From ed0f7d3facec7c541ffd7326f3a7e6b78fe3a846 Mon Sep 17 00:00:00 2001
From: Dasun Pubudumal <pubudumald@gmail.com>
Date: Thu, 14 Aug 2025 14:08:05 +0100
Subject: [PATCH 01/37] Adding some documentation!

---
 config/initializers/settings.rb | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/config/initializers/settings.rb b/config/initializers/settings.rb
index 73f35f132b..df0493dfeb 100644
--- a/config/initializers/settings.rb
+++ b/config/initializers/settings.rb
@@ -12,6 +12,8 @@ def configuration_filename
     private :configuration_filename
 
     def instance # rubocop:todo Metrics/AbcSize
+      # @instance is a Hashie::Mash object that contains all the settings loaded from the YAML file.
+      # It allows for method calls like Settings.pipelines, Settings.purposes, etc.
       return @instance if @instance.present?
 
       # Ideally we'd do Hashie::Mash.load(File.read(configuration_filename)) here
@@ -23,6 +25,8 @@ def instance # rubocop:todo Metrics/AbcSize
 
       # To view a list of pipeline groups and respective pipelines:
       # e.g. Settings.pipelines.group_by(&:pipeline_group).transform_values { |pipelines| pipelines.map(&:name) }
+
+      # This line has specifically been set to customise the behaviour of loading the pipelines.
       @instance.pipelines = ConfigLoader::PipelinesLoader.new.pipelines
 
       @instance
@@ -38,6 +42,9 @@ def instance # rubocop:todo Metrics/AbcSize
       # rubocop:enable Style/StderrPuts
     end
 
+    # This line is making it possible to access configuration using
+    # the Settings.<config> syntax. For example, Settings.pipelines, Settings.purposes, etc.
+    # It delegates all method calls to the instance of Settings.
     delegate_missing_to :instance
 
     def reinitialize

From 5b9431e5f5a5965d24996fe9c4ef3fad2a38e7a9 Mon Sep 17 00:00:00 2001
From: Dasun Pubudumal <pubudumald@gmail.com>
Date: Thu, 14 Aug 2025 14:09:56 +0100
Subject: [PATCH 02/37] [skip ci] Adding some documentation!

---
 config/initializers/settings.rb | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/config/initializers/settings.rb b/config/initializers/settings.rb
index df0493dfeb..1949eb24e9 100644
--- a/config/initializers/settings.rb
+++ b/config/initializers/settings.rb
@@ -11,6 +11,9 @@ def configuration_filename
     end
     private :configuration_filename
 
+    # When invoked, this method will return a Hashie::Mash object that contains all the settings loaded from
+    # the YAML file.
+    # For example, you can access settings like `Settings.pipelines`, `Settings.purposes`, etc.
     def instance # rubocop:todo Metrics/AbcSize
       # @instance is a Hashie::Mash object that contains all the settings loaded from the YAML file.
       # It allows for method calls like Settings.pipelines, Settings.purposes, etc.

From 87503b4b9def689d2bf9574740cd781b935dffd2 Mon Sep 17 00:00:00 2001
From: Dasun Pubudumal <pubudumald@gmail.com>
Date: Thu, 14 Aug 2025 14:18:59 +0100
Subject: [PATCH 03/37] [skip ci] Adding some documentation!

---
 config/initializers/settings.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/initializers/settings.rb b/config/initializers/settings.rb
index 1949eb24e9..d0840d4ab7 100644
--- a/config/initializers/settings.rb
+++ b/config/initializers/settings.rb
@@ -47,7 +47,7 @@ def instance # rubocop:todo Metrics/AbcSize
 
     # This line is making it possible to access configuration using
     # the Settings.<config> syntax. For example, Settings.pipelines, Settings.purposes, etc.
-    # It delegates all method calls to the instance of Settings.
+    # It delegates all method calls to the Mash (which is @instance here).
     delegate_missing_to :instance
 
     def reinitialize

From 7484922e8bec9acad591634264efcb9458ab97a8 Mon Sep 17 00:00:00 2001
From: Dasun Pubudumal <pubudumald@gmail.com>
Date: Fri, 15 Aug 2025 13:29:46 +0100
Subject: [PATCH 04/37] Starting Settions and Configuration V2 mixins.

---
 config/initializers/configurationV2.rb | 39 +++++++++++++++++++++++++
 config/initializers/settingsV2.rb      | 40 ++++++++++++++++++++++++++
 2 files changed, 79 insertions(+)
 create mode 100644 config/initializers/configurationV2.rb
 create mode 100644 config/initializers/settingsV2.rb

