }
-      let(:tube_3_create_args) { { user_id: user.id, asset_id: child_tube_3_v2.id, metadata: metadata_for_tube_3 } }
-
-      let!(:metadata_for_tube_4) { { tube_rack_barcode: 'TR00000002', tube_rack_position: 'B1' } }
-      let(:tube_4_create_args) { { user_id: user.id, asset_id: child_tube_4_v2.id, metadata: metadata_for_tube_4 } }
-
-      let!(:metadata_for_tube_5) { { tube_rack_barcode: 'TR00000002', tube_rack_position: 'C1' } }
-      let(:tube_5_create_args) { { user_id: user.id, asset_id: child_tube_5_v2.id, metadata: metadata_for_tube_5 } }
-
       let(:contingency_file) do
         fixture_file_upload(
           'spec/fixtures/files/scrna_core/scrna_core_contingency_tube_rack_scan_3_tubes.csv',
@@ -840,15 +727,7 @@ def expect_custom_metadatum_collection_posts(tubes_hash)
         )
       end
 
-      before do
-        stub_v2_user(user)
-
-        stub_v2_labware(child_tube_1_v2)
-        stub_v2_labware(child_tube_2_v2)
-        stub_v2_labware(child_tube_3_v2)
-        stub_v2_labware(child_tube_4_v2)
-        stub_v2_labware(child_tube_5_v2)
-      end
+      before { stub_v2_user(user) }
 
       it 'creates the child tubes' do
         expect_specific_tube_creation(child_sequencing_tube_purpose_uuid, sequencing_tubes)
@@ -920,18 +799,6 @@ def expect_custom_metadatum_collection_posts(tubes_hash)
           )
         end
 
-        before do
-          stub_get_labware_metadata(child_tube_1_v2.barcode.machine, child_tube_1_v1)
-          stub_get_labware_metadata(child_tube_2_v2.barcode.machine, child_tube_2_v1)
-          stub_get_labware_metadata(child_tube_3_v2.barcode.machine, child_tube_3_v1)
-          stub_get_labware_metadata(child_tube_4_v2.barcode.machine, child_tube_4_v1)
-
-          stub_asset_search(child_tube_1_v2.barcode.machine, child_tube_1_v1)
-          stub_asset_search(child_tube_2_v2.barcode.machine, child_tube_2_v1)
-          stub_asset_search(child_tube_3_v2.barcode.machine, child_tube_3_v1)
-          stub_asset_search(child_tube_4_v2.barcode.machine, child_tube_4_v1)
-        end
-
         it 'does not create a tube for the failed well' do
           expect_specific_tube_creation(child_sequencing_tube_purpose_uuid, sequencing_tubes)
           expect_specific_tube_creation(child_contingency_tube_purpose_uuid, contingency_tubes)
@@ -968,67 +835,6 @@ def expect_custom_metadatum_collection_posts(tubes_hash)
         }
       end
 
