From 3184c3134595272d1acee0f0d962aa0e7b82a04f Mon Sep 17 00:00:00 2001
From: Stephen Hulme <sh51@sanger.ac.uk>
Date: Thu, 28 Nov 2024 08:24:43 +0000
Subject: [PATCH 01/40] fix: generate plate volumes

---
 .../uat_actions/generate_plate_volumes.rb     | 103 ++++++++++++++++++
 .../generate_plate_volumes_spec.rb            |  37 +++++++
 2 files changed, 140 insertions(+)
 create mode 100644 app/uat_actions/uat_actions/generate_plate_volumes.rb
 create mode 100644 spec/uat_actions/generate_plate_volumes_spec.rb

diff --git a/app/uat_actions/uat_actions/generate_plate_volumes.rb b/app/uat_actions/uat_actions/generate_plate_volumes.rb
new file mode 100644
index 0000000000..4a577abe11
--- /dev/null
+++ b/app/uat_actions/uat_actions/generate_plate_volumes.rb
@@ -0,0 +1,103 @@
+# frozen_string_literal: true
+
+# Will generate volumes for a given plate
+class UatActions::GeneratePlateVolumes < UatActions
+  self.title = 'Generate volumes for a plate'
+  self.description = 'Generate a set of randomised volumes for a plate.'
+  self.category = :quality_control
+
+  form_field :plate_barcode,
+             :text_field,
+             label: 'Plate barcode',
+             help:
+               'Enter the barcode of the plate for which you want to add volumes. ' \
+                 'NB. only well containing aliquots will have volumes set.'
+  form_field :minimum_volume,
+             :number_field,
+             label: 'Minimum volume (µl)',
+             help: 'The minimum volume the wells should have.',
+             options: {
+               minimum: 0
+             }
+  form_field :maximum_volume,
+             :number_field,
+             label: 'Maximum volume (µl)',
+             help: 'The maximum volume the wells should have.',
+             options: {
+               minimum: 0
+             }
+
+
+  #
+  # Returns a default copy of the UatAction which will be used to fill in the form, with values
+  # for the units, and min and max volumes.
+  #
+  # @return [UatActions::GeneratePlateVolumes] A default object for rendering a form
+  def self.default
+    new( minimum_volume: 0, maximum_volume: 100)
+  end
+
+
+  validates :plate_barcode, presence: { message: 'could not be found' }
+  validates :minimum_volume, numericality: { only_integer: false }
+  validates :maximum_volume, numericality: { greater_than: 0, only_integer: false }
+  validate :maximum_greater_than_minimum
+
+  def perform
+    qc_assay_results = construct_qc_assay
+    report['number_well_volumes_written'] = qc_assay_results[:num_wells_written]
+    qc_assay_results[:qc_assay_success]
+  end
+
+  private
+
+  def maximum_greater_than_minimum
+    return true if max_vol > min_vol
+
+    errors.add(:maximum_volume, 'needs to be greater than minimum volume')
+    false
+  end
+
+  def labware
+    @labware ||= Plate.find_by_barcode(plate_barcode.strip)
+  end
+
+  def key
+    @key ||= 'volume'
+  end
+
+  def min_vol
+    @min_vol ||= minimum_volume.to_f
+  end
+
+  def max_vol
+    @max_vol ||= maximum_volume.to_f
+  end
+
+  def create_random_volume
+    value = (rand * (max_vol - min_vol)) + min_vol
+    format('%.3f', value)
+  end
+
+  def construct_qc_assay
+    qc_assay = QcAssay.new
+    num_wells_written = 0
+
+    labware.wells.each do |well|
+      next if well.aliquots.empty?
+
+      QcResult.create!(
+        asset: well,
+        key: key,
+        value: create_random_volume,
+        units: 'µl',
+        assay_type: 'UAT_Testing',
+        assay_version: 'Binning',
+        qc_assay: qc_assay
+      )
+      num_wells_written += 1
+    end
+    qc_assay_success = qc_assay.save
+    { qc_assay_success:, num_wells_written: }
+  end
+end
diff --git a/spec/uat_actions/generate_plate_volumes_spec.rb b/spec/uat_actions/generate_plate_volumes_spec.rb
new file mode 100644
index 0000000000..fcb826677d
--- /dev/null
+++ b/spec/uat_actions/generate_plate_volumes_spec.rb
@@ -0,0 +1,37 @@
+# frozen_string_literal: true
+
+require 'rails_helper'
+
+describe UatActions::GeneratePlateVolumes do
+  context 'with valid options' do
+    let(:plate) { create(:plate_with_untagged_wells, sample_count: 3) }
+    let(:uat_action) { described_class.new(parameters) }
+    let(:report) do
+      # A report is a hash of key value pairs which get returned to the user.
+      # It should include information such as barcodes and identifiers
+      { 'number_well_volumes_written' => 3 }
+    end
+
+    context 'when ul volumes' do
+      let(:parameters) do
+        {
+          plate_barcode: plate.barcodes.first.barcode,
+          minimum_volume: 0,
+          maximum_volume: 30
+        }
+      end
+
+      it 'can be performed' do
+        expect(uat_action.perform).to be true
+        expect(uat_action.report).to eq report
+        expect(plate.wells.map(&:qc_results).size).to eq 3
+        expect(plate.wells.first.qc_results.first.assay_type).to eq 'UAT_Testing'
+      end
+    end
+
+  end
+
+  it 'returns a default' do
+    expect(described_class.default).to be_a described_class
+  end
+end

From 12deaa2c01c3aefe227aed524e04c461b5a8923b Mon Sep 17 00:00:00 2001
From: Stephen Hulme <sh51@sanger.ac.uk>
Date: Thu, 28 Nov 2024 08:33:33 +0000
Subject: [PATCH 02/40] style: lindt

---
 app/uat_actions/uat_actions/generate_plate_volumes.rb | 4 +---
 spec/uat_actions/generate_plate_volumes_spec.rb       | 9 +--------
 2 files changed, 2 insertions(+), 11 deletions(-)

diff --git a/app/uat_actions/uat_actions/generate_plate_volumes.rb b/app/uat_actions/uat_actions/generate_plate_volumes.rb
index 4a577abe11..c316881cf0 100644
--- a/app/uat_actions/uat_actions/generate_plate_volumes.rb
+++ b/app/uat_actions/uat_actions/generate_plate_volumes.rb
@@ -27,17 +27,15 @@ class UatActions::GeneratePlateVolumes < UatActions
                minimum: 0
              }
 
-
   #
   # Returns a default copy of the UatAction which will be used to fill in the form, with values
   # for the units, and min and max volumes.
   #
   # @return [UatActions::GeneratePlateVolumes] A default object for rendering a form
   def self.default
-    new( minimum_volume: 0, maximum_volume: 100)
+    new(minimum_volume: 0, maximum_volume: 100)
   end
 
-
   validates :plate_barcode, presence: { message: 'could not be found' }
   validates :minimum_volume, numericality: { only_integer: false }
   validates :maximum_volume, numericality: { greater_than: 0, only_integer: false }
diff --git a/spec/uat_actions/generate_plate_volumes_spec.rb b/spec/uat_actions/generate_plate_volumes_spec.rb
index fcb826677d..115596e63f 100644
--- a/spec/uat_actions/generate_plate_volumes_spec.rb
+++ b/spec/uat_actions/generate_plate_volumes_spec.rb
@@ -13,13 +13,7 @@
     end
 
     context 'when ul volumes' do
-      let(:parameters) do
-        {
-          plate_barcode: plate.barcodes.first.barcode,
-          minimum_volume: 0,
-          maximum_volume: 30
-        }
-      end
+      let(:parameters) { { plate_barcode: plate.barcodes.first.barcode, minimum_volume: 0, maximum_volume: 30 } }
 
       it 'can be performed' do
         expect(uat_action.perform).to be true
@@ -28,7 +22,6 @@
         expect(plate.wells.first.qc_results.first.assay_type).to eq 'UAT_Testing'
       end
     end
-
   end
 
   it 'returns a default' do

From df603b40d9c980545801a9d75dae7b892487a9db Mon Sep 17 00:00:00 2001
From: Stephen Hulme <sh51@sanger.ac.uk>
Date: Thu, 28 Nov 2024 08:51:56 +0000
Subject: [PATCH 03/40] tests: split out individual expectations

---
 spec/uat_actions/generate_plate_volumes_spec.rb | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/spec/uat_actions/generate_plate_volumes_spec.rb b/spec/uat_actions/generate_plate_volumes_spec.rb
index 115596e63f..1ef656c3e9 100644
--- a/spec/uat_actions/generate_plate_volumes_spec.rb
+++ b/spec/uat_actions/generate_plate_volumes_spec.rb
@@ -17,8 +17,17 @@
 
       it 'can be performed' do
         expect(uat_action.perform).to be true
+      end
+
+      it 'generates the correct report' do
         expect(uat_action.report).to eq report
+      end
+
+      it 'creates the correct number of QC results' do
         expect(plate.wells.map(&:qc_results).size).to eq 3
+      end
+
+      it 'sets the correct assay type for the first QC result' do
         expect(plate.wells.first.qc_results.first.assay_type).to eq 'UAT_Testing'
       end
     end

From b3084f7fd2d62e14760f78ddde638907a2e8508f Mon Sep 17 00:00:00 2001
From: Stephen Hulme <sh51@sanger.ac.uk>
Date: Thu, 28 Nov 2024 09:12:28 +0000
Subject: [PATCH 04/40] tests: refactor and fix expectations

---
 .../generate_plate_volumes_spec.rb            | 49 +++++++++++++------
 1 file changed, 33 insertions(+), 16 deletions(-)

diff --git a/spec/uat_actions/generate_plate_volumes_spec.rb b/spec/uat_actions/generate_plate_volumes_spec.rb
index 1ef656c3e9..043c108636 100644
--- a/spec/uat_actions/generate_plate_volumes_spec.rb
+++ b/spec/uat_actions/generate_plate_volumes_spec.rb
@@ -6,34 +6,51 @@
   context 'with valid options' do
     let(:plate) { create(:plate_with_untagged_wells, sample_count: 3) }
     let(:uat_action) { described_class.new(parameters) }
+    let!(:performed_action) { uat_action.perform }
     let(:report) do
       # A report is a hash of key value pairs which get returned to the user.
       # It should include information such as barcodes and identifiers
       { 'number_well_volumes_written' => 3 }
     end
 
-    context 'when ul volumes' do
-      let(:parameters) { { plate_barcode: plate.barcodes.first.barcode, minimum_volume: 0, maximum_volume: 30 } }
+    let(:parameters) { { plate_barcode: plate.barcodes.first.barcode, minimum_volume: 0, maximum_volume: 30 } }
 
-      it 'can be performed' do
-        expect(uat_action.perform).to be true
-      end
+    it 'can be performed' do
+      expect(performed_action).to be true
+    end
+
+    it 'generates the correct report' do
+      expect(uat_action.report).to eq report
+    end
 
-      it 'generates the correct report' do
-        expect(uat_action.report).to eq report
-      end
+    it 'creates the correct number of QC results' do
+      expect(plate.wells.map(&:qc_results).size).to eq 3
+    end
 
-      it 'creates the correct number of QC results' do
-        expect(plate.wells.map(&:qc_results).size).to eq 3
-      end
+    it 'sets the correct assay type for the first QC result' do
+      expect(plate.wells.first.qc_results.first.assay_type).to eq 'UAT_Testing'
+    end
 
-      it 'sets the correct assay type for the first QC result' do
-        expect(plate.wells.first.qc_results.first.assay_type).to eq 'UAT_Testing'
-      end
+    it 'sets the volumes to be within the specified range' do
+      expect(plate.wells.map { |well| well.qc_results.first.value.to_f }).to all(be_between(0, 30))
     end
   end
 
-  it 'returns a default' do
-    expect(described_class.default).to be_a described_class
+  context 'with default options' do
+    it 'returns an instance of described_class' do
+      expect(described_class.default).to be_a described_class
+    end
+
+    it 'has a nil plate_barcode' do
+      expect(described_class.default.plate_barcode).to be_nil
+    end
+
+    it 'has a minimum_volume of 0' do
+      expect(described_class.default.minimum_volume).to eq 0
+    end
+
+    it 'has a maximum_volume of 100' do
+      expect(described_class.default.maximum_volume).to eq 100
+    end
   end
 end

From ca14fa166dd39107558769aa005c05c1e53f708c Mon Sep 17 00:00:00 2001
From: Stephen Hulme <sh51@sanger.ac.uk>
Date: Mon, 2 Dec 2024 17:00:23 +0000
Subject: [PATCH 05/40] tests: add additional tests for validation

---
 .../generate_plate_volumes_spec.rb            | 37 +++++++++++++++++--
 1 file changed, 33 insertions(+), 4 deletions(-)

diff --git a/spec/uat_actions/generate_plate_volumes_spec.rb b/spec/uat_actions/generate_plate_volumes_spec.rb
index 043c108636..e90521938e 100644
--- a/spec/uat_actions/generate_plate_volumes_spec.rb
+++ b/spec/uat_actions/generate_plate_volumes_spec.rb
@@ -3,17 +3,19 @@
 require 'rails_helper'
 
 describe UatActions::GeneratePlateVolumes do
+  let(:plate) { create(:plate_with_untagged_wells, sample_count: 3) }
+  let(:plate_barcode) { plate.barcodes.first.barcode }
+  let(:uat_action) { described_class.new(parameters) }
+  let!(:performed_action) { uat_action.perform }
+
   context 'with valid options' do
-    let(:plate) { create(:plate_with_untagged_wells, sample_count: 3) }
-    let(:uat_action) { described_class.new(parameters) }
-    let!(:performed_action) { uat_action.perform }
     let(:report) do
       # A report is a hash of key value pairs which get returned to the user.
       # It should include information such as barcodes and identifiers
       { 'number_well_volumes_written' => 3 }
     end
 
-    let(:parameters) { { plate_barcode: plate.barcodes.first.barcode, minimum_volume: 0, maximum_volume: 30 } }
+    let(:parameters) { { plate_barcode: plate_barcode, minimum_volume: 0, maximum_volume: 30 } }
 
     it 'can be performed' do
       expect(performed_action).to be true
@@ -37,6 +39,8 @@
   end
 
   context 'with default options' do
+    let(:parameters) { { plate_barcode: } }
+
     it 'returns an instance of described_class' do
       expect(described_class.default).to be_a described_class
     end
@@ -53,4 +57,29 @@
       expect(described_class.default.maximum_volume).to eq 100
     end
   end
+
+  context 'with invalid options' do
+    let(:parameters) { {plate_barcode: plate_barcode, minimum_volume: 110, maximum_volume: 10 } }
+    let!(:saved_action) { uat_action.save }
+
+    it 'has a minimum_volume of 110' do
+      expect(uat_action.minimum_volume).to eq 110
+    end
+
+    it 'has a maximum_volume of 10' do
+      expect(uat_action.maximum_volume).to eq 10
+    end
+
+    it 'is invalid' do
+      expect(uat_action.valid?).to be false
+    end
+
+    it 'can not be saved' do
+      expect(saved_action).to be false
+    end
+
+    it 'adds an error' do
+      expect(uat_action.errors.full_messages).to include('Maximum volume needs to be greater than minimum volume')
+    end
+  end
 end

From 48a0ba159b6a6dd206b67db42521b59630f6238f Mon Sep 17 00:00:00 2001
From: Stephen Hulme <sh51@sanger.ac.uk>
Date: Tue, 3 Dec 2024 09:25:47 +0000
Subject: [PATCH 06/40] style: lint

---
 spec/uat_actions/generate_plate_volumes_spec.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/spec/uat_actions/generate_plate_volumes_spec.rb b/spec/uat_actions/generate_plate_volumes_spec.rb
index e90521938e..e655213412 100644
--- a/spec/uat_actions/generate_plate_volumes_spec.rb
+++ b/spec/uat_actions/generate_plate_volumes_spec.rb
@@ -59,7 +59,7 @@
   end
 
   context 'with invalid options' do
-    let(:parameters) { {plate_barcode: plate_barcode, minimum_volume: 110, maximum_volume: 10 } }
+    let(:parameters) { { plate_barcode: plate_barcode, minimum_volume: 110, maximum_volume: 10 } }
     let!(:saved_action) { uat_action.save }
 
     it 'has a minimum_volume of 110' do

From 9c82b866e11f196bde1f9fe64764cf0b15a22d78 Mon Sep 17 00:00:00 2001
From: Stephen Hulme <sh51@sanger.ac.uk>
Date: Tue, 3 Dec 2024 15:53:28 +0000
Subject: [PATCH 07/40] fix: allow maximum to equal minimum