diff --git a/config/initializers/configurationV2.rb b/config/initializers/configurationV2.rb
new file mode 100644
index 0000000000..36bcdd3be7
--- /dev/null
+++ b/config/initializers/configurationV2.rb
@@ -0,0 +1,39 @@
+# frozen_string_literal: true
+
+module ConfigurationV2
+  # Configuration for the application, including loaders for various configurations.
+
+  def initialize(config_hash)
+    config_hash.with_indifferent_access.each do |key, value|
+
+    end
+  end
+
+  class Item
+    include Enumerable
+
+    attr_reader :children, :configuration
+
+    def initialize(configuration, children = {})
+      @children = children
+      @configuration = configuration
+
+      children.each do |key, child|
+        if child.is_a?(ActiveSupport::HashWithIndifferentAccess)
+          next if respond_to?(key)
+
+          child_item = Item.new(configuration, child)
+          define_singleton_method(key) { child_item }
+        else
+          define_singleton_method(key) { child }
+        end
+      end
+    end
+
+    def each(...)
+      children.each(...)
+    end
+  end
+
+
+end
\ No newline at end of file
diff --git a/config/initializers/settingsV2.rb b/config/initializers/settingsV2.rb
new file mode 100644
index 0000000000..ce299779f9
--- /dev/null
+++ b/config/initializers/settingsV2.rb
@@ -0,0 +1,40 @@
+# frozen_string_literal: true
+
+module SettingsV2
+
+  CONFIGURATION_TYPES = [
+    :searches,
+    :transfer_templates,
+    :printers,
+    :purposes,
+    :purpose_uuids,
+    :robots,
+    :default_pmb_templates,
+    :default_sprint_templates,
+    :default_printer_type_names,
+    :submission_templates
+  ]*
+
+  CONFIGURATION_TYPES.each do |config|
+    # proc needs to return the configuration value
+    self.class.send(:define_method, config, proc { configuration.send(config) })
+  end
+
+  def self.load_yaml
+    config = Rails.root.join('config', 'settings', "#{Rails.env}.yml")
+    return unless File.exist?(config)
+
+    config_file_descriptor = File.open(configuration_filename, 'r:bom|utf-8')
+    # Returns a Hash with the configuration data
+    config_data = YAML.safe_load(config_file_descriptor, permitted_classes: [Symbol], aliases: true)
+    raise "Configuration file #{config} is not valid YAML." if config_data.blank?
+
+    config_data.with_indifferent_access
+  end
+
+  def self.configuration
+    @configuration ||= ConfigurationV2.new(load_yaml)
+  end
+
+
+end
\ No newline at end of file

From e9a64dfc4a35b2a4f22bb6c21b7bf751c5e2bc62 Mon Sep 17 00:00:00 2001
From: Dasun Pubudumal <pubudumald@gmail.com>
Date: Mon, 18 Aug 2025 09:38:38 +0100
Subject: [PATCH 05/37] Fix linting issues

---
 ...configurationV2.rb => configuration_v2.rb} | 13 ++++---
 .../{settingsV2.rb => settings_v2.rb}         | 39 +++++++++----------
 2 files changed, 25 insertions(+), 27 deletions(-)
 rename config/initializers/{configurationV2.rb => configuration_v2.rb} (78%)
 rename config/initializers/{settingsV2.rb => settings_v2.rb} (58%)

diff --git a/config/initializers/configurationV2.rb b/config/initializers/configuration_v2.rb
similarity index 78%
rename from config/initializers/configurationV2.rb
rename to config/initializers/configuration_v2.rb
index 36bcdd3be7..5d6f9e9252 100644
--- a/config/initializers/configurationV2.rb
+++ b/config/initializers/configuration_v2.rb
@@ -1,19 +1,21 @@
 # frozen_string_literal: true
 
+# Parent configuration mixin.
 module ConfigurationV2
   # Configuration for the application, including loaders for various configurations.
 
   def initialize(config_hash)
-    config_hash.with_indifferent_access.each do |key, value|
-
-    end
+    # config_hash.with_indifferent_access.each do |key, value|
+    # end
   end
 
+  # Configuration item.
   class Item
     include Enumerable
 
     attr_reader :children, :configuration
 
+    # rubocop:disable Metrics/MethodLength
     def initialize(configuration, children = {})
       @children = children
       @configuration = configuration
@@ -29,11 +31,10 @@ def initialize(configuration, children = {})
         end
       end
     end
+    # rubocop:enable Metrics/MethodLength
 
     def each(...)
       children.each(...)
     end
   end
-
-
-end
\ No newline at end of file
+end
diff --git a/config/initializers/settingsV2.rb b/config/initializers/settings_v2.rb
similarity index 58%
rename from config/initializers/settingsV2.rb
rename to config/initializers/settings_v2.rb
index ce299779f9..a0e7f9ef22 100644
--- a/config/initializers/settingsV2.rb
+++ b/config/initializers/settings_v2.rb
@@ -1,24 +1,23 @@
 # frozen_string_literal: true
 
+# Parent settings mixin.
 module SettingsV2
-
-  CONFIGURATION_TYPES = [
-    :searches,
-    :transfer_templates,
-    :printers,
-    :purposes,
-    :purpose_uuids,
-    :robots,
-    :default_pmb_templates,
-    :default_sprint_templates,
-    :default_printer_type_names,
-    :submission_templates
-  ]*
-
-  CONFIGURATION_TYPES.each do |config|
-    # proc needs to return the configuration value
-    self.class.send(:define_method, config, proc { configuration.send(config) })
-  end
+  CONFIGURATION_TYPES = %i[
+    searches
+    transfer_templates
+    printers
+    purposes
+    purpose_uuids
+    robots
+    default_pmb_templates
+    default_sprint_templates
+    default_printer_type_names
+    submission_templates
+  ] *
+    CONFIGURATION_TYPES.each do |config|
+      # proc needs to return the configuration value
+      self.class.send(:define_method, config, proc { configuration.send(config) })
+    end
 
   def self.load_yaml
     config = Rails.root.join('config', 'settings', "#{Rails.env}.yml")
@@ -35,6 +34,4 @@ def self.load_yaml
   def self.configuration
     @configuration ||= ConfigurationV2.new(load_yaml)
   end
-
-
-end
\ No newline at end of file
+end

From 1fbe0030c17d44371009b3b4ca178e0c7c7ee03a Mon Sep 17 00:00:00 2001
From: Dasun Pubudumal <pubudumald@gmail.com>
Date: Mon, 18 Aug 2025 09:41:09 +0100
Subject: [PATCH 06/37] Fix linting issues