-      # child tubes for lookup after creation
-      let(:child_tube_1_v2) do
-        create(
-          :v2_stock_tube,
-          state: 'passed',
-          purpose_name: child_contingency_tube_purpose_name,
-          aliquots: [child_tube_1_aliquot],
-          barcode_prefix: 'FX',
-          barcode_number: 11,
-          uuid: child_tube_1_uuid
-        )
-      end
-
-      let(:child_tube_2_v2) do
-        create(
-          :v2_stock_tube,
-          state: 'passed',
-          purpose_name: child_contingency_tube_purpose_name,
-          aliquots: [child_tube_2_aliquot],
-          barcode_prefix: 'FX',
-          barcode_number: 12,
-          uuid: child_tube_2_uuid
-        )
-      end
-
-      let(:child_tube_3_v2) do
-        create(
-          :v2_stock_tube,
-          state: 'passed',
-          purpose_name: child_contingency_tube_purpose_name,
-          aliquots: [child_tube_3_aliquot],
-          barcode_prefix: 'FX',
-          barcode_number: 13,
-          uuid: child_tube_3_uuid
-        )
-      end
-
-      let(:child_tube_4_v2) do
-        create(
-          :v2_stock_tube,
-          state: 'passed',
-          purpose_name: child_contingency_tube_purpose_name,
-          aliquots: [child_tube_4_aliquot],
-          barcode_prefix: 'FX',
-          barcode_number: 14,
-          uuid: child_tube_4_uuid
-        )
-      end
-
-      let(:child_tube_5_v2) do
-        create(
-          :v2_stock_tube,
-          state: 'passed',
-          purpose_name: child_contingency_tube_purpose_name,
-          aliquots: [child_tube_5_aliquot],
-          barcode_prefix: 'FX',
-          barcode_number: 15,
-          uuid: child_tube_5_uuid
-        )
-      end
-
       let(:contingency_tubes) do
         prepare_created_child_tubes(
           [
@@ -1069,38 +875,7 @@ def expect_custom_metadatum_collection_posts(tubes_hash)
         )
       end
 
-      # need api v1 versions of child tubes
-      let(:child_tube_1_v1) { json :tube, uuid: child_tube_1_uuid, barcode_prefix: 'FX', barcode_number: 11 }
-      let(:child_tube_2_v1) { json :tube, uuid: child_tube_2_uuid, barcode_prefix: 'FX', barcode_number: 12 }
-      let(:child_tube_3_v1) { json :tube, uuid: child_tube_3_uuid, barcode_prefix: 'FX', barcode_number: 13 }
-      let(:child_tube_4_v1) { json :tube, uuid: child_tube_4_uuid, barcode_prefix: 'FX', barcode_number: 14 }
-      let(:child_tube_5_v1) { json :tube, uuid: child_tube_5_uuid, barcode_prefix: 'FX', barcode_number: 15 }
-
-      # need to stub the creation of the tube metadata
-      let!(:metadata_for_tube_1) { { tube_rack_barcode: 'TR00000002', tube_rack_position: 'A1' } }
-      let(:tube_1_create_args) { { user_id: user.id, asset_id: child_tube_1_v2.id, metadata: metadata_for_tube_1 } }
-
-      let!(:metadata_for_tube_2) { { tube_rack_barcode: 'TR00000002', tube_rack_position: 'B1' } }
-      let(:tube_2_create_args) { { user_id: user.id, asset_id: child_tube_2_v2.id, metadata: metadata_for_tube_2 } }
-
-      let!(:metadata_for_tube_3) { { tube_rack_barcode: 'TR00000002', tube_rack_position: 'C1' } }
-      let(:tube_3_create_args) { { user_id: user.id, asset_id: child_tube_3_v2.id, metadata: metadata_for_tube_3 } }
-
-      let!(:metadata_for_tube_4) { { tube_rack_barcode: 'TR00000002', tube_rack_position: 'E1' } }
-      let(:tube_4_create_args) { { user_id: user.id, asset_id: child_tube_4_v2.id, metadata: metadata_for_tube_4 } }
-
-      let!(:metadata_for_tube_5) { { tube_rack_barcode: 'TR00000002', tube_rack_position: 'F1' } }
-      let(:tube_5_create_args) { { user_id: user.id, asset_id: child_tube_5_v2.id, metadata: metadata_for_tube_5 } }
-
-      before do
-        stub_v2_user(user)
-
-        stub_v2_labware(child_tube_1_v2)
-        stub_v2_labware(child_tube_2_v2)
-        stub_v2_labware(child_tube_3_v2)
-        stub_v2_labware(child_tube_4_v2)
-        stub_v2_labware(child_tube_5_v2)
-      end
+      before { stub_v2_user(user) }
 
       it 'creates the child tubes' do
         # Contingency tubes creation

From cd8c643d9a0d64f756d8198a780b1ee9234a0731 Mon Sep 17 00:00:00 2001
From: Stuart McHattie <sm49@sanger.ac.uk>
Date: Tue, 17 Sep 2024 13:37:04 +0100
Subject: [PATCH 6/9] Remove accidental assignment to unused variable