---
 app/uat_actions/uat_actions/generate_plate_volumes.rb | 8 ++++----
 spec/uat_actions/generate_plate_volumes_spec.rb       | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/app/uat_actions/uat_actions/generate_plate_volumes.rb b/app/uat_actions/uat_actions/generate_plate_volumes.rb
index c316881cf0..0afd4cacb9 100644
--- a/app/uat_actions/uat_actions/generate_plate_volumes.rb
+++ b/app/uat_actions/uat_actions/generate_plate_volumes.rb
@@ -39,7 +39,7 @@ def self.default
   validates :plate_barcode, presence: { message: 'could not be found' }
   validates :minimum_volume, numericality: { only_integer: false }
   validates :maximum_volume, numericality: { greater_than: 0, only_integer: false }
-  validate :maximum_greater_than_minimum
+  validate :maximum_greater_than_or_equal_to_minimum
 
   def perform
     qc_assay_results = construct_qc_assay
@@ -49,10 +49,10 @@ def perform
 
   private
 
-  def maximum_greater_than_minimum
-    return true if max_vol > min_vol
+  def maximum_greater_than_or_equal_to_minimum
+    return true if max_vol >= min_vol
 
-    errors.add(:maximum_volume, 'needs to be greater than minimum volume')
+    errors.add(:maximum_volume, 'needs to be greater than or equal to minimum volume')
     false
   end
 
diff --git a/spec/uat_actions/generate_plate_volumes_spec.rb b/spec/uat_actions/generate_plate_volumes_spec.rb
index e655213412..794fefafcb 100644
--- a/spec/uat_actions/generate_plate_volumes_spec.rb
+++ b/spec/uat_actions/generate_plate_volumes_spec.rb
@@ -79,7 +79,7 @@
     end
 
     it 'adds an error' do
-      expect(uat_action.errors.full_messages).to include('Maximum volume needs to be greater than minimum volume')
+      expect(uat_action.errors.full_messages).to include('Maximum volume needs to be greater than or equal to minimum volume')
     end
   end
 end

From 91b78f328d9ce2a432aedf3e24924034634bb392 Mon Sep 17 00:00:00 2001
From: Stephen Hulme <sh51@sanger.ac.uk>
Date: Tue, 3 Dec 2024 17:01:33 +0000
Subject: [PATCH 08/40] fix: allow maximum to equal minimum (concentrations)

---
 .../uat_actions/generate_plate_concentrations.rb          | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/app/uat_actions/uat_actions/generate_plate_concentrations.rb b/app/uat_actions/uat_actions/generate_plate_concentrations.rb
index ac97aacb5a..aaf04ab299 100644
--- a/app/uat_actions/uat_actions/generate_plate_concentrations.rb
+++ b/app/uat_actions/uat_actions/generate_plate_concentrations.rb
@@ -48,7 +48,7 @@ def self.default
   validates :concentration_units, presence: { message: 'needs a choice' }
   validates :minimum_concentration, numericality: { only_integer: false }
   validates :maximum_concentration, numericality: { greater_than: 0, only_integer: false }
-  validate :maximum_greater_than_minimum
+  validate :maximum_greater_than_or_equal_to_minimum
 
   def perform
     qc_assay_results = construct_qc_assay
@@ -58,10 +58,10 @@ def perform
 
   private
 
-  def maximum_greater_than_minimum
-    return true if max_conc > min_conc
+  def maximum_greater_than_or_equal_to_minimum
+    return true if max_conc >= min_conc
 
-    errors.add(:maximum_concentration, 'needs to be greater than minimum concentration')
+    errors.add(:maximum_concentration, 'needs to be greater than or equal to minimum concentration')
     false
   end
 

From a2acfb96a1c46c446381e11c468fef2d5ee9e012 Mon Sep 17 00:00:00 2001
From: Stephen Hulme <sh51@sanger.ac.uk>
Date: Tue, 3 Dec 2024 17:02:34 +0000
Subject: [PATCH 09/40] style: lint

---
 spec/uat_actions/generate_plate_volumes_spec.rb | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/spec/uat_actions/generate_plate_volumes_spec.rb b/spec/uat_actions/generate_plate_volumes_spec.rb
index 794fefafcb..ed51fb389a 100644
--- a/spec/uat_actions/generate_plate_volumes_spec.rb
+++ b/spec/uat_actions/generate_plate_volumes_spec.rb
@@ -79,7 +79,9 @@
     end
 
     it 'adds an error' do
-      expect(uat_action.errors.full_messages).to include('Maximum volume needs to be greater than or equal to minimum volume')
+      expect(uat_action.errors.full_messages).to include(
+        'Maximum volume needs to be greater than or equal to minimum volume'
+      )
     end
   end
 end

From 5b0a3ed3144bbf353fe0b2b2341fe91e4752ddba Mon Sep 17 00:00:00 2001
From: Stephen Hulme <sh51@sanger.ac.uk>
Date: Wed, 4 Dec 2024 10:05:48 +0000
Subject: [PATCH 10/40] tests: add more

---
 .../generate_plate_concentrations_spec.rb     | 61 +++++++++++++++++++
 .../generate_plate_volumes_spec.rb            | 20 ++++++
 2 files changed, 81 insertions(+)

diff --git a/spec/uat_actions/generate_plate_concentrations_spec.rb b/spec/uat_actions/generate_plate_concentrations_spec.rb
index 0c15ece3cb..549fab29d1 100644
--- a/spec/uat_actions/generate_plate_concentrations_spec.rb
+++ b/spec/uat_actions/generate_plate_concentrations_spec.rb
@@ -49,6 +49,67 @@
     end
   end
 
+  context 'with invalid options' do
+    let(:parameters) do
+      {
+        plate_barcode: plate_barcode,
+        concentration_units: 'ng/ul',
+        minimum_concentration: 30,
+        maximum_concentration: 10
+      }
+    end
+    let!(:saved_action) { uat_action.save }
+
+    it 'has a minimum_concentration of 30' do
+      expect(uat_action.minimum_concentration).to eq 30
+    end
+
+    it 'has a maximum_concentration of 10' do
+      expect(uat_action.maximum_concentration).to eq 10
+    end
+
+    it 'is invalid' do
+      expect(uat_action.valid?).to be false
+    end
+
+    it 'can not be saved' do
+      expect(saved_action).to be false
+    end
+
+    it 'adds an error' do
+      expect(uat_action.errors.full_messages).to include(
+        'Maximum concentration needs to be greater than or equal to minimum concentration'
+      )
+    end
+  end
+
+  context 'with equal minimum and maximum concentrations' do
+    let(:parameters) do
+      {
+        plate_barcode: plate_barcode,
+        concentration_units: 'ng/ul',
+        minimum_concentration: 10,
+        maximum_concentration: 10
+      }
+    end
+
+    it 'can be performed' do
+      expect(performed_action).to be true
+    end
+
+    it 'generates the correct report' do
+      expect(uat_action.report).to eq('number_weil_concentrations_written' => 3)
+    end
+
+    it 'creates the correct number of QC results' do
+      expect(plate.wells.map(&:qc_results).size).to eq 3
+    end
+
+    it 'sets the concentrations to be within the specified range' do
+      expect(plate.wells.map { |well| well.qc_results.first.value.to_f }).to all(eq 10)
+    end
+  end
+
   it 'returns a default' do
     expect(described_class.default).to be_a described_class
   end
diff --git a/spec/uat_actions/generate_plate_volumes_spec.rb b/spec/uat_actions/generate_plate_volumes_spec.rb
index ed51fb389a..c169b8d01f 100644
--- a/spec/uat_actions/generate_plate_volumes_spec.rb
+++ b/spec/uat_actions/generate_plate_volumes_spec.rb
@@ -84,4 +84,24 @@
       )
     end
   end
+
+  context 'with equal minimum and maximum volumes' do
+    let(:parameters) { { plate_barcode: plate_barcode, minimum_volume: 10, maximum_volume: 10 } }
+
+    it 'can be performed' do
+      expect(performed_action).to be true
+    end
+
+    it 'generates the correct report' do
+      expect(uat_action.report).to eq('number_well_volumes_written' => 3)
+    end
+
+    it 'creates the correct number of QC results' do
+      expect(plate.wells.map(&:qc_results).size).to eq 3
+    end
+
+    it 'sets the volumes to be within the specified range' do
+      expect(plate.wells.map { |well| well.qc_results.first.value.to_f }).to all(eq 10)
+    end
+  end
 end

From d45119c713f6c9b32ba231b5ae29b9c85451beb4 Mon Sep 17 00:00:00 2001
From: Stephen Hulme <sh51@sanger.ac.uk>
Date: Wed, 4 Dec 2024 10:47:55 +0000
Subject: [PATCH 11/40] tests: repair broken tests

---
 .../generate_plate_concentrations_spec.rb     | 59 ++++++++++++-------
 1 file changed, 38 insertions(+), 21 deletions(-)

diff --git a/spec/uat_actions/generate_plate_concentrations_spec.rb b/spec/uat_actions/generate_plate_concentrations_spec.rb
index 549fab29d1..ed1bb8d8c4 100644
--- a/spec/uat_actions/generate_plate_concentrations_spec.rb
+++ b/spec/uat_actions/generate_plate_concentrations_spec.rb
@@ -3,9 +3,36 @@
 require 'rails_helper'
 
 describe UatActions::GeneratePlateConcentrations do
+  let(:plate) { create(:plate_with_untagged_wells, sample_count: 3) }
+  let(:plate_barcode) { plate.barcodes.first.barcode }
+  let(:uat_action) { described_class.new(parameters) }
+  let!(:saved_action) { uat_action.save }
+
+  context 'with default options' do
+    let(:parameters) { {} }
+
+    it 'returns a default' do
+      expect(described_class.default).to be_a described_class
+    end
+
+    it 'has a nil plate_barcode' do
+      expect(described_class.default.plate_barcode).to be_nil
+    end
+
+    it 'has a minimum_concentration of 0' do
+      expect(described_class.default.minimum_concentration).to eq 0
+    end
+
+    it 'has a maximum_concentration of 100' do
+      expect(described_class.default.maximum_concentration).to eq 100
+    end
+
+    it 'has a concentration_units of ng/ul' do
+      expect(described_class.default.concentration_units).to eq 'ng/ul'
+    end
+  end
+
   context 'with valid options' do
-    let(:plate) { create(:plate_with_untagged_wells, sample_count: 3) }
-    let(:uat_action) { described_class.new(parameters) }
     let(:report) do
       # A report is a hash of key value pairs which get returned to the user.
       # It should include information such as barcodes and identifiers
@@ -15,15 +42,15 @@
     context 'when ng per ul concentrations' do
       let(:parameters) do
         {
-          plate_barcode: plate.barcodes.first.barcode,
+          plate_barcode: plate_barcode,
           concentration_units: 'ng/ul',
           minimum_concentration: 0,
           maximum_concentration: 30
         }
       end
 
-      it 'can be performed' do
-        expect(uat_action.perform).to be true
+      it 'can be saved' do
+        expect(saved_action).to be true
         expect(uat_action.report).to eq report
         expect(plate.wells.map(&:qc_results).size).to eq 3
         expect(plate.wells.first.qc_results.first.assay_type).to eq 'UAT_Testing'
@@ -32,16 +59,11 @@
 
     context 'when nM concentrations' do
       let(:parameters) do
-        {
-          plate_barcode: plate.barcodes.first.barcode,
-          concentration_units: 'nM',
-          minimum_concentration: 0,
-          maximum_concentration: 30
-        }
+        { plate_barcode: plate_barcode, concentration_units: 'nM', minimum_concentration: 0, maximum_concentration: 30 }
       end
 
-      it 'can be performed' do
-        expect(uat_action.perform).to be true
+      it 'can be saved' do
+        expect(saved_action).to be true
         expect(uat_action.report).to eq report
         expect(plate.wells.map(&:qc_results).size).to eq 3
         expect(plate.wells.first.qc_results.first.assay_type).to eq 'UAT_Testing'
@@ -58,7 +80,6 @@
         maximum_concentration: 10
       }
     end
-    let!(:saved_action) { uat_action.save }
 
     it 'has a minimum_concentration of 30' do
       expect(uat_action.minimum_concentration).to eq 30
@@ -93,12 +114,12 @@
       }
     end
 
-    it 'can be performed' do
-      expect(performed_action).to be true
+    it 'can be saved' do
+      expect(saved_action).to be true
     end
 
     it 'generates the correct report' do
-      expect(uat_action.report).to eq('number_weil_concentrations_written' => 3)
+      expect(uat_action.report).to eq('number_well_concentrations_written' => 3)
     end
 
     it 'creates the correct number of QC results' do
@@ -109,8 +130,4 @@
       expect(plate.wells.map { |well| well.qc_results.first.value.to_f }).to all(eq 10)
     end
   end
-
-  it 'returns a default' do
-    expect(described_class.default).to be_a described_class
-  end
 end

From d2a1e636cbe3cdb1e70ffab674b03f94024bd7d9 Mon Sep 17 00:00:00 2001
From: Stuart McHattie <sm49@sanger.ac.uk>
Date: Wed, 4 Dec 2024 12:18:04 +0000
Subject: [PATCH 12/40] Add TODO for removal of order_template.rb

---
 app/models/order_template.rb | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/app/models/order_template.rb b/app/models/order_template.rb
index 17d4c6d0d4..215acc3a1d 100644
--- a/app/models/order_template.rb
+++ b/app/models/order_template.rb
@@ -3,3 +3,6 @@
 # If we remove this, then we break our API endpoints. Some of which, at least at one point, actually had
 # external users.
 OrderTemplate = SubmissionTemplate
+
+# TODO: {API v1 removal} this alias was created for v1 and should not be in v2. When v1 is removed, we should try
+#       to remove this alias as well.

From 2e73bc6029ed76459c6d502bb1df2d0162af875f Mon Sep 17 00:00:00 2001
From: Stephen Hulme <sh51@sanger.ac.uk>
Date: Thu, 5 Dec 2024 11:33:49 +0000
Subject: [PATCH 13/40] fix: specify what b and v stand for

---
 app/views/batches/_cherrypick_single_worksheet.html.erb | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/app/views/batches/_cherrypick_single_worksheet.html.erb b/app/views/batches/_cherrypick_single_worksheet.html.erb
index 91e04b260e..4075619fde 100644
--- a/app/views/batches/_cherrypick_single_worksheet.html.erb
+++ b/app/views/batches/_cherrypick_single_worksheet.html.erb
@@ -92,6 +92,7 @@
 </div>
 
 <div id="footer">
-  Created: <%= batch.updated_at.strftime("%I:%M %p on %A %d %B, %Y") %> for <%= batch.user.login %> -
+  v = receptacle volume; b = buffer volume<br>
+  Created: <%= batch.updated_at.strftime("%I:%M %p on %A %d %B, %Y") %> for <%= batch.user.login %><br>
   Printed: <%= Time.now.strftime("%I:%M %p on %A %d %B, %Y") %> for <%= current_user.login %>
 </div>

From b99815b72dc6e2e9b35efe396658073ab2a1c1bc Mon Sep 17 00:00:00 2001
From: Stuart McHattie <sm49@sanger.ac.uk>
Date: Thu, 5 Dec 2024 12:11:36 +0000
Subject: [PATCH 14/40] Move the overridden method to the top of
 TagLayoutProcessor

---
 .../api/v2/tag_layouts_controller.rb          | 46 ++++++++++---------
 1 file changed, 24 insertions(+), 22 deletions(-)

diff --git a/app/controllers/api/v2/tag_layouts_controller.rb b/app/controllers/api/v2/tag_layouts_controller.rb
index bc2472640e..d3330aea1f 100644
--- a/app/controllers/api/v2/tag_layouts_controller.rb
+++ b/app/controllers/api/v2/tag_layouts_controller.rb
@@ -10,6 +10,30 @@ class TagLayoutsController < JSONAPI::ResourceController
     end
 
     class TagLayoutProcessor < JSONAPI::Processor
+      # Override the default behaviour for a JSONAPI::Processor when creating a new resource.
+      # We need to check whether a template UUID was given, and, if so, copy its data into this
+      # new TagLayoutResource. The creation will be prevented if any data from the template is also
+      # included in the create request as additional values. e.g. a request has a template UUID and
+      # also specifies a direction or a tag_group. In this case, the error will indicate that the
+      # template UUID was not an allowed attribute.
+      def create_resource
+        errors = []
+        template = find_template { |new_errors| errors += new_errors }
+        merge_template_data(template) { |new_errors| errors += new_errors } unless template.nil?
+
+        return JSONAPI::ErrorsOperationResult.new(JSONAPI::BAD_REQUEST, errors) unless errors.empty?
+
+        # Perform the usual create actions.
+        resource = TagLayoutResource.create(context)
+        result = resource.replace_fields(params[:data])
+
+        record_template_use(template, resource)
+
+        JSONAPI::ResourceOperationResult.new((result == :completed ? :created : :accepted), resource)
+      end
+
+      private
+
       def find_template
         template_uuid = params[:data][:attributes][:tag_layout_template_uuid]
         return nil if template_uuid.nil? # No errors -- we just don't have a template.
@@ -72,28 +96,6 @@ def enforce_uniqueness?
       def record_template_use(template, resource)
         template&.record_template_use(TagLayout.find(resource.id).plate, enforce_uniqueness?)
       end
-
-      # Override the default behaviour for a JSONAPI::Processor when creating a new resource.
-      # We need to check whether a template UUID was given, and, if so, copy its data into this
-      # new TagLayoutResource. The creation will be prevented if any data from the template is also
-      # included in the create request as additional values. e.g. a request has a template UUID and
-      # also specifies a direction or a tag_group. In this case, the error will indicate that the
-      # template UUID was not an allowed attribute.
-      def create_resource
-        errors = []
-        template = find_template { |new_errors| errors += new_errors }
-        merge_template_data(template) { |new_errors| errors += new_errors } unless template.nil?
-
-        return JSONAPI::ErrorsOperationResult.new(JSONAPI::BAD_REQUEST, errors) unless errors.empty?
-
-        # Perform the usual create actions.
-        resource = TagLayoutResource.create(context)
-        result = resource.replace_fields(params[:data])
-
-        record_template_use(template, resource)
-
-        JSONAPI::ResourceOperationResult.new((result == :completed ? :created : :accepted), resource)
-      end
     end
   end
 end