---
 config/initializers/settings_v2.rb | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/config/initializers/settings_v2.rb b/config/initializers/settings_v2.rb
index a0e7f9ef22..8c8470801a 100644
--- a/config/initializers/settings_v2.rb
+++ b/config/initializers/settings_v2.rb
@@ -13,11 +13,12 @@ module SettingsV2
     default_sprint_templates
     default_printer_type_names
     submission_templates
-  ] *
-    CONFIGURATION_TYPES.each do |config|
-      # proc needs to return the configuration value
-      self.class.send(:define_method, config, proc { configuration.send(config) })
-    end
+  ].freeze
+
+  CONFIGURATION_TYPES.each do |config|
+    # proc needs to return the configuration value
+    self.class.send(:define_method, config, proc { configuration.send(config) })
+  end
 
   def self.load_yaml
     config = Rails.root.join('config', 'settings', "#{Rails.env}.yml")

From 239458f641ca8b2a0792b36d3b10410b43c8b5dc Mon Sep 17 00:00:00 2001
From: Dasun Pubudumal <pubudumald@gmail.com>
Date: Mon, 18 Aug 2025 11:57:19 +0100
Subject: [PATCH 07/37] Redoing the settings module

---
 config/initializers/configuration_v2.rb     | 40 ---------
 config/initializers/custom_configuration.rb | 44 ++++++++++
 config/initializers/settings.rb             | 94 ++++++++-------------
 config/initializers/settings_v2.rb          | 38 ---------
 4 files changed, 80 insertions(+), 136 deletions(-)
 delete mode 100644 config/initializers/configuration_v2.rb
 create mode 100644 config/initializers/custom_configuration.rb
 delete mode 100644 config/initializers/settings_v2.rb

diff --git a/config/initializers/configuration_v2.rb b/config/initializers/configuration_v2.rb
deleted file mode 100644
index 5d6f9e9252..0000000000
--- a/config/initializers/configuration_v2.rb
+++ /dev/null
@@ -1,40 +0,0 @@
-# frozen_string_literal: true
-
-# Parent configuration mixin.
-module ConfigurationV2
-  # Configuration for the application, including loaders for various configurations.
-
-  def initialize(config_hash)
-    # config_hash.with_indifferent_access.each do |key, value|
-    # end
-  end
-
-  # Configuration item.
-  class Item
-    include Enumerable
-
-    attr_reader :children, :configuration
-
-    # rubocop:disable Metrics/MethodLength
-    def initialize(configuration, children = {})
-      @children = children
-      @configuration = configuration
-
-      children.each do |key, child|
-        if child.is_a?(ActiveSupport::HashWithIndifferentAccess)
-          next if respond_to?(key)
-
-          child_item = Item.new(configuration, child)
-          define_singleton_method(key) { child_item }
-        else
-          define_singleton_method(key) { child }
-        end
-      end
-    end
-    # rubocop:enable Metrics/MethodLength
-
-    def each(...)
-      children.each(...)
-    end
-  end
-end
diff --git a/config/initializers/custom_configuration.rb b/config/initializers/custom_configuration.rb
new file mode 100644
index 0000000000..049c6d7c0f
--- /dev/null
+++ b/config/initializers/custom_configuration.rb
@@ -0,0 +1,44 @@
+# frozen_string_literal: true
+
+# Parent configuration mixin.
+module Settings
+  # Configuration for the application, including loaders for various configurations.
+
+  # Custom configuration class that can be used to build a configuration
+  class CustomConfiguration
+    def initialize(config_hash)
+      config_hash.with_indifferent_access.each do |key, value|
+        define_singleton_method(key) { Item.new(key, value) }
+      end
+    end
+
+    # Configuration item.
+    class Item
+      include Enumerable
+
+      attr_reader :children, :configuration
+
+      # rubocop:disable Metrics/MethodLength
+      def initialize(configuration, children = {})
+        @children = children
+        @configuration = configuration
+
+        children.each do |key, child|
+          if child.is_a?(ActiveSupport::HashWithIndifferentAccess)
+            next if respond_to?(key)
+
+            child_item = Item.new(configuration, child)
+            define_singleton_method(key) { child_item }
+          else
+            define_singleton_method(key) { child }
+          end
+        end
+      end
+      # rubocop:enable Metrics/MethodLength
+
+      def each(...)
+        children.each(...)
+      end
+    end
+  end
+end
diff --git a/config/initializers/settings.rb b/config/initializers/settings.rb
index d0840d4ab7..87cb8f42f9 100644
--- a/config/initializers/settings.rb
+++ b/config/initializers/settings.rb
@@ -1,66 +1,44 @@
 # frozen_string_literal: true
 