---
 spec/models/labware_creators/plate_split_to_tube_racks_spec.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/spec/models/labware_creators/plate_split_to_tube_racks_spec.rb b/spec/models/labware_creators/plate_split_to_tube_racks_spec.rb
index 6fd9a237b..5a0de7246 100644
--- a/spec/models/labware_creators/plate_split_to_tube_racks_spec.rb
+++ b/spec/models/labware_creators/plate_split_to_tube_racks_spec.rb
@@ -165,7 +165,7 @@ def expect_custom_metadatum_collection_posts(tubes_hash)
     expected_call_args =
       tubes_hash.flat_map do |tube_rack_barcode, tubes|
         tubes.map do |tube|
-          metadata = {
+          {
             user_id: user.id,
             asset_id: tube.id,
             metadata: {

From 9f10f6a0e28740510cb47bcccb64df5ae5b0d17a Mon Sep 17 00:00:00 2001
From: Stuart McHattie <sm49@sanger.ac.uk>
Date: Tue, 17 Sep 2024 14:22:20 +0100
Subject: [PATCH 7/9] Fix tests for pooled tubes by submission

---
 .../pooled_tubes_by_submission_spec.rb        | 103 ++++++++----------
 1 file changed, 43 insertions(+), 60 deletions(-)

diff --git a/spec/models/labware_creators/pooled_tubes_by_submission_spec.rb b/spec/models/labware_creators/pooled_tubes_by_submission_spec.rb
index f358503a5..cb8033efe 100644
--- a/spec/models/labware_creators/pooled_tubes_by_submission_spec.rb
+++ b/spec/models/labware_creators/pooled_tubes_by_submission_spec.rb
@@ -11,6 +11,8 @@
 RSpec.describe LabwareCreators::PooledTubesBySubmission do
   include FeatureHelpers
 
+  has_a_working_api
+
   it_behaves_like 'it only allows creation from charged and passed plates with defined downstream pools'
 
   subject { LabwareCreators::PooledTubesBySubmission.new(api, form_attributes) }
@@ -31,10 +33,25 @@
   before { stub_v2_plate(source_plate, stub_search: false) }
 
   context '#save!' do
-    has_a_working_api
-
-    let(:child_1_name) { 'DN5 A1:C1' }
-    let(:child_2_name) { 'DN5 D1:A2' }
+    def expect_specific_tube_creation(child_tubes)
+      # Create a mock for the specific tube creation.
+      specific_tube_creation = double
+      allow(specific_tube_creation).to receive(:children).and_return(child_tubes)
+
+      # Expect the post request and return the mock.
+      expect_api_v2_posts(
+        'SpecificTubeCreation',
+        [
+          {
+            child_purpose_uuids: [purpose_uuid] * child_tubes.size,
+            parent_uuids: [parent_uuid],
+            tube_attributes: child_tubes.map { |tube| { name: tube.name } },
+            user_uuid: user_uuid
+          }
+        ],
+        [specific_tube_creation]
+      )
+    end
 
     # Used to fetch the pools. This is the kind of thing we could pass through from a custom form
     let!(:parent_request) do
@@ -42,40 +59,20 @@
       stub_api_get(parent_uuid, 'wells', body: wells_json)
     end
 
-    let(:creation_payload) do
-      {
-        user: user_uuid,
-        parent: parent_uuid,
-        child_purposes: [purpose_uuid, purpose_uuid],
-        tube_attributes: [{ name: child_1_name }, { name: child_2_name }]
-      }
-    end
+    let(:child_1_name) { 'DN5 A1:C1' }
+    let(:child_2_name) { 'DN5 D1:A2' }
 