From 6abc012e4b8ab53f381f9dcb4e79bb3e3848b30f Mon Sep 17 00:00:00 2001
From: Stuart McHattie <sm49@sanger.ac.uk>
Date: Thu, 5 Dec 2024 14:39:01 +0000
Subject: [PATCH 15/40] Make OrderResource work

Particularly when it comes to creating new Orders from a SubmissionTemplate
---
 app/controllers/api/v2/orders_controller.rb |  98 +++++++++++++++
 app/resources/api/v2/base_resource.rb       |   1 +
 app/resources/api/v2/order_resource.rb      | 127 +++++++++++++++++---
 config/routes.rb                            |   2 +-
 4 files changed, 212 insertions(+), 16 deletions(-)

diff --git a/app/controllers/api/v2/orders_controller.rb b/app/controllers/api/v2/orders_controller.rb
index 63a1e71e45..07b871d200 100644
--- a/app/controllers/api/v2/orders_controller.rb
+++ b/app/controllers/api/v2/orders_controller.rb
@@ -8,5 +8,103 @@ class OrdersController < JSONAPI::ResourceController
       # By default JSONAPI::ResourceController provides most the standard
       # behaviour, and in many cases this file may be left empty.
     end
+
+    class OrderProcessor < JSONAPI::Processor
+      # Override the default behaviour for a JSONAPI::Processor when creating a new resource.
+      # We need to check whether a template UUID was given, and, if so, use it to create the Order directly.
+      # Where no template is given, the Order will be created via the base JSONAPI::Processor.
+      def create_resource
+        errors = []
+        template = find_template { |new_errors| errors += new_errors }
+        attributes = template_attributes { |new_errors| errors += new_errors } unless template.nil?
+
+        return JSONAPI::ErrorsOperationResult.new(JSONAPI::BAD_REQUEST, errors) unless errors.empty?
+        return super if template.nil? # No template means we should use the default behaviour.
+
+        create_order_from_template(template, attributes)
+      end
+
+      private
+
+      def find_template
+        template_uuid = params[:data][:attributes][:submission_template_uuid]
+        return nil if template_uuid.nil? # No errors -- we just don't have a template.
+
+        template = SubmissionTemplate.with_uuid(template_uuid).first
+
+        if template.nil?
+          yield JSONAPI::Exceptions::InvalidFieldValue.new(:submission_template_uuid, template_uuid).errors
+        end
+
+        template
+      end
+
+      def template_attributes(&)
+        parameters = params[:data][:attributes][:submission_template_attributes]
+
+        if parameters.nil?
+          yield JSONAPI::Exceptions::ParameterMissing.new(:submission_template_attributes).errors
+          return
+        end
+
+        make_template_attributes(permitted_attributes(parameters), &)
+      end
+
+      def permitted_attributes(attributes)
+        attributes.permit(
+          { asset_uuids: [], request_options: {} },
+          :autodetect_projects,
+          :autodetect_studies,
+          :user_uuid
+        )
+      end
+
+      def make_template_attributes(attributes, &)
+        {}.tap do |result|
+          result[:assets] = extract_assets(attributes, &)
+          result[:autodetect_projects] = attributes[:autodetect_projects] unless attributes[:autodetect_projects].nil?
+          result[:autodetect_studies] = attributes[:autodetect_studies] unless attributes[:autodetect_studies].nil?
+          result[:request_options] = require_attribute(attributes, :request_options)
+          result[:user] = extract_user(attributes, &)
+        end
+      end
+
+      def extract_assets(attributes, &)
+        asset_uuids = require_attribute(attributes, :asset_uuids, &)
+        return nil if asset_uuids.nil?
+
+        asset_uuids.map do |uuid|
+          uuid = Uuid.find_by(external_id: uuid)
+          yield JSONAPI::Exceptions::InvalidFieldValue.new(:asset_uuids, uuid).errors if uuid.nil?
+          uuid&.resource
+        end
+      end
+
+      def extract_user(attributes, &)
+        user_uuid = require_attribute(attributes, :user_uuid, &)
+        return nil if user_uuid.nil?
+
+        user = User.with_uuid(user_uuid).first
+        yield JSONAPI::Exceptions::InvalidFieldValue.new(:user_uuid, user_uuid).errors if user.nil?
+        user
+      end
+
+      def require_attribute(attributes, key)
+        value = attributes.require(key)
+        value = value.to_h if value.instance_of?(ActionController::Parameters) && value.permitted?
+        value
+      rescue ActionController::ParameterMissing
+        yield JSONAPI::Exceptions::ParameterMissing.new("submission_template_attributes.#{key}").errors
+        nil
+      end
+
+      def create_order_from_template(template, attributes)
+        order = template.create_order!(attributes)
+        resource = OrderResource.new(order, context)
+        result = resource.replace_fields(params[:data])
+
+        JSONAPI::ResourceOperationResult.new((result == :completed ? :created : :accepted), resource)
+      end
+    end
   end
 end
diff --git a/app/resources/api/v2/base_resource.rb b/app/resources/api/v2/base_resource.rb
index 0a9dbd2495..a713b3dfaa 100644
--- a/app/resources/api/v2/base_resource.rb
+++ b/app/resources/api/v2/base_resource.rb
@@ -17,6 +17,7 @@ class BaseResource < JSONAPI::Resource
       abstract
 
       # Loaded on the base class so that they can be loaded globally.
+      Order.descendants.each { |subclass| model_hint model: subclass, resource: :order }
       Purpose.descendants.each { |subclass| model_hint model: subclass, resource: :purpose }
       Plate.descendants.each { |subclass| model_hint model: subclass, resource: :plate }
       Tube.descendants.each { |subclass| model_hint model: subclass, resource: :tube }
diff --git a/app/resources/api/v2/order_resource.rb b/app/resources/api/v2/order_resource.rb
index e06622ea27..9dbc55b8a0 100644
--- a/app/resources/api/v2/order_resource.rb
+++ b/app/resources/api/v2/order_resource.rb
@@ -2,37 +2,134 @@
 
 module Api
   module V2
-    # @todo This documentation does not yet include a detailed description of what this resource represents.
-    # @todo This documentation does not yet include detailed descriptions for relationships, attributes and filters.
-    # @todo This documentation does not yet include any example usage of the API via cURL or similar.
+    # Provides a JSON:API representation of {Order} which are used as the main means of requesting work.
+    # Creation of this resource via a `POST` request which must include a {#submission_template_uuid=} and a
+    # {#submission_template_attributes=} hash.
     #
-    # @note Access this resource via the `/api/v2/orders/` endpoint.
+    # @note This resource cannot be modified after creation: its endpoint will not accept `PATCH` requests.
+    # @note Access this resource via the `/api/v2/tube_from_tube_creations/` endpoint.
     #
-    # Provides a JSON:API representation of {Order}.
+    # @example POST request with child purpose and parent tube specified by UUID (deprecated)
+    #   POST /api/v2/tube_from_tube_creations/
+    #   {
+    #     "data": {
+    #       "type": "tube_from_tube_creations",
+    #       "attributes": {
+    #         "child_purpose_uuid": "11111111-2222-3333-4444-555555666666",
+    #         "parent_uuid": "33333333-4444-5555-6666-777777888888",
+    #         "user_uuid": "99999999-0000-1111-2222-333333444444"
+    #       }
+    #     }
+    #   }
+    #
+    # @example POST request with child purpose and parent tube specified by relationship
+    #   POST /api/v2/tube_from_tube_creations/
+    #   {
+    #     "data": {
+    #       "type": "tube_from_tube_creations",
+    #       "attributes": {},
+    #       "relationships": {
+    #         "child_purpose": {
+    #           "data": { "type": "tube_purposes", "id": "123" }
+    #         },
+    #         "parent": {
+    #           "data": { "type": "tubes", "id": "456" }
+    #         },
+    #         "user": {
+    #           "data": { "type": "users", "id": "789" }
+    #         }
+    #       }
+    #     }
+    #   }
+    #
+    # @example GET request for all TubeFromTubeCreation resources
+    #   GET /api/v2/tube_from_tube_creations/
+    #
+    # @example GET request for a TubeFromTubeCreation with ID 123
+    #   GET /api/v2/tube_from_tube_creations/123/
     #
     # For more information about JSON:API see the [JSON:API Specifications](https://jsonapi.org/format/)
     # or look at the [JSONAPI::Resources](http://jsonapi-resources.com/) package for Sequencescape's implementation
     # of the JSON:API standard.
     class OrderResource < BaseResource
-      # Constants...
+      ###
+      # Attributes
+      ###
 
-      # model_name / model_hint if required
+      # @!attribute [r] order_type
+      #   @return [String] the STI type of the {Order}.
+      attribute :order_type, delegate: :sti_type, readonly: true
 
-      default_includes :uuid_object
+      # @!attribute [r] request_options
+      #   @return [Hash] request options for the {Order}.
+      #   @note These can only be set once upon creation of the {Order}.
+      attribute :request_options, readonly: true
 
-      # Associations:
+      # @!attribute [r] request_types
+      #   @return [Array<Integer>] the IDs of types of request in this {Order}.
+      #   @note These can only be set once upon creation of the {Order}.
+      attribute :request_types, readonly: true
 
       # Attributes
+      # @!attribute [r] uuid
+      #   @return [String] the UUID for this {Order}.
       attribute :uuid, readonly: true
-      attribute :request_options, write_once: true
 
-      # Filters
+      ###
+      # Relationships
+      ###
+
+      # @!attribute [r] project
+      #   @return [ProjectResource] the project associated with this Order.
+      #   @note This can only be set once upon creation of the Order.
+      has_one :project, readonly: true
+
+      # @!attribute [r] study
+      #   @return [StudyResource] the study associated with this Order.
+      #   @note This can only be set once upon creation of the {Order}.
+      has_one :study, readonly: true
+
+      # @!attribute [r] user
+      #   @return [UserResource] the user who created this {Order}.
+      #   @note This can only be set once upon creation of the {Order}.
+      has_one :user, readonly: true
+
+      ###
+      # Template attributes
+      ###
+
+      # These are defined here to assist with the creation of Orders from SubmissionTemplates.
+      # The values given are not stored in the Order and will be consumed by the OrderProcessor.
+
+      # @!attribute [w] submission_template_uuid
+      #   The UUID of the {SubmissionTemplate} to use when creating this {Order}.
+      #   @note This is mandatory when creating new {Order}s via the API. It is not stored.
+      attribute :submission_template_uuid, writeonly: true
+
+      def submission_template_uuid=(value)
+        # Do nothing with this value as it's consumed by the OrderProcessor.
+      end
 
-      # Custom methods
-      # These shouldn't be used for business logic, and a more about
-      # I/O and isolating implementation details.
+      # @!attribute [w] submission_template_attributes
+      #   A hash of additional attributes to use when creating this {Order} from a given {SubmissionTemplate}.
+      #   The structure of this hash is as follows:
+      #
+      #   ```json
+      #   {
+      #     "asset_uuids": [String],
+      #     "autodetect_projects": Boolean,  // optional
+      #     "autodetect_studies": Boolean,   // optional
+      #     "request_options": Hash,
+      #     "user_uuid": String
+      #   }
+      #   ```
+      #
+      #   @note This is mandatory when creating new {Order}s via the API. It is not stored.
+      attribute :submission_template_attributes, writeonly: true
 
-      # Class method overrides
+      def submission_template_attributes=(value)
+        # Do nothing with this value as it's consumed by the OrderProcessor.
+      end
     end
   end
 end
diff --git a/config/routes.rb b/config/routes.rb
index 2be4715c9e..3a2223498c 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -34,7 +34,7 @@
       jsonapi_resources :lanes
       jsonapi_resources :lot_types
       jsonapi_resources :lots
-      jsonapi_resources :orders
+      jsonapi_resources :orders, except: %i[update]
       jsonapi_resources :pick_lists
       jsonapi_resources :plate_conversions, except: %i[update]
       jsonapi_resources :plate_creations, except: %i[update]

From dc4d9e2ce9d4242b3007799b7314c022dc2ae58c Mon Sep 17 00:00:00 2001
From: Stuart McHattie <sm49@sanger.ac.uk>
Date: Thu, 5 Dec 2024 15:02:58 +0000
Subject: [PATCH 16/40] Clean up code for creating the template attributes

---
 app/controllers/api/v2/orders_controller.rb | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/app/controllers/api/v2/orders_controller.rb b/app/controllers/api/v2/orders_controller.rb
index 07b871d200..f05d8347c8 100644
--- a/app/controllers/api/v2/orders_controller.rb
+++ b/app/controllers/api/v2/orders_controller.rb
@@ -60,13 +60,13 @@ def permitted_attributes(attributes)
       end
 
       def make_template_attributes(attributes, &)
-        {}.tap do |result|
-          result[:assets] = extract_assets(attributes, &)
-          result[:autodetect_projects] = attributes[:autodetect_projects] unless attributes[:autodetect_projects].nil?
-          result[:autodetect_studies] = attributes[:autodetect_studies] unless attributes[:autodetect_studies].nil?
-          result[:request_options] = require_attribute(attributes, :request_options)
-          result[:user] = extract_user(attributes, &)
-        end
+        {
+          assets: extract_assets(attributes, &),
+          autodetect_projects: attributes[:autodetect_projects],
+          autodetect_studies: attributes[:autodetect_studies],
+          request_options: require_attribute(attributes, :request_options),
+          user: extract_user(attributes, &)
+        }.compact
       end
 
       def extract_assets(attributes, &)

From 0e5e9c44e7d0088ca39a21784cff7339c4c4a272 Mon Sep 17 00:00:00 2001
From: Stuart McHattie <sm49@sanger.ac.uk>
Date: Mon, 9 Dec 2024 15:25:26 +0000
Subject: [PATCH 17/40] Add tests for orders

There are more to add, but this is WIP
---
 spec/factories/submission_factories.rb        |  11 +-
 .../patient_consent_withdrawl_spec.rb         |   2 +-
 spec/requests/api/v2/orders_spec.rb           | 420 ++++++++++++++++--
 spec/resources/api/v2/order_resource_spec.rb  |  35 +-
 4 files changed, 417 insertions(+), 51 deletions(-)

diff --git a/spec/factories/submission_factories.rb b/spec/factories/submission_factories.rb
index dfb79715f1..62d56d9dcb 100644
--- a/spec/factories/submission_factories.rb
+++ b/spec/factories/submission_factories.rb
@@ -12,13 +12,20 @@
 
   factory :submission_template do
     transient do
-      request_type_ids_list { request_types.map { |rt| [rt.id] } }
+      project { nil }
+      study { nil }
       request_types { [] }
     end
 
     submission_class_name { LinearSubmission.name }
     sequence(:name) { |i| "Template #{i}" }
-    submission_parameters { { request_type_ids_list: } }
+    submission_parameters do
+      {
+        request_type_ids_list: request_types.map { |rt| [rt.id] },
+        project_id: project&.id,
+        study_id: study&.id
+      }.compact
+    end
     product_catalogue { |pc| pc.association(:single_product_catalogue) }
 
     factory :cherrypick_submission_template do
diff --git a/spec/features/patient_consent_withdrawl_spec.rb b/spec/features/patient_consent_withdrawl_spec.rb
index 027e1eebf6..ee860f1931 100644
--- a/spec/features/patient_consent_withdrawl_spec.rb
+++ b/spec/features/patient_consent_withdrawl_spec.rb
@@ -55,7 +55,7 @@
     context 'an order' do
       # Lifted straight from the feature test with minimal rspecification
       # and optimization
-      let(:submission_template) { create(:submission_template, request_type_ids_list: [[create(:request_type).id]]) }
+      let(:submission_template) { create(:submission_template, request_types: [create(:request_type)]) }
       let(:sample_tube) { create(:sample_tube, sample:) }
       let(:asset_group) { create(:asset_group, assets: [sample_tube.receptacle]) }
 
diff --git a/spec/requests/api/v2/orders_spec.rb b/spec/requests/api/v2/orders_spec.rb
index 0faeec1378..c34a23116b 100644
--- a/spec/requests/api/v2/orders_spec.rb
+++ b/spec/requests/api/v2/orders_spec.rb
@@ -2,56 +2,416 @@
 
 require 'rails_helper'
 require './spec/requests/api/v2/shared_examples/api_key_authenticatable'
+require './spec/requests/api/v2/shared_examples/requests'
 
 describe 'Orders API', with: :api_v2 do
-  let(:base_endpoint) { '/api/v2/orders' }
+  let(:model_class) { Order }
+  let(:base_endpoint) { "/api/v2/#{resource_type}" }
+  let(:resource_type) { model_class.name.demodulize.pluralize.underscore }
 
   it_behaves_like 'ApiKeyAuthenticatable'
 