-require 'config_loader/pipelines_loader'
-
-# Global setting object loaded from `config/settings/_environment_.yml` which is
-# generated on running `rake config:generate`
-class Settings
-  class << self
-    def configuration_filename
-      Rails.root.join('config', 'settings', "#{Rails.env}.yml")
-    end
-    private :configuration_filename
-
-    # When invoked, this method will return a Hashie::Mash object that contains all the settings loaded from
-    # the YAML file.
-    # For example, you can access settings like `Settings.pipelines`, `Settings.purposes`, etc.
-    def instance # rubocop:todo Metrics/AbcSize
-      # @instance is a Hashie::Mash object that contains all the settings loaded from the YAML file.
-      # It allows for method calls like Settings.pipelines, Settings.purposes, etc.
-      return @instance if @instance.present?
-
-      # Ideally we'd do Hashie::Mash.load(File.read(configuration_filename)) here
-      # but the creates an immutable setting object that messes with tests.
-      # Immutability is good here though, so we should probably fix that.
-      # Added flag onto safe_load to allow read of anchors (aliases) in yml files.
-      config_file_descriptor = File.open(configuration_filename, 'r:bom|utf-8')
-      @instance = Hashie::Mash.new(YAML.safe_load(config_file_descriptor, permitted_classes: [Symbol], aliases: true))
-
-      # To view a list of pipeline groups and respective pipelines:
-      # e.g. Settings.pipelines.group_by(&:pipeline_group).transform_values { |pipelines| pipelines.map(&:name) }
-
-      # This line has specifically been set to customise the behaviour of loading the pipelines.
-      @instance.pipelines = ConfigLoader::PipelinesLoader.new.pipelines
+# Parent settings mixin.
+module Settings
+  CONFIGURATION_TYPES = %i[
+    searches
+    transfer_templates
+    printers
+    purposes
+    purpose_uuids
+    robots
+    default_pmb_templates
+    default_sprint_templates
+    default_printer_type_names
+    submission_templates
+  ].freeze
+
+  CONFIGURATION_TYPES.each do |config|
+    # Accessor methods
+    self.class.send(:define_method, config, proc {
+      Settings.configuration.send(config)
+    })
+    # Mutator methods
+    self.class.send(:define_method, "#{config}=", proc { |value|
+      Settings.configuration.send("#{config}=", value)
+    })
+  end
 
-      @instance
-    rescue Errno::ENOENT
-      # This before we've fully initialized and is intended to report issues to
-      # the user.
-      # rubocop:disable Style/StderrPuts
-      star_length = [96, 12 + configuration_filename.to_s.length].max
-      $stderr.puts('*' * star_length)
-      $stderr.puts "WARNING! No #{configuration_filename}"
-      $stderr.puts "You need to run 'rake config:generate' and can ignore this message if that's what you are doing!"
-      $stderr.puts('*' * star_length)
-      # rubocop:enable Style/StderrPuts
-    end
+  def self.load_yaml
+    config = Rails.root.join('config', 'settings', "#{Rails.env}.yml")
+    return unless File.exist?(config)
 
-    # This line is making it possible to access configuration using
-    # the Settings.<config> syntax. For example, Settings.pipelines, Settings.purposes, etc.
-    # It delegates all method calls to the Mash (which is @instance here).
-    delegate_missing_to :instance
+    config_file_descriptor = File.open(config, 'r:bom|utf-8')
+    # Returns a Hash with the configuration data
+    config_data = YAML.safe_load(config_file_descriptor, permitted_classes: [Symbol], aliases: true)
+    raise "Configuration file #{config} is not valid YAML." if config_data.blank?
 
-    def reinitialize
-      @instance = nil
-      self
-    end
+    config_data.with_indifferent_access
   end
-end
 
-Rails.application.config.to_prepare do
-  # By re-initializing here we gain:
-  # - Clear hot-reloading of classes like PipelineList when in development mode
-  # - Reloading of the settings in development mode, meaning you don't need to
-  #   restart following a rake config:generate
-  Settings.reinitialize.instance
+  def self.configuration
+    @configuration ||= CustomConfiguration.new(load_yaml)
+  end
 end
diff --git a/config/initializers/settings_v2.rb b/config/initializers/settings_v2.rb
deleted file mode 100644
index 8c8470801a..0000000000
--- a/config/initializers/settings_v2.rb
+++ /dev/null
@@ -1,38 +0,0 @@
-# frozen_string_literal: true
-
-# Parent settings mixin.
-module SettingsV2
-  CONFIGURATION_TYPES = %i[
-    searches
-    transfer_templates
-    printers
-    purposes
-    purpose_uuids
-    robots
-    default_pmb_templates
-    default_sprint_templates
-    default_printer_type_names
-    submission_templates
-  ].freeze
-
-  CONFIGURATION_TYPES.each do |config|
-    # proc needs to return the configuration value
-    self.class.send(:define_method, config, proc { configuration.send(config) })
-  end
-
-  def self.load_yaml
-    config = Rails.root.join('config', 'settings', "#{Rails.env}.yml")
-    return unless File.exist?(config)
-
-    config_file_descriptor = File.open(configuration_filename, 'r:bom|utf-8')
-    # Returns a Hash with the configuration data
-    config_data = YAML.safe_load(config_file_descriptor, permitted_classes: [Symbol], aliases: true)
-    raise "Configuration file #{config} is not valid YAML." if config_data.blank?
-
-    config_data.with_indifferent_access
-  end
-
-  def self.configuration
-    @configuration ||= ConfigurationV2.new(load_yaml)
-  end
-end

From 0f356ff1f7b33019f9085f05279054619bae1429 Mon Sep 17 00:00:00 2001
From: Dasun Pubudumal <pubudumald@gmail.com>
Date: Mon, 18 Aug 2025 15:36:06 +0100
Subject: [PATCH 08/37] Redoing the settings module

---
 config/initializers/custom_configuration.rb | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/config/initializers/custom_configuration.rb b/config/initializers/custom_configuration.rb
index 049c6d7c0f..7682bea092 100644
--- a/config/initializers/custom_configuration.rb
+++ b/config/initializers/custom_configuration.rb
@@ -7,8 +7,11 @@ module Settings
   # Custom configuration class that can be used to build a configuration
   class CustomConfiguration
     def initialize(config_hash)
-      config_hash.with_indifferent_access.each do |key, value|
+      @children = config_hash.with_indifferent_access
+
+      @children.each do |key, value|
         define_singleton_method(key) { Item.new(key, value) }
+        define_singleton_method("#{key}=") { |new_value| @children[key] = new_value }
       end
     end
 