-    let(:tube_creation_request_uuid) { SecureRandom.uuid }
+    let(:tube_attributes) { [{ name: child_1_name }, { name: child_2_name }] }
 
-    let!(:tube_creation_request) do
-      stub_api_post(
-        'specific_tube_creations',
-        payload: {
-          specific_tube_creation: creation_payload
-        },
-        body:
-          json(
-            :specific_tube_creation,
-            uuid: tube_creation_request_uuid,
-            children_count: 2,
-            names: [child_1_name, child_2_name]
-          )
-      )
-    end
+    let(:child_tubes) do
+      # Prepare child tubes and stub their lookups.
+      child_tubes =
+        tube_attributes.each_with_index.map do |attrs, index|
+          create(:v2_tube, name: attrs[:name], uuid: "tube-#{index}")
+        end
+      child_tubes.each { |child_tube| stub_v2_labware(child_tube) }
 
-    # Find out what tubes we've just made!
-    let!(:tube_creation_children_request) do
-      stub_api_get(
-        tube_creation_request_uuid,
-        'children',
-        body: json(:tube_collection, names: [child_1_name, child_2_name])
-      )
+      child_tubes
     end
 
     let(:transfer_requests) do
@@ -106,9 +103,10 @@
     end
 
     context 'without parent metadata' do
+      before { expect_specific_tube_creation(child_tubes) }
+
       it 'pools by submission' do
         expect(subject.save!).to be_truthy
-        expect(tube_creation_request).to have_been_made.once
         expect(transfer_creation_request).to have_been_made.once
       end
 
@@ -133,24 +131,11 @@
              for_multiplexing: true
       end
 
-      setup do
-        stub_get_labware_metadata('DN10', parent, metadata: { stock_barcode: 'DN6' })
-        stub_api_post(
-          'specific_tube_creations',
-          payload: {
-            specific_tube_creation: creation_payload
-          },
-          body:
-            json(
-              :specific_tube_creation,
-              uuid: tube_creation_request_uuid,
-              children_count: 2,
-              names: [child_1_name, child_2_name]
-            )
-        )
-      end
+      setup { stub_get_labware_metadata('DN10', parent, metadata: { stock_barcode: 'DN6' }) }
 
       it 'sets the correct tube name' do
+        expect_specific_tube_creation(child_tubes)
+
         expect(subject.save!).to be_truthy
         expect(subject.child_stock_tubes.length).to eq(2)
         expect(subject.child_stock_tubes).to have_key(child_1_name)
@@ -172,6 +157,9 @@
           { 'source_asset' => 'example-well-uuid-7', 'target_asset' => 'tube-1', 'submission' => 'pool-2-uuid' }
         ]
       end
+
+      before { expect_specific_tube_creation(child_tubes) }
+
       it 'pools by submission' do
         expect(subject.save!).to be_truthy
         expect(transfer_creation_request).to have_been_made.once
@@ -191,14 +179,9 @@
         ]
       end
 
-      let(:creation_payload) do
-        {
-          user: user_uuid,
-          parent: parent_uuid,
-          child_purposes: [purpose_uuid],
-          tube_attributes: [{ name: child_1_name }]
-        }
-      end
+      let(:tube_attributes) { [{ name: child_1_name }] }
+
+      before { expect_specific_tube_creation(child_tubes) }
 
       it 'pools by submission' do
         expect(subject.save!).to be_truthy

From 8ca6cc86c93c599807c30ad669882cdde07827d8 Mon Sep 17 00:00:00 2001
From: Stuart McHattie <sm49@sanger.ac.uk>
Date: Tue, 17 Sep 2024 14:34:43 +0100
Subject: [PATCH 8/9] Fix tests for custom_pooled_tubes