-  context 'with multiple orders' do
-    before { create_list(:order, 5) }
+  context 'with a list of resources' do
+    let(:resource_count) { 5 }
 
-    it 'sends a list of orders' do
-      api_get base_endpoint
+    before { create_list(:order, resource_count) }
 
-      # test for the 200 status-code
-      expect(response).to have_http_status(:success)
+    describe '#GET all resources' do
+      before { api_get base_endpoint }
 
-      # check to make sure the right amount of messages are returned
-      expect(json['data'].length).to eq(5)
+      it 'responds with a success http code' do
+        expect(response).to have_http_status(:success)
+      end
+
+      it 'returns all the resources' do
+        expect(json['data'].length).to eq(resource_count)
+      end
     end
+  end
+
+  context 'with a single resource' do
+    describe '#GET resource by ID' do
+      let(:resource) { create(:order) }
+
+      context 'without included relationships' do
+        before { api_get "#{base_endpoint}/#{resource.id}" }
+
+        it 'responds with a success http code' do
+          expect(response).to have_http_status(:success)
+        end
+
+        it 'returns the resource with the correct id' do
+          expect(json.dig('data', 'id')).to eq(resource.id.to_s)
+        end
+
+        it 'returns the resource with the correct type' do
+          expect(json.dig('data', 'type')).to eq(resource_type)
+        end
+
+        it 'returns the correct value for the order_type attributes' do
+          expect(json.dig('data', 'attributes', 'order_type')).to eq(resource.sti_type)
+        end
+
+        it 'returns the correct value for the request_options attributes' do
+          expect(json.dig('data', 'attributes', 'request_options')).to eq(resource.request_options)
+        end
+
+        it 'returns the correct value for the request_types attributes' do
+          expect(json.dig('data', 'attributes', 'request_types')).to eq(resource.request_types)
+        end
 
-    # Check filters, ESPECIALLY if they aren't simple attribute filters
+        it 'returns the correct value for the uuid attributes' do
+          expect(json.dig('data', 'attributes', 'uuid')).to eq(resource.uuid)
+        end
+
+        it 'excludes the unfetchable submission_template_uuid' do
+          expect(json.dig('data', 'attributes', 'submission_template_uuid')).not_to be_present
+        end
+
+        it 'excludes the unfetchable submission_template_attributes' do
+          expect(json.dig('data', 'attributes', 'submission_template_attributes')).not_to be_present
+        end
+
+        it 'returns a reference to the project relationship' do
+          expect(json.dig('data', 'relationships', 'project')).to be_present
+        end
+
+        it 'returns a reference to the study relationship' do
+          expect(json.dig('data', 'relationships', 'study')).to be_present
+        end
+
+        it 'returns a reference to the user relationship' do
+          expect(json.dig('data', 'relationships', 'user')).to be_present
+        end
+
+        it 'does not include attributes for related resources' do
+          expect(json['included']).not_to be_present
+        end
+      end
+
+      context 'with included relationships' do
+        it_behaves_like 'a GET request including a has_one relationship', 'project'
+        it_behaves_like 'a GET request including a has_one relationship', 'study'
+        it_behaves_like 'a GET request including a has_one relationship', 'user'
+      end
+    end
   end
 
-  context 'with a order' do
+  describe '#PATCH a resource' do
     let(:resource_model) { create(:order) }
-
+    let(:purpose) { create(:tube_purpose) }
     let(:payload) do
-      {
-        'data' => {
-          'id' => resource_model.id,
-          'type' => 'orders',
-          'attributes' => {
-            # Set new attributes
+      { data: { id: resource_model.id, type: resource_type, attributes: { child_purpose_uuid: [purpose.uuid] } } }
+    end
+
+    it 'finds no route for the method' do
+      expect { api_patch "#{base_endpoint}/#{resource_model.id}", payload }.to raise_error(
+        ActionController::RoutingError
+      )
+    end
+  end
+
+  describe '#POST a create request' do
+    let(:project) { create(:project) }
+    let(:study) { create(:study) }
+    let(:request_types) { create_list(:request_type, 1, asset_type: 'Well') }
+    let(:template) { create(:submission_template, request_types:, project:, study:) }
+    let(:assets) { create(:plate_with_tagged_wells).wells[0..2] }
+    let(:user) { create(:user) }
+
+    context 'with a valid payload' do
+      shared_examples 'a valid request' do
+        before { api_post base_endpoint, payload }
+
+        it 'creates a new resource' do
+          expect { api_post base_endpoint, payload }.to change(model_class, :count).by(1)
+        end
+
+        it 'responds with success' do
+          expect(response).to have_http_status(:success)
+        end
+
+        it 'returns the resource with the correct type' do
+          expect(json.dig('data', 'type')).to eq(resource_type)
+        end
+
+        it 'returns the correct value for the order_type attributes' do
+          new_record = model_class.last
+          expect(json.dig('data', 'attributes', 'order_type')).to eq(new_record.sti_type)
+        end
+
+        it 'returns the correct value for the request_options attributes' do
+          new_record = model_class.last
+          expect(json.dig('data', 'attributes', 'request_options')).to eq(new_record.request_options)
+        end
+
+        it 'returns the correct value for the request_types attributes' do
+          new_record = model_class.last
+          expect(json.dig('data', 'attributes', 'request_types')).to eq(new_record.request_types)
+        end
+
+        it 'returns the correct value for the uuid attributes' do
+          new_record = model_class.last
+          expect(json.dig('data', 'attributes', 'uuid')).to eq(new_record.uuid)
+        end
+
+        it 'excludes the unfetchable submission_template_uuid' do
+          expect(json.dig('data', 'attributes', 'submission_template_uuid')).not_to be_present
+        end
+
+        it 'excludes the unfetchable submission_template_attributes' do
+          expect(json.dig('data', 'attributes', 'submission_template_attributes')).not_to be_present
+        end
+
+        it 'returns a reference to the project relationship' do
+          expect(json.dig('data', 'relationships', 'project')).to be_present
+        end
+
+        it 'returns a reference to the study relationship' do
+          expect(json.dig('data', 'relationships', 'study')).to be_present
+        end
+
+        it 'returns a reference to the user relationship' do
+          expect(json.dig('data', 'relationships', 'user')).to be_present
+        end
+
+        it "associates the template's project with the new record" do
+          new_record = model_class.last
+          expect(new_record.project).to eq(project)
+        end
+
+        it "associates the template's study with the new record" do
+          new_record = model_class.last
+          expect(new_record.study).to eq(study)
+        end
+
+        it 'associates the user with the new record' do
+          new_record = model_class.last
+          expect(new_record.user).to eq(user)
+        end
+      end
+
+      context 'with complete attributes' do
+        let(:payload) do
+          {
+            data: {
+              type: resource_type,
+              attributes: {
+                submission_template_uuid: template.uuid,
+                submission_template_attributes: {
+                  asset_uuids: assets.map(&:uuid),
+                  autodetect_projects: false,
+                  autodetect_studies: false,
+                  request_options: {
+                    library_type: 'Chromium single cell 3 prime v3',
+                    fragment_size_required_from: '200',
+                    fragment_size_required_to: '800'
+                  },
+                  user_uuid: user.uuid
+                }
+              }
+            }
+          }
+        end
+
+        it_behaves_like 'a valid request'
+      end
+
+      context 'with minimal attributes' do
+        let(:payload) do
+          {
+            data: {
+              type: resource_type,
+              attributes: {
+                submission_template_uuid: template.uuid,
+                submission_template_attributes: {
+                  asset_uuids: assets.map(&:uuid),
+                  request_options: {
+                    no_options: true
+                  },
+                  user_uuid: user.uuid
+                }
+              }
+            }
+          }
+        end
+
+        it_behaves_like 'a valid request'
+      end
+    end
+
+    describe 'with the project specified by the template' do
+      let(:template) { create(:submission_template, request_types:, project:, study:) }
+      let(:autodetect_projects) { false }
+      let(:payload) do
+        {
+          data: {
+            type: resource_type,
+            attributes: {
+              submission_template_uuid: template.uuid,
+              submission_template_attributes: {
+                asset_uuids: assets.map(&:uuid),
+                autodetect_projects: autodetect_projects,
+                request_options: {
+                  no_options: true
+                },
+                user_uuid: user.uuid
+              }
+            }
+          }
+        }
+      end
+
+      before { api_post base_endpoint, payload }
+
+      context 'when autocomplete is false' do
+        let(:autodetect_projects) { false }
+
+        it "associates the template's project with the new record" do
+          new_record = model_class.last
+          expect(new_record.project).to eq(project)
+        end
+      end
+
+      context 'when autocomplete is true' do
+        let(:autodetect_projects) { true }
+
+        it "associates the template's project with the new record" do
+          new_record = model_class.last
+          expect(new_record.project).to eq(project)
+        end
+      end
+    end
+
+    describe 'without the project specified by the template' do
+      let(:template) { create(:submission_template, request_types:, study:) }
+      let(:autodetect_projects) { false }
+      let(:payload) do
+        {
+          data: {
+            type: resource_type,
+            attributes: {
+              submission_template_uuid: template.uuid,
+              submission_template_attributes: {
+                asset_uuids: assets.map(&:uuid),
+                autodetect_projects: autodetect_projects,
+                request_options: {
+                  no_options: true
+                },
+                user_uuid: user.uuid
+              }
+            }
           }
         }
-      }
+      end
+
+      before { api_post base_endpoint, payload }
+
+      context 'when autocomplete is false' do
+        let(:autodetect_projects) { false }
+
+        it 'fails validation on the model' do
+          # Not ideal, but we haven't implemented handling of validation errors for Order from the model via this
+          # processor.
+          expect(json.dig('errors', 0, 'meta', 'exception')).to include("Project can't be blank")
+        end
+      end
+
+      context 'when autocomplete is true' do
+        let(:autodetect_projects) { true }
+
+        it 'associates the unique project from assets with the new record' do
+          new_record = model_class.last
+          expect(new_record.project).to eq(assets.first.projects.first)
+        end
+      end
     end
 
-    it 'sends an individual order' do
-      api_get "#{base_endpoint}/#{resource_model.id}"
-      expect(response).to have_http_status(:success)
-      expect(json.dig('data', 'type')).to eq('orders')
+    describe 'with the study specified by the template' do
+      let(:template) { create(:submission_template, request_types:, project:, study:) }
+      let(:autodetect_studies) { false }
+      let(:payload) do
+        {
+          data: {
+            type: resource_type,
+            attributes: {
+              submission_template_uuid: template.uuid,
+              submission_template_attributes: {
+                asset_uuids: assets.map(&:uuid),
+                autodetect_studies: autodetect_studies,
+                request_options: {
+                  no_options: true
+                },
+                user_uuid: user.uuid
+              }
+            }
+          }
+        }
+      end
+
+      before { api_post base_endpoint, payload }
+
+      context 'when autocomplete is false' do
+        let(:autodetect_studies) { false }
+
+        it "associates the template's study with the new record" do
+          new_record = model_class.last
+          expect(new_record.study).to eq(study)
+        end
+      end
+
+      context 'when autocomplete is true' do
+        let(:autodetect_studies) { true }
+
+        it "associates the template's study with the new record" do
+          new_record = model_class.last
+          expect(new_record.study).to eq(study)
+        end
+      end
     end
 
-    # Remove if immutable
-    it 'allows update of a order' do
-      api_patch "#{base_endpoint}/#{resource_model.id}", payload
-      expect(response).to have_http_status(:success)
-      expect(json.dig('data', 'type')).to eq('orders')
-      # Double check at least one of the attributes
-      # eg. expect(json.dig('data', 'attributes', 'state')).to eq('started')
+    describe 'without the study specified by the template' do
+      let(:template) { create(:submission_template, request_types:, project:) }
+      let(:autodetect_studies) { false }
+      let(:payload) do
+        {
+          data: {
+            type: resource_type,
+            attributes: {
+              submission_template_uuid: template.uuid,
+              submission_template_attributes: {
+                asset_uuids: assets.map(&:uuid),
+                autodetect_studies: autodetect_studies,
+                request_options: {
+                  no_options: true
+                },
+                user_uuid: user.uuid
+              }
+            }
+          }
+        }
+      end
+
+      before { api_post base_endpoint, payload }
+
+      context 'when autocomplete is false' do
+        let(:autodetect_studies) { false }
+
+        it 'fails validation on the model' do
+          # Not ideal, but we haven't implemented handling of validation errors for Order from the model via this
+          # processor.
+          expect(json.dig('errors', 0, 'meta', 'exception')).to include("Study can't be blank")
+        end
+      end
+
+      context 'when autocomplete is true' do
+        let(:autodetect_studies) { true }
+
+        it 'associates the unique study from assets with the new record' do
+          new_record = model_class.last
+          expect(new_record.study).to eq(assets.first.studies.first)
+        end
+      end
     end
   end
 end
diff --git a/spec/resources/api/v2/order_resource_spec.rb b/spec/resources/api/v2/order_resource_spec.rb
index 43f815ae86..d0334541fa 100644
--- a/spec/resources/api/v2/order_resource_spec.rb
+++ b/spec/resources/api/v2/order_resource_spec.rb
@@ -8,22 +8,21 @@
 
   let(:resource_model) { build_stubbed(:order) }
 
-  # Test attributes
-  it 'works', :aggregate_failures do # rubocop:todo RSpec/ExampleWording
-    expect(resource).to have_attribute :uuid
-    expect(resource).not_to have_updatable_field(:id)
-    expect(resource).not_to have_updatable_field(:uuid)
-  end
-
-  # Updatable fields
-  # eg. it { is_expected.to have_updatable_field(:state) }
-
-  # Filters
-  # eg. it { is_expected.to filter(:order_type) }
-
-  # Associations
-  # eg. it { is_expected.to have_many(:samples).with_class_name('Sample') }
-
-  # Custom method tests
-  # Add tests for any custom methods you've added.
+  # Model Name
+  it { is_expected.to have_model_name 'Order' }
+
+  # Attributes
+  it { is_expected.to have_readonly_attribute :order_type }
+  it { is_expected.to have_readonly_attribute :request_options }
+  it { is_expected.to have_readonly_attribute :request_types }
+  it { is_expected.to have_readonly_attribute :uuid }
+
+  # Relationships
+  it { is_expected.to have_a_readonly_has_one(:project).with_class_name('Project') }
+  it { is_expected.to have_a_readonly_has_one(:study).with_class_name('Study') }
+  it { is_expected.to have_a_readonly_has_one(:user).with_class_name('User') }
+
+  # Template attributes
+  it { is_expected.to have_writeonly_attribute :submission_template_uuid }
+  it { is_expected.to have_writeonly_attribute :submission_template_attributes }
 end

From a8b9d8b486f228f08ac4272369f8fd65e3d47d92 Mon Sep 17 00:00:00 2001
From: Stuart McHattie <sm49@sanger.ac.uk>
Date: Mon, 9 Dec 2024 16:32:21 +0000
Subject: [PATCH 18/40] Complete tests for OrderResource requests

---
 app/controllers/api/v2/orders_controller.rb   |   8 +-
 spec/requests/api/v2/orders_spec.rb           | 224 ++++++++++++++++++
 .../api/v2/shared_examples/requests.rb        |  16 ++
 3 files changed, 244 insertions(+), 4 deletions(-)

diff --git a/app/controllers/api/v2/orders_controller.rb b/app/controllers/api/v2/orders_controller.rb
index f05d8347c8..da30f615e6 100644
--- a/app/controllers/api/v2/orders_controller.rb
+++ b/app/controllers/api/v2/orders_controller.rb
@@ -64,7 +64,7 @@ def make_template_attributes(attributes, &)
           assets: extract_assets(attributes, &),
           autodetect_projects: attributes[:autodetect_projects],
           autodetect_studies: attributes[:autodetect_studies],
-          request_options: require_attribute(attributes, :request_options),
+          request_options: require_attribute(attributes, :request_options, &),
           user: extract_user(attributes, &)
         }.compact
       end
@@ -74,9 +74,9 @@ def extract_assets(attributes, &)
         return nil if asset_uuids.nil?
 