@@ -32,6 +35,7 @@ def initialize(configuration, children = {})
           else
             define_singleton_method(key) { child }
           end
+          define_singleton_method("#{key}=") { |new_value| @children[key] = new_value }
         end
       end
       # rubocop:enable Metrics/MethodLength

From d9f17e63336c83567af0495f8c995f09857ad90b Mon Sep 17 00:00:00 2001
From: Dasun Pubudumal <pubudumald@gmail.com>
Date: Mon, 18 Aug 2025 15:44:15 +0100
Subject: [PATCH 09/37] [skip ci] Adding comments

---
 config/initializers/custom_configuration.rb | 22 +++++++++++++++++++--
 1 file changed, 20 insertions(+), 2 deletions(-)

diff --git a/config/initializers/custom_configuration.rb b/config/initializers/custom_configuration.rb
index 7682bea092..f21b4ad71c 100644
--- a/config/initializers/custom_configuration.rb
+++ b/config/initializers/custom_configuration.rb
@@ -4,18 +4,36 @@
 module Settings
   # Configuration for the application, including loaders for various configurations.
 
-  # Custom configuration class that can be used to build a configuration
+  # This will create class-level functions so that they could be accessed like
+  # Settings.searches, Settings.transfer_templates, etc.
   class CustomConfiguration
     def initialize(config_hash)
       @children = config_hash.with_indifferent_access
 
+      # When you invoke, Settings.configuration.searches in settings.rb, it would invoke static
+      # methods declared through this block.
       @children.each do |key, value|
+        # For every getter method, it creates a method that returns an Item instance
+        # with the key and value from the configuration hash.
         define_singleton_method(key) { Item.new(key, value) }
+        # For every setter method, it creates a method that sets the value in the children hash.
+        # This allows you to do Settings.configuration.searches = new_value.
         define_singleton_method("#{key}=") { |new_value| @children[key] = new_value }
       end
     end
 
-    # Configuration item.
+    # Configuration item. It recursively builds a structure
+    # that allows for nested configurations to be accessed easily.
+    # It includes Enumerable to allow iteration over its children.
+    #
+    # Each child can be a nested configuration or a simple value.
+    # This allows for a flexible and dynamic configuration structure.
+    #
+    # @example
+    #   config = Settings.configuration
+    #   config.searches.some_child.some_grandchild
+    #   config.searches.some_child.some_grandchild = new_value
+    #
     class Item
       include Enumerable
 

From 741672a2e35060cadc4f411644ff6a9b1080fd62 Mon Sep 17 00:00:00 2001
From: Dasun Pubudumal <pubudumald@gmail.com>
Date: Mon, 18 Aug 2025 16:05:02 +0100
Subject: [PATCH 10/37] [skip ci] Adding more configuration stuff

---
 config/initializers/settings.rb | 2 ++
 config/settings/test.yml        | 8 +++++++-
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/config/initializers/settings.rb b/config/initializers/settings.rb
index 87cb8f42f9..6ed68fc48e 100644
--- a/config/initializers/settings.rb
+++ b/config/initializers/settings.rb
@@ -13,6 +13,8 @@ module Settings
     default_sprint_templates
     default_printer_type_names
     submission_templates
+    pipelines
+    poolings
   ].freeze
 
   CONFIGURATION_TYPES.each do |config|
diff --git a/config/settings/test.yml b/config/settings/test.yml
index 3034a3623e..7067f22eb8 100644
--- a/config/settings/test.yml
+++ b/config/settings/test.yml
@@ -7,5 +7,11 @@
 :purposes: {}
 :purpose_uuids: {}
 :robots: {}
-:locations: {}
+:default_pmb_templates: {}
+:default_sprint_templates: {}
+:default_printer_type_names: []
+:submission_templates: {}
 :qc_purposes: []
+:locations: {}
+:pipelines: {}
+:poolings: {}
\ No newline at end of file

From 31e5575d9a633d97f8ccf1f45d3cacc7e78dacd7 Mon Sep 17 00:00:00 2001
From: Dasun Pubudumal <pubudumald@gmail.com>
Date: Tue, 19 Aug 2025 09:28:49 +0100
Subject: [PATCH 11/37] [skip ci] Adding more configuration stuff

---
 config/initializers/custom_configuration.rb | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/config/initializers/custom_configuration.rb b/config/initializers/custom_configuration.rb
index f21b4ad71c..9678beb895 100644
--- a/config/initializers/custom_configuration.rb
+++ b/config/initializers/custom_configuration.rb
@@ -58,6 +58,12 @@ def initialize(configuration, children = {})
       end
       # rubocop:enable Metrics/MethodLength
 
+      delegate :[]=, to: :@children
+
+      def fetch(key, default = nil)
+        @children.fetch(key, default)
+      end
+
       def each(...)
         children.each(...)
       end

From 887a18325b10361a2befea6fd30b45b71b63c96f Mon Sep 17 00:00:00 2001
From: Dasun Pubudumal <pubudumald@gmail.com>
Date: Tue, 19 Aug 2025 09:30:21 +0100
Subject: [PATCH 12/37] [skip ci] Adding more configuration stuff

---
 config/settings/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/settings/test.yml b/config/settings/test.yml
index 7067f22eb8..80293ca9ae 100644
--- a/config/settings/test.yml
+++ b/config/settings/test.yml
@@ -14,4 +14,4 @@
 :qc_purposes: []
 :locations: {}
 :pipelines: {}
-:poolings: {}
\ No newline at end of file
+:poolings: {}

From a68b52d1a743e6a610cf9dc7992717043eeaca2b Mon Sep 17 00:00:00 2001
From: Dasun Pubudumal <pubudumald@gmail.com>
Date: Tue, 19 Aug 2025 10:55:15 +0100
Subject: [PATCH 13/37] Refactor search_helper to use children method for
 accessing purposes