---
 .../custom_pooled_tubes_spec.rb               | 48 +++++++++----------
 1 file changed, 23 insertions(+), 25 deletions(-)

diff --git a/spec/models/labware_creators/custom_pooled_tubes_spec.rb b/spec/models/labware_creators/custom_pooled_tubes_spec.rb
index c9ed9f2e9..489727e2f 100644
--- a/spec/models/labware_creators/custom_pooled_tubes_spec.rb
+++ b/spec/models/labware_creators/custom_pooled_tubes_spec.rb
@@ -73,29 +73,28 @@
         )
     end
 
-    let(:tube_creation_request_uuid) { SecureRandom.uuid }
-
-    let(:tube_creation_request) do
-      stub_api_post(
-        'specific_tube_creations',
-        payload: {
-          specific_tube_creation: {
-            user: user_uuid,
-            parent: parent_uuid,
-            child_purposes: [purpose_uuid, purpose_uuid],
-            tube_attributes: [{ name: 'DN5 A1:B2' }, { name: 'DN5 C1:G2' }]
+    def expect_specific_tube_creation
+      child_tubes = [
+        create(:v2_tube, name: 'DN5 A1:B2', uuid: 'tube-0'),
+        create(:v2_tube, name: 'DN5 C1:G2', uuid: 'tube-1')
+      ]
+
+      # Create a mock for the specific tube creation.
+      specific_tube_creation = double
+      allow(specific_tube_creation).to receive(:children).and_return(child_tubes)
+
+      # Expect the post request and return the mock.
+      expect_api_v2_posts(
+        'SpecificTubeCreation',
+        [
+          {
+            child_purpose_uuids: [purpose_uuid, purpose_uuid],
+            parent_uuids: [parent_uuid],
+            tube_attributes: child_tubes.map { |tube| { name: tube.name } },
+            user_uuid: user_uuid
           }
-        },
-        body: json(:specific_tube_creation, uuid: tube_creation_request_uuid, children_count: 2)
-      )
-    end
-
-    # Find out what tubes we've just made!
-    let(:tube_creation_children_request) do
-      stub_api_get(
-        tube_creation_request_uuid,
-        'children',
-        body: json(:tube_collection, names: ['DN5 A1:B2', 'DN5 C1:G2'])
+        ],
+        [specific_tube_creation]
       )
     end
 
@@ -138,8 +137,6 @@
     before do
       stub_parent_request
       stub_qc_file_creation
-      tube_creation_children_request
-      tube_creation_request
       transfer_creation_request
     end
 
@@ -149,9 +146,10 @@
       end
 
       it 'pools according to the file' do
+        expect_specific_tube_creation
+
         expect(subject.save).to be_truthy
         expect(stub_qc_file_creation).to have_been_made.once
-        expect(tube_creation_request).to have_been_made.once
         expect(transfer_creation_request).to have_been_made.once
       end
     end

From 3d096e488460e4814521d907b16f227b0a6eadef Mon Sep 17 00:00:00 2001
From: Stuart McHattie <sm49@sanger.ac.uk>
Date: Tue, 17 Sep 2024 16:42:22 +0100
Subject: [PATCH 9/9] Change parents relationship to Labware instead of Asset

---
 .../sequencescape/api/v2/specific_tube_creation.rb              | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/sequencescape/sequencescape/api/v2/specific_tube_creation.rb b/app/sequencescape/sequencescape/api/v2/specific_tube_creation.rb
index 035a70c5a..4b3235552 100644
--- a/app/sequencescape/sequencescape/api/v2/specific_tube_creation.rb
+++ b/app/sequencescape/sequencescape/api/v2/specific_tube_creation.rb
@@ -3,6 +3,6 @@
 # Represents a specific tube creation in Limber via the Sequencescape API
 class Sequencescape::Api::V2::SpecificTubeCreation < Sequencescape::Api::V2::Base
   has_many :children, class_name: 'Sequencescape::Api::V2::Tube'
-  has_many :parents, class_name: 'Sequencescape::Api::V2::Asset'
+  has_many :parents, class_name: 'Sequencescape::Api::V2::Labware'
   has_one :user, class_name: 'Sequencescape::Api::V2::User'
 end