         asset_uuids.map do |uuid|
-          uuid = Uuid.find_by(external_id: uuid)
-          yield JSONAPI::Exceptions::InvalidFieldValue.new(:asset_uuids, uuid).errors if uuid.nil?
-          uuid&.resource
+          uuid_obj = Uuid.find_by(external_id: uuid)
+          yield JSONAPI::Exceptions::InvalidFieldValue.new(:asset_uuids, uuid).errors if uuid_obj.nil?
+          uuid_obj&.resource
         end
       end
 
diff --git a/spec/requests/api/v2/orders_spec.rb b/spec/requests/api/v2/orders_spec.rb
index c34a23116b..89b9618da2 100644
--- a/spec/requests/api/v2/orders_spec.rb
+++ b/spec/requests/api/v2/orders_spec.rb
@@ -413,5 +413,229 @@
         end
       end
     end
+
+    context 'with a read-only attribute in the payload' do
+      context 'with order_type' do
+        let(:disallowed_value) { 'order_type' }
+        let(:payload) { { data: { type: resource_type, attributes: { order_type: 'read-only' } } } }
+
+        it_behaves_like 'a POST request with a disallowed value'
+      end
+
+      context 'with request_options' do
+        let(:disallowed_value) { 'request_options' }
+        let(:payload) { { data: { type: resource_type, attributes: { request_options: 'read-only' } } } }
+
+        it_behaves_like 'a POST request with a disallowed value'
+      end
+
+      context 'with request_types' do
+        let(:disallowed_value) { 'request_types' }
+        let(:payload) { { data: { type: resource_type, attributes: { request_types: 'read-only' } } } }
+
+        it_behaves_like 'a POST request with a disallowed value'
+      end
+
+      context 'with uuid' do
+        let(:disallowed_value) { 'uuid' }
+        let(:payload) { { data: { type: resource_type, attributes: { uuid: 'read-only' } } } }
+
+        it_behaves_like 'a POST request with a disallowed value'
+      end
+    end
+
+    context 'with a read-only relationship in the payload' do
+      context 'with project' do
+        let(:disallowed_value) { 'project' }
+        let(:payload) do
+          { data: { type: resource_type, relationships: { project: { data: { id: '1', type: 'projects' } } } } }
+        end
+
+        it_behaves_like 'a POST request with a disallowed value'
+      end
+
+      context 'with study' do
+        let(:disallowed_value) { 'study' }
+        let(:payload) do
+          { data: { type: resource_type, relationships: { study: { data: { id: '1', type: 'studies' } } } } }
+        end
+
+        it_behaves_like 'a POST request with a disallowed value'
+      end
+
+      context 'with user' do
+        let(:disallowed_value) { 'user' }
+        let(:payload) do
+          { data: { type: resource_type, relationships: { user: { data: { id: '1', type: 'users' } } } } }
+        end
+
+        it_behaves_like 'a POST request with a disallowed value'
+      end
+    end
+
+    context 'without a required attribute' do
+      let(:project) { create(:project) }
+      let(:study) { create(:study) }
+      let(:request_types) { create_list(:request_type, 1, asset_type: 'Well') }
+      let(:template) { create(:submission_template, request_types:, project:, study:) }
+      let(:assets) { create(:plate_with_tagged_wells).wells[0..2] }
+      let(:user) { create(:user) }
+
+      context 'without a submission_template_uuid' do
+        let(:payload) do
+          {
+            data: {
+              type: resource_type,
+              attributes: {
+                submission_template_attributes: {
+                  asset_uuids: assets.map(&:uuid),
+                  request_options: {
+                    no_options: true
+                  },
+                  user_uuid: user.uuid
+                }
+              }
+            }
+          }
+        end
+
+        it 'fails to create the resource' do
+          # Not providing a submission_template_uuid is a valid use case as we default to the normal JSONAPI::Resources
+          # behaviour, but it will fail validation on the new Order model as it needs certain attributes set, but
+          # they're all read-only on the API.
+          api_post base_endpoint, payload
+
+          expect(json['errors'].map { |err| err['detail'] }).to match_array(
+            [
+              'user - must exist',
+              "study - can't be blank",
+              "project - can't be blank",
+              "request_types - can't be blank"
+            ]
+          )
+        end
+      end
+
+      context 'without submission_template_attributes' do
+        let(:payload) { { data: { type: resource_type, attributes: { submission_template_uuid: template.uuid } } } }
+        let(:error_detail_message) { 'The required parameter, submission_template_attributes, is missing.' }
+
+        it_behaves_like 'a bad POST request with a specific error'
+      end
+
+      context 'without submission_template_attributes.asset_uuids' do
+        let(:payload) do
+          {
+            data: {
+              type: resource_type,
+              attributes: {
+                submission_template_uuid: template.uuid,
+                submission_template_attributes: {
+                  request_options: {
+                    no_options: true
+                  },
+                  user_uuid: user.uuid
+                }
+              }
+            }
+          }
+        end
+        let(:error_detail_message) { 'The required parameter, submission_template_attributes.asset_uuids, is missing.' }
+
+        it_behaves_like 'a bad POST request with a specific error'
+      end
+
+      context 'without submission_template_attributes.request_options' do
+        let(:payload) do
+          {
+            data: {
+              type: resource_type,
+              attributes: {
+                submission_template_uuid: template.uuid,
+                submission_template_attributes: {
+                  asset_uuids: assets.map(&:uuid),
+                  user_uuid: user.uuid
+                }
+              }
+            }
+          }
+        end
+        let(:error_detail_message) do
+          'The required parameter, submission_template_attributes.request_options, is missing.'
+        end
+
+        it_behaves_like 'a bad POST request with a specific error'
+      end
+
+      context 'without submission_template_attributes.user_uuid' do
+        let(:payload) do
+          {
+            data: {
+              type: resource_type,
+              attributes: {
+                submission_template_uuid: template.uuid,
+                submission_template_attributes: {
+                  asset_uuids: assets.map(&:uuid),
+                  request_options: {
+                    no_options: true
+                  }
+                }
+              }
+            }
+          }
+        end
+        let(:error_detail_message) { 'The required parameter, submission_template_attributes.user_uuid, is missing.' }
+
+        it_behaves_like 'a bad POST request with a specific error'
+      end
+    end
+
+    context 'with an invalid UUID' do
+      context 'with an invalid asset_uuid' do
+        let(:payload) do
+          {
+            data: {
+              type: resource_type,
+              attributes: {
+                submission_template_uuid: template.uuid,
+                submission_template_attributes: {
+                  asset_uuids: ['not-a-valid-uuid'],
+                  request_options: {
+                    no_options: true
+                  },
+                  user_uuid: user.uuid
+                }
+              }
+            }
+          }
+        end
+        let(:error_detail_message) { 'not-a-valid-uuid is not a valid value for asset_uuids.' }
+
+        it_behaves_like 'a bad POST request with a specific error'
+      end
+
+      context 'with an invalid user_uuid' do
+        let(:payload) do
+          {
+            data: {
+              type: resource_type,
+              attributes: {
+                submission_template_uuid: template.uuid,
+                submission_template_attributes: {
+                  asset_uuids: assets.map(&:uuid),
+                  request_options: {
+                    no_options: true
+                  },
+                  user_uuid: 'not-a-valid-uuid'
+                }
+              }
+            }
+          }
+        end
+        let(:error_detail_message) { 'not-a-valid-uuid is not a valid value for user_uuid.' }
+
+        it_behaves_like 'a bad POST request with a specific error'
+      end
+    end
   end
 end
diff --git a/spec/requests/api/v2/shared_examples/requests.rb b/spec/requests/api/v2/shared_examples/requests.rb
index 829b65e79c..3e3ec9c9d6 100644
--- a/spec/requests/api/v2/shared_examples/requests.rb
+++ b/spec/requests/api/v2/shared_examples/requests.rb
@@ -50,6 +50,22 @@
   end
 end
 
+shared_examples 'a bad POST request with a specific error' do
+  before { api_post base_endpoint, payload }
+
+  it 'does not create a new resource' do
+    expect { api_post base_endpoint, payload }.not_to change(model_class, :count)
+  end
+
+  it 'responds with unprocessable_entity' do
+    expect(response).to have_http_status(:bad_request)
+  end
+
+  it 'specifies the expected error message' do
+    expect(json.dig('errors', 0, 'detail')).to eq(error_detail_message)
+  end
+end
+
 shared_examples 'a GET request including a has_one relationship' do |related_name|
   before { api_get "#{base_endpoint}/#{resource.id}?include=#{related_name}" }
 

From 44fb0657c4b3306f327e74ad181f60ba378afe4e Mon Sep 17 00:00:00 2001
From: Stuart McHattie <sm49@sanger.ac.uk>
Date: Mon, 9 Dec 2024 16:58:41 +0000
Subject: [PATCH 19/40] Fix Rubocop issues

---
 spec/requests/api/v2/orders_spec.rb | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/spec/requests/api/v2/orders_spec.rb b/spec/requests/api/v2/orders_spec.rb
index 89b9618da2..d4ac5ae21a 100644
--- a/spec/requests/api/v2/orders_spec.rb
+++ b/spec/requests/api/v2/orders_spec.rb
@@ -498,6 +498,9 @@
             }
           }
         end
+        let(:expected_error_details) do
+          ['user - must exist', "study - can't be blank", "project - can't be blank", "request_types - can't be blank"]
+        end
 
         it 'fails to create the resource' do
           # Not providing a submission_template_uuid is a valid use case as we default to the normal JSONAPI::Resources
@@ -505,14 +508,7 @@
           # they're all read-only on the API.
           api_post base_endpoint, payload
 
-          expect(json['errors'].map { |err| err['detail'] }).to match_array(
-            [
-              'user - must exist',
-              "study - can't be blank",
-              "project - can't be blank",
-              "request_types - can't be blank"
-            ]
-          )
+          expect(json['errors'].pluck('detail')).to contain_exactly(*expected_error_details)
         end
       end
 

From d26dfcebca3a5c15f6a1e1b60a9b94cb08728faf Mon Sep 17 00:00:00 2001
From: Stuart McHattie <sm49@sanger.ac.uk>
Date: Tue, 10 Dec 2024 21:20:43 +0000
Subject: [PATCH 20/40] Fix rubocop complaint

---
 spec/requests/api/v2/orders_spec.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/spec/requests/api/v2/orders_spec.rb b/spec/requests/api/v2/orders_spec.rb
index d4ac5ae21a..fcda248506 100644
--- a/spec/requests/api/v2/orders_spec.rb
+++ b/spec/requests/api/v2/orders_spec.rb
@@ -508,7 +508,7 @@
           # they're all read-only on the API.
           api_post base_endpoint, payload
 
-          expect(json['errors'].pluck('detail')).to contain_exactly(*expected_error_details)
+          expect(json['errors'].pluck('detail')).to match_array(expected_error_details)
         end
       end
 

From 1e4dd24f2d163cbb646fb1396ccb2d97662eb28b Mon Sep 17 00:00:00 2001
From: sabrine33 <sa33@sanger.ac.uk>
Date: Thu, 12 Dec 2024 11:57:55 +0000
Subject: [PATCH 21/40] add huMFre code field to the samples

---
 app/controllers/samples_controller.rb         |  1 +
 app/models/api/sample_io.rb                   |  1 +
 app/models/sample.rb                          | 10 ++++++++
 .../shared/metadata/edit/_sample.html.erb     |  2 ++
 .../shared/metadata/show/_sample.html.erb     |  2 ++
 config/locales/metadata/en.yml                |  2 ++
 ...36_add_hu_m_fre_code_to_sample_metadata.rb |  6 +++++
 db/schema.rb                                  |  3 ++-
 spec/models/api/sample_io_spec.rb             |  6 +++--
 spec/models/sample_spec.rb                    | 24 +++++++++++++++++++
 10 files changed, 54 insertions(+), 3 deletions(-)
 create mode 100644 db/migrate/20241211143636_add_hu_m_fre_code_to_sample_metadata.rb

diff --git a/app/controllers/samples_controller.rb b/app/controllers/samples_controller.rb
index 2e21f2782e..a9aa814e8f 100644
--- a/app/controllers/samples_controller.rb
+++ b/app/controllers/samples_controller.rb
@@ -248,6 +248,7 @@ def default_permitted_metadata_fields
         subject
         treatment
         donor_id
+        huMFre_code
       ]
     }
   end
diff --git a/app/models/api/sample_io.rb b/app/models/api/sample_io.rb
index 5acaac3742..b54b90443a 100644
--- a/app/models/api/sample_io.rb
+++ b/app/models/api/sample_io.rb
@@ -98,6 +98,7 @@ def json_root
     map_attribute_to_json_attribute(:treatment)
     map_attribute_to_json_attribute(:date_of_consent_withdrawn)
     map_attribute_to_json_attribute(:user_id_of_consent_withdrawn, 'marked_as_consent_withdrawn_by')
+    map_attribute_to_json_attribute(:huMFre_code)
   end
 
   extra_json_attributes do |_object, json_attributes|
diff --git a/app/models/sample.rb b/app/models/sample.rb
index 105b86ef96..2ea4e9d0da 100644
--- a/app/models/sample.rb
+++ b/app/models/sample.rb
@@ -147,6 +147,8 @@ class Current < ActiveSupport::CurrentAttributes
     custom_attribute(:date_of_consent_withdrawn)
     custom_attribute(:user_id_of_consent_withdrawn)
 
+    custom_attribute(:huMFre_code)
+
     # These fields are warehoused, so need to match the encoding restrictions there
     # This excludes supplementary characters, which include emoji and rare kanji
     # @note phenotype isn't currently broadcast but has a field waiting in the warehouse
@@ -226,6 +228,14 @@ class Current < ActiveSupport::CurrentAttributes
   # Sample::Metadata tracks sample information, either for use in the lab, or passing to
   # the EBI
   class Metadata
+
+    validates :huMFre_code,
+              format: {
+                with: %r{\A\d{2}/\d{2,}|\d{2}/\d{4}-\d{3}\z},
+                message: 'must match a valid format, e.g. 12/34 or 12/2023-001'
+              },
+              allow_blank: true
+
     # This constraint doesn't match that described in the manifest, and is more permissive
     # It was added on conversion of out database to utf8 to address concerns that this would
     # lead to an increase in characters that their pipeline cannot process. Only a handful
diff --git a/app/views/shared/metadata/edit/_sample.html.erb b/app/views/shared/metadata/edit/_sample.html.erb
index 999a30919e..02f1f264fc 100644
--- a/app/views/shared/metadata/edit/_sample.html.erb
+++ b/app/views/shared/metadata/edit/_sample.html.erb
@@ -80,6 +80,8 @@
     <%= metadata_fields.text_field(:disease) %>
     <%= metadata_fields.text_field(:treatment)%>
 
+    <%= metadata_fields.text_field(:huMFre_code)%>
+
     <%  metadata_fields.finalize_related_fields %>
   <% end %>
 <% end %>
diff --git a/app/views/shared/metadata/show/_sample.html.erb b/app/views/shared/metadata/show/_sample.html.erb
index 23f5aa732f..d75a44439e 100644
--- a/app/views/shared/metadata/show/_sample.html.erb
+++ b/app/views/shared/metadata/show/_sample.html.erb
@@ -64,5 +64,7 @@
     <%= metadata_fields.plain_value(:disease) %>
     <%= metadata_fields.plain_value(:treatment)%>
 
+    <%= metadata_fields.plain_value(:huMFre_code)%>
+
   <% end %>
 <% end %>
diff --git a/config/locales/metadata/en.yml b/config/locales/metadata/en.yml
index 2abb785013..db6ed0d4de 100644
--- a/config/locales/metadata/en.yml
+++ b/config/locales/metadata/en.yml
@@ -325,6 +325,8 @@ en:
           edit_info: "EGA"
         genome_size:
           label: Genome Size
+        huMFre_code:
+          label: HuMFre Code
 
     study:
       metadata:
diff --git a/db/migrate/20241211143636_add_hu_m_fre_code_to_sample_metadata.rb b/db/migrate/20241211143636_add_hu_m_fre_code_to_sample_metadata.rb
new file mode 100644
index 0000000000..d16094607d
--- /dev/null
+++ b/db/migrate/20241211143636_add_hu_m_fre_code_to_sample_metadata.rb
@@ -0,0 +1,6 @@
+# frozen_string_literal: true
+class AddHuMFreCodeToSampleMetadata < ActiveRecord::Migration[7.0]
+  def change
+    add_column :sample_metadata, :huMFre_code, :string, limit: 16
+  end
+end
diff --git a/db/schema.rb b/db/schema.rb
index 11da36d9d8..187e3c4e3e 100644
--- a/db/schema.rb
+++ b/db/schema.rb
@@ -10,7 +10,7 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema[7.0].define(version: 2024_11_06_103710) do
+ActiveRecord::Schema[7.0].define(version: 2024_12_11_143636) do
   create_table "aliquot_indices", id: :integer, charset: "utf8mb4", collation: "utf8mb4_unicode_ci", options: "ENGINE=InnoDB ROW_FORMAT=DYNAMIC", force: :cascade do |t|
     t.integer "aliquot_id", null: false
     t.integer "lane_id", null: false
@@ -1395,6 +1395,7 @@
     t.integer "user_id_of_consent_withdrawn"
     t.boolean "consent_withdrawn", default: false, null: false
     t.string "collected_by", comment: "Name of persons or institute who collected the specimen"
+    t.string "huMFre_code", limit: 16
     t.index ["sample_ebi_accession_number"], name: "index_sample_metadata_on_sample_ebi_accession_number"
     t.index ["sample_id"], name: "index_sample_metadata_on_sample_id"
     t.index ["supplier_name"], name: "index_sample_metadata_on_supplier_name"
diff --git a/spec/models/api/sample_io_spec.rb b/spec/models/api/sample_io_spec.rb
index 3a24a4e9c7..a219f9150e 100644
--- a/spec/models/api/sample_io_spec.rb
+++ b/spec/models/api/sample_io_spec.rb
@@ -62,7 +62,8 @@
         sample_strain_att: 'stuff about strain',
         consent_withdrawn: false,
         donor_id: 2,
-        developmental_stage: 'thing'
+        developmental_stage: 'thing',
+        huMFre_code: '23/21'
       }
     )
   end
@@ -133,7 +134,8 @@
       'developmental_stage' => 'thing',
       'donor_id' => '2',
       'reference_genome' => 'ReferenceGenome1',
-      'component_sample_uuids' => [{ uuid: comp_sample1.uuid }, { uuid: comp_sample2.uuid }]
+      'component_sample_uuids' => [{ uuid: comp_sample1.uuid }, { uuid: comp_sample2.uuid }],
+      'huMFre_code' => '23/21'
     }
   end
 
diff --git a/spec/models/sample_spec.rb b/spec/models/sample_spec.rb
index daa588a53d..838ff5f62c 100644
--- a/spec/models/sample_spec.rb
+++ b/spec/models/sample_spec.rb
@@ -259,6 +259,30 @@
     end
   end
 