---
 app/helpers/search_helper.rb | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/app/helpers/search_helper.rb b/app/helpers/search_helper.rb
index 15f8dd83dd..854f96f3a9 100644
--- a/app/helpers/search_helper.rb
+++ b/app/helpers/search_helper.rb
@@ -2,20 +2,20 @@
 
 module SearchHelper # rubocop:todo Style/Documentation
   def stock_plate_uuids
-    Settings.purposes.select { |_uuid, config| config.input_plate }.keys
+    Settings.purposes.children.select { |_uuid, config| config.input_plate }.keys
   end
 
   def self.stock_plate_names
-    Settings.purposes.values.select(&:input_plate).map(&:name)
+    Settings.purposes.children.values.select(&:input_plate).map(&:name)
   end
 
   # Returns purpose names of stock plates using stock_plate flag instead of input_plate.
   def self.stock_plate_names_with_flag
-    Settings.purposes.values.select(&:stock_plate).map(&:name)
+    Settings.purposes.children.values.select(&:stock_plate).map(&:name)
   end
 
   def self.purpose_config_for_purpose_name(purpose_name)
-    Settings.purposes.values.find { |obj| obj[:name] == purpose_name }
+    Settings.purposes.children.values.find { |obj| obj[:name] == purpose_name }
   end
 
   def self.alternative_workline_reference_name(labware)
@@ -26,12 +26,13 @@ def self.alternative_workline_reference_name(labware)
   end
 
   def self.merger_plate_names
-    Settings.purposes.values.select(&:merger_plate).map(&:name)
+    Settings.purposes.children.values.select(&:merger_plate).map(&:name)
   end
 
   def purpose_options(type)
     Settings
       .purposes
+      .children
       .select { |_uuid, settings| settings[:asset_type] == type }
       .map { |uuid, settings| [settings[:name], uuid] }
   end

From f50a9f46e1aa9fad1fdd5fdee5419828dece9c6d Mon Sep 17 00:00:00 2001
From: Dasun Pubudumal <pubudumald@gmail.com>
Date: Tue, 19 Aug 2025 14:17:06 +0100
Subject: [PATCH 14/37] Enhance CustomConfiguration to dynamically define
 getter and setter methods for nested configuration access; add initial
 settings_spec for pipelines

---
 config/initializers/custom_configuration.rb | 14 ++++++++
 config/initializers/settings.rb             | 10 +++++-
 spec/initializers/settings_spec.rb          | 39 +++++++++++++++++++++
 3 files changed, 62 insertions(+), 1 deletion(-)
 create mode 100644 spec/initializers/settings_spec.rb

diff --git a/config/initializers/custom_configuration.rb b/config/initializers/custom_configuration.rb
index 9678beb895..a38dfd71a4 100644
--- a/config/initializers/custom_configuration.rb
+++ b/config/initializers/custom_configuration.rb
@@ -44,6 +44,20 @@ def initialize(configuration, children = {})
         @children = children
         @configuration = configuration
 
+        # Dynamically defines getter and setter methods for each child key in the configuration.
+        #
+        # For each key-value pair in the children hash:
+        # - If the value is a nested hash (ActiveSupport::HashWithIndifferentAccess),
+        #   it creates a getter method that returns a new Item instance, allowing for recursive access.
+        # - If the value is a simple value, it creates a getter method that returns the value directly.
+        # - For every key, it also creates a setter method to update the value in the children hash.
+        #
+        # This enables flexible, dot-notation access and assignment for deeply nested configuration structures.
+        #
+        # Example:
+        #   config = Settings.configuration
+        #   config.searches.some_child.some_grandchild        # Access nested value
+        #   config.searches.some_child.some_grandchild = val  # Set nested value
         children.each do |key, child|
           if child.is_a?(ActiveSupport::HashWithIndifferentAccess)
             next if respond_to?(key)
diff --git a/config/initializers/settings.rb b/config/initializers/settings.rb
index 6ed68fc48e..98cab22b68 100644
--- a/config/initializers/settings.rb
+++ b/config/initializers/settings.rb
@@ -13,7 +13,6 @@ module Settings
     default_sprint_templates
     default_printer_type_names
     submission_templates
-    pipelines
     poolings
   ].freeze
 
@@ -28,6 +27,15 @@ module Settings
     })
   end
 
+  # Delegates Settings.pipelines to the PipelinesLoader
+  def self.pipelines
+    @pipelines ||= ConfigLoader::PipelinesLoader.new.pipelines
+  end
+
+  def self.pipelines=(value)
+    @pipelines = value
+  end
+
   def self.load_yaml
     config = Rails.root.join('config', 'settings', "#{Rails.env}.yml")
     return unless File.exist?(config)
diff --git a/spec/initializers/settings_spec.rb b/spec/initializers/settings_spec.rb
new file mode 100644
index 0000000000..b77d53936d
--- /dev/null
+++ b/spec/initializers/settings_spec.rb
@@ -0,0 +1,39 @@
+# frozen_string_literal: true
+
+require 'rails_helper'
+
+RSpec.describe Settings, skip: 'Skipping as WIP' do
+  let(:yaml_data) do
+    {
+      'searches' => %w[search1 search2],
+      'transfer_templates' => ['template1'],
+      'printers' => ['printer1'],
+      'purposes' => ['purpose1'],
+      'purpose_uuids' => ['uuid1'],
+      'robots' => ['robot1'],
+      'default_pmb_templates' => ['pmb1'],
+      'default_sprint_templates' => ['sprint1'],
+      'default_printer_type_names' => ['type1'],
+      'submission_templates' => ['submission1'],
+      'poolings' => ['pooling1']
+    }
+  end
+
+  before do
+    allow(Rails).to receive_messages(root: Pathname.new(File.dirname(__FILE__)), env: 'test')
+    file_double = StringIO.new(yaml_data.to_yaml)
+    allow(File).to receive_messages(exist?: true, open: file_double)
+    stub_const('CustomConfiguration', Struct.new(*Settings::CONFIGURATION_TYPES) do
+      def initialize(hash)
+        hash.each { |k, v| send("#{k}=", v) }
+      end
+    end)
+    described_class.instance_variable_set(:@configuration, nil)
+  end
+
+  describe 'Settings configuration setting the pipelines' do
+    it 'when invoked, returns the pipelines properly' do
+      skip 'WIP'
+    end
+  end
+end