+  context 'huMFre code' do
+    let(:sample) { create(:sample) }
+
+    it 'defaults to null when not specified' do
+      expect(sample.sample_metadata.huMFre_code).to be_nil
+    end
+
+    it 'fails to update/save when huMFre code value is invalid' do
+      expect(sample.sample_metadata.huMFre_code).to be_nil
+      sample.sample_metadata.huMFre_code = 'humFre1'
+      expect(sample.sample_metadata.save).to be false
+    end
+
+    it 'contains huMFre code value when it is correctly specified' do
+      sample.sample_metadata.update!(huMFre_code: '12/12')
+      expect(sample.sample_metadata.huMFre_code).to eq '12/12'
+    end
+
+    it 'can have the huMFre code blanked' do
+      sample.sample_metadata.update!(huMFre_code: nil)
+      expect(sample.sample_metadata.huMFre_code).to be_nil
+    end
+  end
+
   context '(DPL-148) on updating sample metadata' do
     let(:sample) { create(:sample) }
 

From 487419153735f7f3eb0d54c97e33f1fa6e6f9e0d Mon Sep 17 00:00:00 2001
From: sabrine33 <sa33@sanger.ac.uk>
Date: Thu, 12 Dec 2024 12:01:53 +0000
Subject: [PATCH 22/40] run prettier

---
 app/models/sample.rb | 1 -
 1 file changed, 1 deletion(-)

diff --git a/app/models/sample.rb b/app/models/sample.rb
index 2ea4e9d0da..5ea3f68a78 100644
--- a/app/models/sample.rb
+++ b/app/models/sample.rb
@@ -228,7 +228,6 @@ class Current < ActiveSupport::CurrentAttributes
   # Sample::Metadata tracks sample information, either for use in the lab, or passing to
   # the EBI
   class Metadata
-
     validates :huMFre_code,
               format: {
                 with: %r{\A\d{2}/\d{2,}|\d{2}/\d{4}-\d{3}\z},

From 569962a0fd94decc086d1a5647c84011b4f7b738 Mon Sep 17 00:00:00 2001
From: sabrine33 <sa33@sanger.ac.uk>
Date: Thu, 12 Dec 2024 13:20:37 +0000
Subject: [PATCH 23/40] fix cucumber test

---
 features/samples/xml_interface.feature | 1 +
 1 file changed, 1 insertion(+)

diff --git a/features/samples/xml_interface.feature b/features/samples/xml_interface.feature
index 26f533159e..960ec1e0d4 100644
--- a/features/samples/xml_interface.feature
+++ b/features/samples/xml_interface.feature
@@ -68,6 +68,7 @@ Feature: The XML interface to the samples
           <property><name>Time Point</name><value></value></property>
           <property><name>Donor Id</name><value></value></property>
           <property><name>Collected By</name><value/></property>
+          <property><name>HuMFre Code</name><value/></property>
         </properties>
       </sample>
       """

From 5a080e0e0a95fe4b5343ef1ab13f9eaf048ef97a Mon Sep 17 00:00:00 2001
From: Stephen Hulme <sh51@sanger.ac.uk>
Date: Thu, 12 Dec 2024 13:23:04 +0000
Subject: [PATCH 24/40] fix: show units

---
 app/views/batches/_cherrypick_single_worksheet.html.erb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/views/batches/_cherrypick_single_worksheet.html.erb b/app/views/batches/_cherrypick_single_worksheet.html.erb
index 4075619fde..f10384d5bb 100644
--- a/app/views/batches/_cherrypick_single_worksheet.html.erb
+++ b/app/views/batches/_cherrypick_single_worksheet.html.erb
@@ -92,7 +92,7 @@
 </div>
 
 <div id="footer">
-  v = receptacle volume; b = buffer volume<br>
+  v = receptacle volume µl; b = buffer volume µl<br>
   Created: <%= batch.updated_at.strftime("%I:%M %p on %A %d %B, %Y") %> for <%= batch.user.login %><br>
   Printed: <%= Time.now.strftime("%I:%M %p on %A %d %B, %Y") %> for <%= current_user.login %>
 </div>

From 6f66d94df59a5e874251139247a1b87227d8e8fb Mon Sep 17 00:00:00 2001
From: Stephen Hulme <sh51@sanger.ac.uk>
Date: Thu, 12 Dec 2024 13:24:14 +0000
Subject: [PATCH 25/40] fix: reword receptacle volume -> picking volume

---
 app/views/batches/_cherrypick_single_worksheet.html.erb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/views/batches/_cherrypick_single_worksheet.html.erb b/app/views/batches/_cherrypick_single_worksheet.html.erb
index f10384d5bb..6bb66c2c36 100644
--- a/app/views/batches/_cherrypick_single_worksheet.html.erb
+++ b/app/views/batches/_cherrypick_single_worksheet.html.erb
@@ -92,7 +92,7 @@
 </div>
 
 <div id="footer">
-  v = receptacle volume µl; b = buffer volume µl<br>
+  v = picking volume µl; b = buffer volume µl<br>
   Created: <%= batch.updated_at.strftime("%I:%M %p on %A %d %B, %Y") %> for <%= batch.user.login %><br>
   Printed: <%= Time.now.strftime("%I:%M %p on %A %d %B, %Y") %> for <%= current_user.login %>
 </div>

From 9da0e253ff7983124c78bb94d23cd025ad91cdd5 Mon Sep 17 00:00:00 2001
From: Stephen Hulme <sh51@sanger.ac.uk>
Date: Fri, 13 Dec 2024 12:11:18 +0000
Subject: [PATCH 26/40] fix: replace assay_version Binning with more suitable
 UAT_version

---
 app/uat_actions/uat_actions/generate_plate_volumes.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/uat_actions/uat_actions/generate_plate_volumes.rb b/app/uat_actions/uat_actions/generate_plate_volumes.rb
index 0afd4cacb9..ddb1033609 100644
--- a/app/uat_actions/uat_actions/generate_plate_volumes.rb
+++ b/app/uat_actions/uat_actions/generate_plate_volumes.rb
@@ -90,7 +90,7 @@ def construct_qc_assay
         value: create_random_volume,
         units: 'µl',
         assay_type: 'UAT_Testing',
-        assay_version: 'Binning',
+        assay_version: 'UAT_version',
         qc_assay: qc_assay
       )
       num_wells_written += 1

From 95a65bb56a5ffe89cdd9a86d66f0a807f3a84a9c Mon Sep 17 00:00:00 2001
From: Stuart McHattie <sm49@sanger.ac.uk>
Date: Mon, 16 Dec 2024 12:39:34 +0000
Subject: [PATCH 27/40] Clean up the OrdersProcessor and OrderResource

---
 app/controllers/api/v2/orders_controller.rb  | 65 +++++++-------------
 app/resources/api/v2/order_resource.rb       | 15 ++---
 spec/resources/api/v2/order_resource_spec.rb | 34 ++++++++++
 3 files changed, 64 insertions(+), 50 deletions(-)

diff --git a/app/controllers/api/v2/orders_controller.rb b/app/controllers/api/v2/orders_controller.rb
index da30f615e6..553298c46c 100644
--- a/app/controllers/api/v2/orders_controller.rb
+++ b/app/controllers/api/v2/orders_controller.rb
@@ -10,44 +10,31 @@ class OrdersController < JSONAPI::ResourceController
     end
 
     class OrderProcessor < JSONAPI::Processor
-      # Override the default behaviour for a JSONAPI::Processor when creating a new resource.
-      # We need to check whether a template UUID was given, and, if so, use it to create the Order directly.
-      # Where no template is given, the Order will be created via the base JSONAPI::Processor.
-      def create_resource
-        errors = []
-        template = find_template { |new_errors| errors += new_errors }
-        attributes = template_attributes { |new_errors| errors += new_errors } unless template.nil?
-
-        return JSONAPI::ErrorsOperationResult.new(JSONAPI::BAD_REQUEST, errors) unless errors.empty?
-        return super if template.nil? # No template means we should use the default behaviour.
-
-        create_order_from_template(template, attributes)
-      end
+      before_create_resource :prepare_context
 
       private
 
+      def prepare_context
+        context[:template] = find_template
+        context[:template_attributes] = template_attributes unless context[:template].nil?
+      end
+
       def find_template
         template_uuid = params[:data][:attributes][:submission_template_uuid]
         return nil if template_uuid.nil? # No errors -- we just don't have a template.
 
         template = SubmissionTemplate.with_uuid(template_uuid).first
-
-        if template.nil?
-          yield JSONAPI::Exceptions::InvalidFieldValue.new(:submission_template_uuid, template_uuid).errors
-        end
+        raise JSONAPI::Exceptions::InvalidFieldValue.new(:submission_template_uuid, template_uuid) if template.nil?
 
         template
       end
 
-      def template_attributes(&)
+      def template_attributes
         parameters = params[:data][:attributes][:submission_template_attributes]
 
-        if parameters.nil?
-          yield JSONAPI::Exceptions::ParameterMissing.new(:submission_template_attributes).errors
-          return
-        end
+        raise JSONAPI::Exceptions::ParameterMissing, :submission_template_attributes if parameters.nil?
 
-        make_template_attributes(permitted_attributes(parameters), &)
+        make_template_attributes(permitted_attributes(parameters))
       end
 
       def permitted_attributes(attributes)
@@ -59,33 +46,34 @@ def permitted_attributes(attributes)
         )
       end
 
-      def make_template_attributes(attributes, &)
+      def make_template_attributes(attributes)
         {
-          assets: extract_assets(attributes, &),
+          assets: extract_assets(attributes),
           autodetect_projects: attributes[:autodetect_projects],
           autodetect_studies: attributes[:autodetect_studies],
-          request_options: require_attribute(attributes, :request_options, &),
-          user: extract_user(attributes, &)
+          request_options: require_attribute(attributes, :request_options),
+          user: extract_user(attributes)
         }.compact
       end
 
-      def extract_assets(attributes, &)
-        asset_uuids = require_attribute(attributes, :asset_uuids, &)
+      def extract_assets(attributes)
+        asset_uuids = require_attribute(attributes, :asset_uuids)
         return nil if asset_uuids.nil?
 
         asset_uuids.map do |uuid|
           uuid_obj = Uuid.find_by(external_id: uuid)
-          yield JSONAPI::Exceptions::InvalidFieldValue.new(:asset_uuids, uuid).errors if uuid_obj.nil?
+          raise JSONAPI::Exceptions::InvalidFieldValue.new(:asset_uuids, uuid) if uuid_obj.nil?
           uuid_obj&.resource
         end
       end
 
-      def extract_user(attributes, &)
-        user_uuid = require_attribute(attributes, :user_uuid, &)
+      def extract_user(attributes)
+        user_uuid = require_attribute(attributes, :user_uuid)
         return nil if user_uuid.nil?
 
         user = User.with_uuid(user_uuid).first
-        yield JSONAPI::Exceptions::InvalidFieldValue.new(:user_uuid, user_uuid).errors if user.nil?
+        raise JSONAPI::Exceptions::InvalidFieldValue.new(:user_uuid, user_uuid) if user.nil?
+
         user
       end
 
@@ -94,16 +82,7 @@ def require_attribute(attributes, key)
         value = value.to_h if value.instance_of?(ActionController::Parameters) && value.permitted?
         value
       rescue ActionController::ParameterMissing
-        yield JSONAPI::Exceptions::ParameterMissing.new("submission_template_attributes.#{key}").errors
-        nil
-      end
-
-      def create_order_from_template(template, attributes)
-        order = template.create_order!(attributes)
-        resource = OrderResource.new(order, context)
-        result = resource.replace_fields(params[:data])
-
-        JSONAPI::ResourceOperationResult.new((result == :completed ? :created : :accepted), resource)
+        raise JSONAPI::Exceptions::ParameterMissing, "submission_template_attributes.#{key}"
       end
     end
   end
diff --git a/app/resources/api/v2/order_resource.rb b/app/resources/api/v2/order_resource.rb
index 9dbc55b8a0..52859bd4e8 100644
--- a/app/resources/api/v2/order_resource.rb
+++ b/app/resources/api/v2/order_resource.rb
@@ -95,7 +95,7 @@ class OrderResource < BaseResource
       has_one :user, readonly: true
 
       ###
-      # Template attributes
+      # Templated creation
       ###
 
       # These are defined here to assist with the creation of Orders from SubmissionTemplates.
@@ -105,10 +105,7 @@ class OrderResource < BaseResource
       #   The UUID of the {SubmissionTemplate} to use when creating this {Order}.
       #   @note This is mandatory when creating new {Order}s via the API. It is not stored.
       attribute :submission_template_uuid, writeonly: true
-
-      def submission_template_uuid=(value)
-        # Do nothing with this value as it's consumed by the OrderProcessor.
-      end
+      attr_writer :submission_template_uuid # Do not store this on the model. It's consumed by the OrderProcessor.
 
       # @!attribute [w] submission_template_attributes
       #   A hash of additional attributes to use when creating this {Order} from a given {SubmissionTemplate}.
@@ -126,9 +123,13 @@ def submission_template_uuid=(value)
       #
       #   @note This is mandatory when creating new {Order}s via the API. It is not stored.
       attribute :submission_template_attributes, writeonly: true
+      attr_writer :submission_template_attributes # Do not store this on the model. It's consumed by the OrderProcessor.
+
+      def self.create(context)
+        return super if context[:template].nil?
 
-      def submission_template_attributes=(value)
-        # Do nothing with this value as it's consumed by the OrderProcessor.
+        order = context[:template].create_order!(context[:template_attributes])
+        new(order, context)
       end
     end
   end
diff --git a/spec/resources/api/v2/order_resource_spec.rb b/spec/resources/api/v2/order_resource_spec.rb
index d0334541fa..d8bad10f00 100644
--- a/spec/resources/api/v2/order_resource_spec.rb
+++ b/spec/resources/api/v2/order_resource_spec.rb
@@ -25,4 +25,38 @@
   # Template attributes
   it { is_expected.to have_writeonly_attribute :submission_template_uuid }
   it { is_expected.to have_writeonly_attribute :submission_template_attributes }
+
+  # Custom methods
+  describe '#self.create' do
+    context 'without a template in the context' do
+      let(:context) { {} }
+      let(:resource) { double('OrderResource') }
+
+      it 'returns an OrderResource created by the super class' do
+        expect(described_class.superclass).to receive(:create).with(context).and_return(resource)
+
+        expect(described_class.create(context)).to eq(resource)
+      end
+    end
+
+    context 'with a template in the context' do
+      let(:context) { { template:, template_attributes: } }
+      let(:template) { double('SubmissionTemplate') }
+      let(:template_attributes) { {} }
+      let(:order) { create(:order) }
+
+      it 'does not call create on the super class' do
+        expect(described_class.superclass).not_to receive(:create).with(context)
+      end
+
+      it 'creates a new OrderResource with a new Order created by the SubmissionTemplate' do
+        allow(template).to receive(:create_order!).and_return(order)
+        allow(described_class).to receive(:new).and_call_original
+
+        described_class.create(context)
+
+        expect(described_class).to have_received(:new).with(order, context)
+      end
+    end
+  end
 end

From 70c8ee39d02a442edfc0d3bc127d055f42f06fdb Mon Sep 17 00:00:00 2001
From: Stuart McHattie <sm49@sanger.ac.uk>
Date: Mon, 16 Dec 2024 12:51:06 +0000
Subject: [PATCH 28/40] Fix Rubocop issues

---
 spec/resources/api/v2/order_resource_spec.rb | 19 +++++++++++--------
 1 file changed, 11 insertions(+), 8 deletions(-)

diff --git a/spec/resources/api/v2/order_resource_spec.rb b/spec/resources/api/v2/order_resource_spec.rb
index d8bad10f00..5428ac9f7e 100644
--- a/spec/resources/api/v2/order_resource_spec.rb
+++ b/spec/resources/api/v2/order_resource_spec.rb
@@ -30,10 +30,9 @@
   describe '#self.create' do
     context 'without a template in the context' do
       let(:context) { {} }
-      let(:resource) { double('OrderResource') }
 
       it 'returns an OrderResource created by the super class' do
-        expect(described_class.superclass).to receive(:create).with(context).and_return(resource)
+        allow(described_class.superclass).to receive(:create).with(context).and_return(resource)
 
         expect(described_class.create(context)).to eq(resource)
       end
@@ -41,21 +40,25 @@
 
     context 'with a template in the context' do
       let(:context) { { template:, template_attributes: } }
-      let(:template) { double('SubmissionTemplate') }
+      let(:template) { instance_double(SubmissionTemplate) }
       let(:template_attributes) { {} }
-      let(:order) { create(:order) }
+
+      before { allow(template).to receive(:create_order!).with(template_attributes).and_return(resource_model) }
 
       it 'does not call create on the super class' do
-        expect(described_class.superclass).not_to receive(:create).with(context)
+        allow(described_class.superclass).to receive(:create)
+
+        described_class.create(context)
+
+        expect(described_class.superclass).not_to have_received(:create)
       end
 
       it 'creates a new OrderResource with a new Order created by the SubmissionTemplate' do
-        allow(template).to receive(:create_order!).and_return(order)
-        allow(described_class).to receive(:new).and_call_original
+        allow(described_class).to receive(:new)
 
         described_class.create(context)
 
-        expect(described_class).to have_received(:new).with(order, context)
+        expect(described_class).to have_received(:new).with(resource_model, context)
       end
     end
   end

From 44df6507c041409fad9384d712a2152762b606c0 Mon Sep 17 00:00:00 2001
From: sabrine33 <sa33@sanger.ac.uk>
Date: Thu, 12 Dec 2024 11:57:55 +0000
Subject: [PATCH 29/40] add huMFre code field to the samples

---
 app/controllers/samples_controller.rb         |  1 +
 app/models/api/sample_io.rb                   |  1 +
 app/models/sample.rb                          | 10 ++++++++
 .../shared/metadata/edit/_sample.html.erb     |  2 ++
 .../shared/metadata/show/_sample.html.erb     |  2 ++
 config/locales/metadata/en.yml                |  2 ++
 ...36_add_hu_m_fre_code_to_sample_metadata.rb |  6 +++++
 db/schema.rb                                  |  3 ++-
 spec/models/api/sample_io_spec.rb             |  6 +++--
 spec/models/sample_spec.rb                    | 24 +++++++++++++++++++
 10 files changed, 54 insertions(+), 3 deletions(-)
 create mode 100644 db/migrate/20241211143636_add_hu_m_fre_code_to_sample_metadata.rb

diff --git a/app/controllers/samples_controller.rb b/app/controllers/samples_controller.rb
index 2e21f2782e..a9aa814e8f 100644
--- a/app/controllers/samples_controller.rb
+++ b/app/controllers/samples_controller.rb
@@ -248,6 +248,7 @@ def default_permitted_metadata_fields
         subject
         treatment
         donor_id
+        huMFre_code
       ]
     }
   end
diff --git a/app/models/api/sample_io.rb b/app/models/api/sample_io.rb
index 5acaac3742..b54b90443a 100644
--- a/app/models/api/sample_io.rb
+++ b/app/models/api/sample_io.rb
@@ -98,6 +98,7 @@ def json_root
     map_attribute_to_json_attribute(:treatment)
     map_attribute_to_json_attribute(:date_of_consent_withdrawn)
     map_attribute_to_json_attribute(:user_id_of_consent_withdrawn, 'marked_as_consent_withdrawn_by')
+    map_attribute_to_json_attribute(:huMFre_code)
   end
 
   extra_json_attributes do |_object, json_attributes|
diff --git a/app/models/sample.rb b/app/models/sample.rb
index 105b86ef96..2ea4e9d0da 100644
--- a/app/models/sample.rb
+++ b/app/models/sample.rb
@@ -147,6 +147,8 @@ class Current < ActiveSupport::CurrentAttributes
     custom_attribute(:date_of_consent_withdrawn)
     custom_attribute(:user_id_of_consent_withdrawn)
 
+    custom_attribute(:huMFre_code)
+
     # These fields are warehoused, so need to match the encoding restrictions there
     # This excludes supplementary characters, which include emoji and rare kanji
     # @note phenotype isn't currently broadcast but has a field waiting in the warehouse
@@ -226,6 +228,14 @@ class Current < ActiveSupport::CurrentAttributes
   # Sample::Metadata tracks sample information, either for use in the lab, or passing to
   # the EBI
   class Metadata
+
+    validates :huMFre_code,
+              format: {
+                with: %r{\A\d{2}/\d{2,}|\d{2}/\d{4}-\d{3}\z},
+                message: 'must match a valid format, e.g. 12/34 or 12/2023-001'
+              },
+              allow_blank: true
+
     # This constraint doesn't match that described in the manifest, and is more permissive
     # It was added on conversion of out database to utf8 to address concerns that this would
     # lead to an increase in characters that their pipeline cannot process. Only a handful
diff --git a/app/views/shared/metadata/edit/_sample.html.erb b/app/views/shared/metadata/edit/_sample.html.erb
index 999a30919e..02f1f264fc 100644
--- a/app/views/shared/metadata/edit/_sample.html.erb
+++ b/app/views/shared/metadata/edit/_sample.html.erb
@@ -80,6 +80,8 @@
     <%= metadata_fields.text_field(:disease) %>
     <%= metadata_fields.text_field(:treatment)%>
 
+    <%= metadata_fields.text_field(:huMFre_code)%>
+
     <%  metadata_fields.finalize_related_fields %>
   <% end %>
 <% end %>
diff --git a/app/views/shared/metadata/show/_sample.html.erb b/app/views/shared/metadata/show/_sample.html.erb
index 23f5aa732f..d75a44439e 100644
--- a/app/views/shared/metadata/show/_sample.html.erb
+++ b/app/views/shared/metadata/show/_sample.html.erb
@@ -64,5 +64,7 @@
     <%= metadata_fields.plain_value(:disease) %>
     <%= metadata_fields.plain_value(:treatment)%>
 
+    <%= metadata_fields.plain_value(:huMFre_code)%>
+
   <% end %>
 <% end %>
diff --git a/config/locales/metadata/en.yml b/config/locales/metadata/en.yml
index 2abb785013..db6ed0d4de 100644
--- a/config/locales/metadata/en.yml
+++ b/config/locales/metadata/en.yml
@@ -325,6 +325,8 @@ en:
           edit_info: "EGA"
         genome_size:
           label: Genome Size
+        huMFre_code:
+          label: HuMFre Code
 
     study:
       metadata:
diff --git a/db/migrate/20241211143636_add_hu_m_fre_code_to_sample_metadata.rb b/db/migrate/20241211143636_add_hu_m_fre_code_to_sample_metadata.rb
new file mode 100644
index 0000000000..d16094607d
--- /dev/null
+++ b/db/migrate/20241211143636_add_hu_m_fre_code_to_sample_metadata.rb
@@ -0,0 +1,6 @@
+# frozen_string_literal: true
+class AddHuMFreCodeToSampleMetadata < ActiveRecord::Migration[7.0]
+  def change
+    add_column :sample_metadata, :huMFre_code, :string, limit: 16
+  end
+end
diff --git a/db/schema.rb b/db/schema.rb
index 11da36d9d8..187e3c4e3e 100644
--- a/db/schema.rb
+++ b/db/schema.rb
@@ -10,7 +10,7 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema[7.0].define(version: 2024_11_06_103710) do
+ActiveRecord::Schema[7.0].define(version: 2024_12_11_143636) do
   create_table "aliquot_indices", id: :integer, charset: "utf8mb4", collation: "utf8mb4_unicode_ci", options: "ENGINE=InnoDB ROW_FORMAT=DYNAMIC", force: :cascade do |t|
     t.integer "aliquot_id", null: false
     t.integer "lane_id", null: false
@@ -1395,6 +1395,7 @@
     t.integer "user_id_of_consent_withdrawn"
     t.boolean "consent_withdrawn", default: false, null: false
     t.string "collected_by", comment: "Name of persons or institute who collected the specimen"
+    t.string "huMFre_code", limit: 16
     t.index ["sample_ebi_accession_number"], name: "index_sample_metadata_on_sample_ebi_accession_number"
     t.index ["sample_id"], name: "index_sample_metadata_on_sample_id"
     t.index ["supplier_name"], name: "index_sample_metadata_on_supplier_name"
diff --git a/spec/models/api/sample_io_spec.rb b/spec/models/api/sample_io_spec.rb
index 3a24a4e9c7..a219f9150e 100644
--- a/spec/models/api/sample_io_spec.rb
+++ b/spec/models/api/sample_io_spec.rb
@@ -62,7 +62,8 @@
         sample_strain_att: 'stuff about strain',
         consent_withdrawn: false,
         donor_id: 2,
-        developmental_stage: 'thing'
+        developmental_stage: 'thing',
+        huMFre_code: '23/21'
       }
     )
   end
@@ -133,7 +134,8 @@
       'developmental_stage' => 'thing',
       'donor_id' => '2',
       'reference_genome' => 'ReferenceGenome1',
-      'component_sample_uuids' => [{ uuid: comp_sample1.uuid }, { uuid: comp_sample2.uuid }]
+      'component_sample_uuids' => [{ uuid: comp_sample1.uuid }, { uuid: comp_sample2.uuid }],
+      'huMFre_code' => '23/21'
     }
   end
 
diff --git a/spec/models/sample_spec.rb b/spec/models/sample_spec.rb
index daa588a53d..838ff5f62c 100644
--- a/spec/models/sample_spec.rb
+++ b/spec/models/sample_spec.rb
@@ -259,6 +259,30 @@
     end
   end
 
+  context 'huMFre code' do
+    let(:sample) { create(:sample) }
+
+    it 'defaults to null when not specified' do
+      expect(sample.sample_metadata.huMFre_code).to be_nil
+    end
+
+    it 'fails to update/save when huMFre code value is invalid' do
+      expect(sample.sample_metadata.huMFre_code).to be_nil
+      sample.sample_metadata.huMFre_code = 'humFre1'
+      expect(sample.sample_metadata.save).to be false
+    end
+
+    it 'contains huMFre code value when it is correctly specified' do
+      sample.sample_metadata.update!(huMFre_code: '12/12')
+      expect(sample.sample_metadata.huMFre_code).to eq '12/12'
+    end
+
+    it 'can have the huMFre code blanked' do
+      sample.sample_metadata.update!(huMFre_code: nil)
+      expect(sample.sample_metadata.huMFre_code).to be_nil
+    end
+  end
+
   context '(DPL-148) on updating sample metadata' do
     let(:sample) { create(:sample) }
 

From debfce3821877fe8eb28519c0e29dd95919cbb55 Mon Sep 17 00:00:00 2001
From: sabrine33 <sa33@sanger.ac.uk>
Date: Thu, 12 Dec 2024 12:01:53 +0000
Subject: [PATCH 30/40] run prettier

---
 app/models/sample.rb | 1 -
 1 file changed, 1 deletion(-)

diff --git a/app/models/sample.rb b/app/models/sample.rb
index 2ea4e9d0da..5ea3f68a78 100644
--- a/app/models/sample.rb
+++ b/app/models/sample.rb
@@ -228,7 +228,6 @@ class Current < ActiveSupport::CurrentAttributes
   # Sample::Metadata tracks sample information, either for use in the lab, or passing to
   # the EBI
   class Metadata
-
     validates :huMFre_code,
               format: {
                 with: %r{\A\d{2}/\d{2,}|\d{2}/\d{4}-\d{3}\z},

From 7ef8fb8564bd5c61c77e7ddf281b466dfda8ec5e Mon Sep 17 00:00:00 2001
From: sabrine33 <sa33@sanger.ac.uk>
Date: Thu, 12 Dec 2024 13:20:37 +0000
Subject: [PATCH 31/40] fix cucumber test

---
 features/samples/xml_interface.feature | 1 +
 1 file changed, 1 insertion(+)

diff --git a/features/samples/xml_interface.feature b/features/samples/xml_interface.feature
index 26f533159e..960ec1e0d4 100644
--- a/features/samples/xml_interface.feature
+++ b/features/samples/xml_interface.feature
@@ -68,6 +68,7 @@ Feature: The XML interface to the samples
           <property><name>Time Point</name><value></value></property>
           <property><name>Donor Id</name><value></value></property>
           <property><name>Collected By</name><value/></property>
+          <property><name>HuMFre Code</name><value/></property>
         </properties>
       </sample>
       """

From 168c92e638339062f6e2704e327b853e3220fc3f Mon Sep 17 00:00:00 2001
From: sabrine33 <sa33@sanger.ac.uk>
Date: Wed, 18 Dec 2024 10:57:14 +0000
Subject: [PATCH 32/40] add length constrain to the huMFre code

---
 app/models/sample.rb | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/app/models/sample.rb b/app/models/sample.rb
index 5ea3f68a78..1dc5ee358b 100644
--- a/app/models/sample.rb
+++ b/app/models/sample.rb
@@ -228,9 +228,13 @@ class Current < ActiveSupport::CurrentAttributes
   # Sample::Metadata tracks sample information, either for use in the lab, or passing to
   # the EBI
   class Metadata
+    # HuMFre numbers contain tissue information, which is only relevant for human samples.
     validates :huMFre_code,
+              length: {
+                maximum: 16
+              },
               format: {
-                with: %r{\A\d{2}/\d{2,}|\d{2}/\d{4}-\d{3}\z},
+                with: %r{\A(?:\d{2}/\d{2,}|\d{2}/\d{4}-\d{3})\z},
                 message: 'must match a valid format, e.g. 12/34 or 12/2023-001'
               },
               allow_blank: true

From 1ee65bb199f200583f6cd03c8fc08f189ebcf0bf Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Wed, 8 Jan 2025 11:34:36 +0000
Subject: [PATCH 33/40] Update rails to version 7.0.8.7