From f9d574fd26f0ea66254907728d9db7a10112e61f Mon Sep 17 00:00:00 2001
From: Dasun Pubudumal <pubudumald@gmail.com>
Date: Tue, 19 Aug 2025 15:59:57 +0100
Subject: [PATCH 15/37] Refactor CreationBehaviour and Settings to improve
 configuration handling; add config.yml for testing

---
 .../concerns/presenters/creation_behaviour.rb |  10 +-
 config/initializers/settings.rb               |   3 +
 spec/data/config.yml                          | 109 ++++++++++++++++++
 spec/initializers/settings_spec.rb            |  39 ++-----
 4 files changed, 126 insertions(+), 35 deletions(-)
 create mode 100644 spec/data/config.yml

diff --git a/app/models/concerns/presenters/creation_behaviour.rb b/app/models/concerns/presenters/creation_behaviour.rb
index 6e0771d6bc..6691f047a0 100644
--- a/app/models/concerns/presenters/creation_behaviour.rb
+++ b/app/models/concerns/presenters/creation_behaviour.rb
@@ -34,9 +34,9 @@ def construct_buttons(scope)
           parent_uuid: uuid,
           parent: labware,
           purpose_uuid: purpose_uuid,
-          name: purpose_settings.name,
-          type: purpose_settings.asset_type,
-          filters: purpose_settings.filters || {}
+          name: purpose_settings[:name],
+          type: purpose_settings[:asset_type],
+          filters: purpose_settings[:filters] || {}
         )
       end
       .force
@@ -62,6 +62,8 @@ def suggested_purpose_options
   end
 
   def compatible_purposes
-    Settings.purposes.lazy.select { |uuid, _purpose_settings| LabwareCreators.class_for(uuid).support_parent?(labware) }
+    Settings.purposes.children.lazy.select do |uuid, _purpose_settings|
+      LabwareCreators.class_for(uuid).support_parent?(labware)
+    end
   end
 end
diff --git a/config/initializers/settings.rb b/config/initializers/settings.rb
index 98cab22b68..d68315a9a4 100644
--- a/config/initializers/settings.rb
+++ b/config/initializers/settings.rb
@@ -16,6 +16,9 @@ module Settings
     poolings
   ].freeze
 