---
 Gemfile.lock | 133 ++++++++++++++++++++++++++-------------------------
 1 file changed, 67 insertions(+), 66 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 60c8c361b3..f9f71d0799 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -34,34 +34,34 @@ GEM
   specs:
     aasm (5.5.0)
       concurrent-ruby (~> 1.0)
-    actioncable (7.0.8.1)
-      actionpack (= 7.0.8.1)
-      activesupport (= 7.0.8.1)
+    actioncable (7.0.8.7)
+      actionpack (= 7.0.8.7)
+      activesupport (= 7.0.8.7)
       nio4r (~> 2.0)
       websocket-driver (>= 0.6.1)
-    actionmailbox (7.0.8.1)
-      actionpack (= 7.0.8.1)
-      activejob (= 7.0.8.1)
-      activerecord (= 7.0.8.1)
-      activestorage (= 7.0.8.1)
-      activesupport (= 7.0.8.1)
+    actionmailbox (7.0.8.7)
+      actionpack (= 7.0.8.7)
+      activejob (= 7.0.8.7)
+      activerecord (= 7.0.8.7)
+      activestorage (= 7.0.8.7)
+      activesupport (= 7.0.8.7)
       mail (>= 2.7.1)
       net-imap
       net-pop
       net-smtp
-    actionmailer (7.0.8.1)
-      actionpack (= 7.0.8.1)
-      actionview (= 7.0.8.1)
-      activejob (= 7.0.8.1)
-      activesupport (= 7.0.8.1)
+    actionmailer (7.0.8.7)
+      actionpack (= 7.0.8.7)
+      actionview (= 7.0.8.7)
+      activejob (= 7.0.8.7)
+      activesupport (= 7.0.8.7)
       mail (~> 2.5, >= 2.5.4)
       net-imap
       net-pop
       net-smtp
       rails-dom-testing (~> 2.0)
-    actionpack (7.0.8.1)
-      actionview (= 7.0.8.1)
-      activesupport (= 7.0.8.1)
+    actionpack (7.0.8.7)
+      actionview (= 7.0.8.7)
+      activesupport (= 7.0.8.7)
       rack (~> 2.0, >= 2.2.4)
       rack-test (>= 0.6.3)
       rails-dom-testing (~> 2.0)
@@ -69,37 +69,37 @@ GEM
     actionpack-xml_parser (2.0.1)
       actionpack (>= 5.0)
       railties (>= 5.0)
-    actiontext (7.0.8.1)
-      actionpack (= 7.0.8.1)
-      activerecord (= 7.0.8.1)
-      activestorage (= 7.0.8.1)
-      activesupport (= 7.0.8.1)
+    actiontext (7.0.8.7)
+      actionpack (= 7.0.8.7)
+      activerecord (= 7.0.8.7)
+      activestorage (= 7.0.8.7)
+      activesupport (= 7.0.8.7)
       globalid (>= 0.6.0)
       nokogiri (>= 1.8.5)
-    actionview (7.0.8.1)
-      activesupport (= 7.0.8.1)
+    actionview (7.0.8.7)
+      activesupport (= 7.0.8.7)
       builder (~> 3.1)
       erubi (~> 1.4)
       rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.1, >= 1.2.0)
-    activejob (7.0.8.1)
-      activesupport (= 7.0.8.1)
+    activejob (7.0.8.7)
+      activesupport (= 7.0.8.7)
       globalid (>= 0.3.6)
-    activemodel (7.0.8.1)
-      activesupport (= 7.0.8.1)
-    activerecord (7.0.8.1)
-      activemodel (= 7.0.8.1)
-      activesupport (= 7.0.8.1)
+    activemodel (7.0.8.7)
+      activesupport (= 7.0.8.7)
+    activerecord (7.0.8.7)
+      activemodel (= 7.0.8.7)
+      activesupport (= 7.0.8.7)
     activerecord-import (1.7.0)
       activerecord (>= 4.2)
-    activestorage (7.0.8.1)
-      actionpack (= 7.0.8.1)
-      activejob (= 7.0.8.1)
-      activerecord (= 7.0.8.1)
-      activesupport (= 7.0.8.1)
+    activestorage (7.0.8.7)
+      actionpack (= 7.0.8.7)
+      activejob (= 7.0.8.7)
+      activerecord (= 7.0.8.7)
+      activesupport (= 7.0.8.7)
       marcel (~> 1.0)
       mini_mime (>= 1.1.0)
-    activesupport (7.0.8.1)
+    activesupport (7.0.8.7)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 1.6, < 2)
       minitest (>= 5.1)
@@ -196,7 +196,7 @@ GEM
       activerecord (>= 5.a)
       database_cleaner-core (~> 2.0.0)
     database_cleaner-core (2.0.1)
-    date (3.4.0)
+    date (3.4.1)
     delayed_job (4.1.11)
       activesupport (>= 3.0, < 8.0)
     delayed_job_active_record (4.1.8)
@@ -206,7 +206,7 @@ GEM
     docile (1.4.0)
     domain_name (0.6.20240107)
     dry-cli (1.0.0)
-    erubi (1.13.0)
+    erubi (1.13.1)
     exception_notification (4.5.0)
       actionmailer (>= 5.2, < 8)
       activesupport (>= 5.2, < 8)
@@ -257,7 +257,7 @@ GEM
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
     logger (1.6.1)
-    loofah (2.23.1)
+    loofah (2.24.0)
       crass (~> 1.0.2)
       nokogiri (>= 1.12.0)
     mail (2.8.1)
@@ -273,7 +273,7 @@ GEM
     mime-types-data (3.2024.0305)
     mini_magick (4.12.0)
     mini_mime (1.1.5)
-    minitest (5.25.1)
+    minitest (5.25.4)
     minitest-profiler (0.0.2)
       activesupport (>= 4.1.0)
       minitest (>= 5.3.3)
@@ -285,7 +285,7 @@ GEM
     mustermann (3.0.0)
       ruby2_keywords (~> 0.0.1)
     mysql2 (0.5.6)
-    net-imap (0.5.1)
+    net-imap (0.5.5)
       date
       net-protocol
     net-ldap (0.19.0)
@@ -297,11 +297,11 @@ GEM
       net-protocol
     netrc (0.11.0)
     nio4r (2.7.4)
-    nokogiri (1.16.7-arm64-darwin)
+    nokogiri (1.18.1-arm64-darwin)
       racc (~> 1.4)
-    nokogiri (1.16.7-x86_64-darwin)
+    nokogiri (1.18.1-x86_64-darwin)
       racc (~> 1.4)
-    nokogiri (1.16.7-x86_64-linux)
+    nokogiri (1.18.1-x86_64-linux-gnu)
       racc (~> 1.4)
     ostruct (0.6.0)
     parallel (1.26.3)
@@ -334,22 +334,22 @@ GEM
       rack (~> 2.2, >= 2.2.4)
     rack-proxy (0.7.7)
       rack
-    rack-test (2.1.0)
+    rack-test (2.2.0)
       rack (>= 1.3)
-    rails (7.0.8.1)
-      actioncable (= 7.0.8.1)
-      actionmailbox (= 7.0.8.1)
-      actionmailer (= 7.0.8.1)
-      actionpack (= 7.0.8.1)
-      actiontext (= 7.0.8.1)
-      actionview (= 7.0.8.1)
-      activejob (= 7.0.8.1)
-      activemodel (= 7.0.8.1)
-      activerecord (= 7.0.8.1)
-      activestorage (= 7.0.8.1)
-      activesupport (= 7.0.8.1)
+    rails (7.0.8.7)
+      actioncable (= 7.0.8.7)
+      actionmailbox (= 7.0.8.7)
+      actionmailer (= 7.0.8.7)
+      actionpack (= 7.0.8.7)
+      actiontext (= 7.0.8.7)
+      actionview (= 7.0.8.7)
+      activejob (= 7.0.8.7)
+      activemodel (= 7.0.8.7)
+      activerecord (= 7.0.8.7)
+      activestorage (= 7.0.8.7)
+      activesupport (= 7.0.8.7)
       bundler (>= 1.15.0)
-      railties (= 7.0.8.1)
+      railties (= 7.0.8.7)
     rails-controller-testing (1.0.5)
       actionpack (>= 5.0.1.rc1)
       actionview (>= 5.0.1.rc1)
@@ -363,13 +363,13 @@ GEM
       activesupport (>= 4.2)
       choice (~> 0.2.0)
       ruby-graphviz (~> 1.2)
-    rails-html-sanitizer (1.6.0)
+    rails-html-sanitizer (1.6.2)
       loofah (~> 2.21)
-      nokogiri (~> 1.14)
+      nokogiri (>= 1.15.7, != 1.16.7, != 1.16.6, != 1.16.5, != 1.16.4, != 1.16.3, != 1.16.2, != 1.16.1, != 1.16.0.rc1, != 1.16.0)
     rails-perftest (0.0.7)
-    railties (7.0.8.1)
-      actionpack (= 7.0.8.1)
-      activesupport (= 7.0.8.1)
+    railties (7.0.8.7)
+      actionpack (= 7.0.8.7)
+      activesupport (= 7.0.8.7)
       method_source
       rake (>= 12.2)
       thor (~> 1.0)
@@ -515,7 +515,7 @@ GEM
     thor (1.3.2)
     tilt (2.4.0)
     timecop (0.9.10)
-    timeout (0.4.2)
+    timeout (0.4.3)
     traceroute (0.8.1)
       rails (>= 3.0.0)
     tzinfo (2.0.6)
@@ -535,7 +535,8 @@ GEM
       crack (>= 0.3.2)
       hashdiff (>= 0.4.0, < 2.0.0)
     websocket (1.2.11)
-    websocket-driver (0.7.6)
+    websocket-driver (0.7.7)
+      base64
       websocket-extensions (>= 0.1.0)
     websocket-extensions (0.1.5)
     whenever (1.0.0)

From 1e862057780917791dbbcf17da4d72cf23b5d04a Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Wed, 8 Jan 2025 19:06:10 +0000
Subject: [PATCH 34/40] Update factory_bot_rails to version 6.4.4

---
 Gemfile.lock | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index f9f71d0799..d6d9f67284 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -210,10 +210,10 @@ GEM
     exception_notification (4.5.0)
       actionmailer (>= 5.2, < 8)
       activesupport (>= 5.2, < 8)
-    factory_bot (6.4.6)
+    factory_bot (6.5.0)
       activesupport (>= 5.0.0)
-    factory_bot_rails (6.4.3)
-      factory_bot (~> 6.4)
+    factory_bot_rails (6.4.4)
+      factory_bot (~> 6.5)
       railties (>= 5.0.0)
     ffi (1.16.3)
     flipper (0.25.4)

From 7238682efc8ca76417f5014a4759447b1eec22bd Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Thu, 9 Jan 2025 07:17:05 +0000
Subject: [PATCH 35/40] Update Node.js to version 22.13.0

---
 .nvmrc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.nvmrc b/.nvmrc
index 7af24b7ddb..6fa8dec4cd 100644
--- a/.nvmrc
+++ b/.nvmrc
@@ -1 +1 @@
-22.11.0
+22.13.0

From 350bf8d240bdbd9b972661738ae5596dba5d81d4 Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Thu, 9 Jan 2025 13:54:18 +0000
Subject: [PATCH 36/40] Update postcss to version 8.4.49

---
 package.json |  2 +-
 yarn.lock    | 19 +++++++++++++++++++
 2 files changed, 20 insertions(+), 1 deletion(-)

diff --git a/package.json b/package.json
index 7f11641e6b..af53721034 100644
--- a/package.json
+++ b/package.json
@@ -16,7 +16,7 @@
     "jsbarcode": "^3.11.6",
     "jszip": "^3.10.1",
     "popper.js": "^1.16.1",
-    "postcss": "^8.4.39",
+    "postcss": "^8.4.49",
     "postcss-flexbugs-fixes": "^5.0.2",
     "postcss-import": "^14.1.0",
     "postcss-preset-env": "^7.8.3",
diff --git a/yarn.lock b/yarn.lock
index 5f00b9aca4..360d2c0f3d 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -5769,6 +5769,11 @@ picocolors@^1.0.0, picocolors@^1.0.1:
   resolved "https://registry.yarnpkg.com/picocolors/-/picocolors-1.0.1.tgz#a8ad579b571952f0e5d25892de5445bcfe25aaa1"
   integrity sha512-anP1Z8qwhkbmu7MFP5iTt+wQKXgwzf7zTyGlcdzabySa9vd0Xt392U0rVmz9poOaBj0uHJKyyo9/upk0HrEQew==
 
+picocolors@^1.1.1:
+  version "1.1.1"
+  resolved "https://registry.yarnpkg.com/picocolors/-/picocolors-1.1.1.tgz#3d321af3eab939b083c8f929a1d12cda81c26b6b"
+  integrity sha512-xceH2snhtb5M9liqDsmEw56le376mTZkEX/jEb/RxNFyegNul7eNslCXP9FDj/Lcu0X8KEyMceP2ntpaHrDEVA==
+
 picomatch@^2.0.4, picomatch@^2.2.1, picomatch@^2.2.2, picomatch@^2.2.3:
   version "2.3.1"
   resolved "https://registry.yarnpkg.com/picomatch/-/picomatch-2.3.1.tgz#3ba3833733646d9d3e4995946c1365a67fb07a42"
@@ -6130,6 +6135,15 @@ postcss@^8.4.33:
     picocolors "^1.0.0"
     source-map-js "^1.2.0"
 
+postcss@^8.4.49:
+  version "8.4.49"
+  resolved "https://registry.yarnpkg.com/postcss/-/postcss-8.4.49.tgz#4ea479048ab059ab3ae61d082190fabfd994fe19"
+  integrity sha512-OCVPnIObs4N29kxTjzLfUryOkvZEq+pf8jTF0lg8E7uETuWHA+v7j3c/xJmiqpX450191LlmZfUKkXxkTry7nA==
+  dependencies:
+    nanoid "^3.3.7"
+    picocolors "^1.1.1"
+    source-map-js "^1.2.1"
+
 prelude-ls@^1.2.1:
   version "1.2.1"
   resolved "https://registry.yarnpkg.com/prelude-ls/-/prelude-ls-1.2.1.tgz#debc6489d7a6e6b0e7611888cec880337d316396"
@@ -6724,6 +6738,11 @@ sortablejs@^1.15.2:
   resolved "https://registry.yarnpkg.com/source-map-js/-/source-map-js-1.2.0.tgz#16b809c162517b5b8c3e7dcd315a2a5c2612b2af"
   integrity sha512-itJW8lvSA0TXEphiRoawsCksnlf8SyvmFzIhltqAHluXd88pkCd+cXJVHTDwdCr0IzwptSm035IHQktUu1QUMg==
 
+source-map-js@^1.2.1:
+  version "1.2.1"
+  resolved "https://registry.yarnpkg.com/source-map-js/-/source-map-js-1.2.1.tgz#1ce5650fddd87abc099eda37dcff024c2667ae46"
+  integrity sha512-UXWMKhLOwVKb728IUtQPXxfYU+usdybtUrK/8uGE8CQMvrhOpwvzDBwj0QhSL7MQc7vIsISBG8VQ8+IDQxpfQA==
+
 source-map-resolve@^0.5.0, source-map-resolve@^0.5.2:
   version "0.5.3"
   resolved "https://registry.yarnpkg.com/source-map-resolve/-/source-map-resolve-0.5.3.tgz#190866bece7553e1f8f267a2ee82c606b5509a1a"

From 2875b4b59bfd643a66923450f65d0444e0cac79e Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Thu, 9 Jan 2025 13:58:57 +0000
Subject: [PATCH 37/40] Update @rails/ujs to version 7.1.501

---
 package.json | 2 +-
 yarn.lock    | 8 ++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/package.json b/package.json
index 7f11641e6b..542b2c006c 100644
--- a/package.json
+++ b/package.json
@@ -1,7 +1,7 @@
 {
   "dependencies": {
     "@fortawesome/fontawesome-free": "^6.5.2",
-    "@rails/ujs": "^7.1.3",
+    "@rails/ujs": "^7.1.501",
     "@ttskch/select2-bootstrap4-theme": "^1.5.2",
     "bootstrap": "^4.6.2",
     "css-loader": "^6.0.0",
diff --git a/yarn.lock b/yarn.lock
index 5f00b9aca4..85cabb6a73 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -1911,10 +1911,10 @@
   resolved "https://registry.yarnpkg.com/@prettier/plugin-ruby/-/plugin-ruby-4.0.4.tgz#73d85fc2a1731a3f62b57ac3116cf1c234027cb6"
   integrity sha512-lCpvfS/dQU5WrwN3AQ5vR8qrvj2h5gE41X08NNzAAXvHdM4zwwGRcP2sHSxfu6n6No+ljWCVx95NvJPFTTjCTg==
 
-"@rails/ujs@^7.1.3":
-  version "7.1.3"
-  resolved "https://registry.yarnpkg.com/@rails/ujs/-/ujs-7.1.3.tgz#6d94a68b7da5046147d31716e0c187a4ead4fb93"
-  integrity sha512-FxtgKNvvIonoBE1TK7U10VMf6CYvzq8SIZ1XZ1Q8zcn/BEXzPzid3zC9qFiojuI5WXVwWhO8GFqApq0stD+OqQ==
+"@rails/ujs@^7.1.501":
+  version "7.1.501"
+  resolved "https://registry.yarnpkg.com/@rails/ujs/-/ujs-7.1.501.tgz#e560a7b6885a12a659c4beb47f4336c8a9353056"
+  integrity sha512-7EDRGUlgns12IgP3SXVSaxA3CwRzbLOypPXn1EqEZiZ/NS/PwaQ/oa7Z2VRO4B46JifoVr0PYg+G5ERSGQJHxQ==
 
 "@rollup/pluginutils@^4.1.1":
   version "4.1.2"

From bcf93b1883d9178e58e459091b353a278157f91c Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Thu, 9 Jan 2025 20:41:57 +0000
Subject: [PATCH 38/40] Update Ruby to version 3.2.6

---
 .ruby-version | 2 +-
 Dockerfile    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.ruby-version b/.ruby-version
index 5ae69bd5f0..34cde5690e 100644
--- a/.ruby-version
+++ b/.ruby-version
@@ -1 +1 @@
-3.2.5
+3.2.6
diff --git a/Dockerfile b/Dockerfile
index f64ba4780f..53d2b9e0ea 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -2,7 +2,7 @@ ARG CHIPSET=default
 
 # Use the correct base image depending on the architecture
 # For Apple M1 Chip, run: docker build --build-arg CHIPSET=m1 .
-FROM ruby:3.2.5-slim AS base_default
+FROM ruby:3.2.6-slim AS base_default
 FROM --platform=linux/amd64 ruby:3.2.5-slim AS base_m1
 FROM base_${CHIPSET} AS base
 

From edecf3750d294b3658f3c7de8ee377941e027d50 Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Thu, 9 Jan 2025 22:47:57 +0000
Subject: [PATCH 39/40] Update Ruby to version 3.3.6

---
 .ruby-version | 2 +-
 Dockerfile    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.ruby-version b/.ruby-version
index 34cde5690e..9c25013dbb 100644
--- a/.ruby-version
+++ b/.ruby-version
@@ -1 +1 @@
-3.2.6
+3.3.6
diff --git a/Dockerfile b/Dockerfile
index 53d2b9e0ea..8209798ccf 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -2,7 +2,7 @@ ARG CHIPSET=default
 
 # Use the correct base image depending on the architecture
 # For Apple M1 Chip, run: docker build --build-arg CHIPSET=m1 .
-FROM ruby:3.2.6-slim AS base_default
+FROM ruby:3.3.6-slim AS base_default
 FROM --platform=linux/amd64 ruby:3.2.5-slim AS base_m1
 FROM base_${CHIPSET} AS base
 

From 4262bc5115e82cccbdce140db084356203dcc2a5 Mon Sep 17 00:00:00 2001
From: "depfu[bot]" <23717796+depfu[bot]@users.noreply.github.com>
Date: Thu, 9 Jan 2025 23:34:38 +0000
Subject: [PATCH 40/40] Update ruby-prof to version 1.7.1

---
 Gemfile.lock | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index d6d9f67284..1c4933d500 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -454,7 +454,7 @@ GEM
       rubocop-rspec (~> 3, >= 3.0.1)
     ruby-graphviz (1.2.5)
       rexml
-    ruby-prof (1.7.0)
+    ruby-prof (1.7.1)
     ruby-progressbar (1.13.0)
     ruby-units (4.0.3)
     ruby-vips (2.2.1)