+  # This loop declares Settings.<CONFIGURATION_TYPE> method declarations
+  # using metaprogramming. For example, when it will add purposes method for Settings, and
+  # when it is invoked, it will use the CustomConfiguration class to send the value for it.
   CONFIGURATION_TYPES.each do |config|
     # Accessor methods
     self.class.send(:define_method, config, proc {
diff --git a/spec/data/config.yml b/spec/data/config.yml
new file mode 100644
index 0000000000..92153b095d
--- /dev/null
+++ b/spec/data/config.yml
@@ -0,0 +1,109 @@
+# The current file has been automatically generated by running the task:
+#   > rake config:generate
+# It is recommended if you need to do any changes in config to modify the
+# required config file under config/pipelines or config/purposes and rerun
+# the task
+---
+:searches:
+  Find assets by barcode: 7e660cbc-6951-11f0-8c10-ded867e19c6b
+  Find project by name: 7e668c82-6951-11f0-8c10-ded867e19c6b
+  Find study by name: 7e66e272-6951-11f0-8c10-ded867e19c6b
+:transfer_templates:
+  384 plate to tube: 7c673a8a-6951-11f0-8c10-ded867e19c6b
+  Transfer columns 1-1: 7d590ff4-6951-11f0-8c10-ded867e19c6b
+:printers:
+  :plate_a: g316bc
+  :plate_b: g311bc2
+  :tube_rack: heron-bc2
+  :tube: g311bc1
+  :limit: 5
+  :default_count: 2
+:purposes:
+  9e42476c-6951-11f0-b542-ded867e19c6b:
+    :name: LBC 5p GEX Dil
+    :default_printer_type: :plate_a
+    :presenter_class: Presenters::NormalisedBinnedPlatePresenter
+    :creator_class: LabwareCreators::NormalisedBinnedPlate
+    :label_class: Labels::PlateLabel
+    :file_links:
+      - name: Download Hamilton Cherrypick to 5 prime Dilution CSV
+        id: hamilton_cherrypick_to_5p_gex_dilution
+      - name: Download Concentration (ng/ul) CSV
+        id: concentrations_ngul
+    :state_changer_class: StateChangers::PlateStateChanger
+    :submission: {}
+    :printer_type: 96 Well Plate
+    :pmb_template: sqsc_96plate_label_template_code39
+    :sprint_template: plate_96.yml.erb
+    :asset_type: plate
+    :dilutions:
+      :target_amount_ng: 50
+      :target_volume: 20
+      :minimum_source_volume: 0.2
+      :bins:
+        - colour: 1
+          pcr_cycles: 16
+          max: 26
+        - colour: 2
+          pcr_cycles: 14
+          min: 26
+:purpose_uuids:
+  LBC 5p GEX Dil: 9e42476c-6951-11f0-b542-ded867e19c6b
+  LBC 5p GEX Frag 2XP: 9e5190f0-6951-11f0-b542-ded867e19c6b
+  LBC 5p GEX LigXP: 9e5424dc-6951-11f0-b542-ded867e19c6b
+:robots:
+  bravo-lb-cherrypick-to-lb-shear:
+    :name: bravo LB Cherrypick => LB Shear
+    :verify_robot: false
+    :require_robot: false
+    :beds:
+      '580000007860':
+        :purpose: LB Cherrypick
+        :states:
+          - passed
+        :label: Bed 7
+        :shared_parent: false
+      '580000009659':
+        :purpose: LB Shear
+        :states:
+          - pending
+        :label: Bed 9
+        :parent: '580000007860'
+        :target_state: passed
+  bravo-lb-shear-to-lb-post-shear:
+    :name: bravo LB Shear => LB Post Shear
+    :verify_robot: false
+    :require_robot: false
+    :beds:
+      '580000009659':
+        :purpose: LB Shear
+        :states:
+          - passed
+        :label: Bed 9
+        :shared_parent: false
+      '580000007860':
+        :purpose: LB Post Shear
+        :states:
+          - pending
+        :label: Bed 7
+        :parent: '580000009659'
+        :target_state: passed
+:default_pmb_templates:
+  :plate_double: plate_6mm_double_code39
+  :plate_a: sqsc_96plate_label_template_code39
+  :tube_rack: sqsc_96plate_label_template_code39
+  :tube: tube_label_template_1d
+:default_sprint_templates:
+  :plate_double: plate_384.yml.erb
+  :plate_a: plate_96.yml.erb
+  :tube_rack: plate_96.yml.erb
+  :tube: tube_label_template_1d.yml.erb
+:default_printer_type_names:
+  :plate_double: 384 Well Plate Double
+  :plate_a: 96 Well Plate
+  :tube_rack: 96 Well Plate
+  :tube: 1D Tube
+:submission_templates:
+  Limber - Cardinal: 7b7a63e0-6951-11f0-8c10-ded867e19c6b
+  Limber - Cardinal cell banking: 7b7bc1e0-6951-11f0-8c10-ded867e19c6b
+poolings:
diff --git a/spec/initializers/settings_spec.rb b/spec/initializers/settings_spec.rb
index b77d53936d..614a08e4ed 100644
--- a/spec/initializers/settings_spec.rb
+++ b/spec/initializers/settings_spec.rb
@@ -2,38 +2,15 @@
 
 require 'rails_helper'
 
-RSpec.describe Settings, skip: 'Skipping as WIP' do
-  let(:yaml_data) do
-    {
-      'searches' => %w[search1 search2],
-      'transfer_templates' => ['template1'],
-      'printers' => ['printer1'],
-      'purposes' => ['purpose1'],
-      'purpose_uuids' => ['uuid1'],
-      'robots' => ['robot1'],
-      'default_pmb_templates' => ['pmb1'],
-      'default_sprint_templates' => ['sprint1'],
-      'default_printer_type_names' => ['type1'],
-      'submission_templates' => ['submission1'],
-      'poolings' => ['pooling1']
-    }
-  end
-
+# rubocop:disable RSpec/EmptyExampleGroup
+RSpec.describe Settings, skip: 'WIP' do
   before do
-    allow(Rails).to receive_messages(root: Pathname.new(File.dirname(__FILE__)), env: 'test')
-    file_double = StringIO.new(yaml_data.to_yaml)
-    allow(File).to receive_messages(exist?: true, open: file_double)
-    stub_const('CustomConfiguration', Struct.new(*Settings::CONFIGURATION_TYPES) do
-      def initialize(hash)
-        hash.each { |k, v| send("#{k}=", v) }
-      end
-    end)
+    config = Rails.root.join('spec/data/config.yml')
+    config_file_descriptor = File.open(config, 'r:bom|utf-8')
+    # Returns a Hash with the configuration data
+    config_data = YAML.safe_load(config_file_descriptor, permitted_classes: [Symbol], aliases: true)
+    allow(described_class).to receive(:load_yaml).and_return(config_data)
     described_class.instance_variable_set(:@configuration, nil)
   end
-
-  describe 'Settings configuration setting the pipelines' do
-    it 'when invoked, returns the pipelines properly' do
-      skip 'WIP'
-    end
-  end
 end
+# rubocop:enable RSpec/EmptyExampleGroup

From ed2ac0c2d0ab257a5db963e0220c5167b9bbdfc5 Mon Sep 17 00:00:00 2001
From: Dasun Pubudumal <pubudumald@gmail.com>
Date: Tue, 19 Aug 2025 16:05:35 +0100
Subject: [PATCH 16/37] Refactor accessor method in Settings module to handle
 children for configuration values

---
 config/initializers/settings.rb | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/config/initializers/settings.rb b/config/initializers/settings.rb
index d68315a9a4..3ec2a80810 100644
--- a/config/initializers/settings.rb
+++ b/config/initializers/settings.rb
@@ -22,7 +22,8 @@ module Settings
   CONFIGURATION_TYPES.each do |config|
     # Accessor methods
     self.class.send(:define_method, config, proc {
-      Settings.configuration.send(config)
+      value = Settings.configuration.send(config)
+      value.respond_to?(:children) ? value.children : value
     })
     # Mutator methods
     self.class.send(:define_method, "#{config}=", proc { |value|

From 950887b02fb0aa355a41a3e629adfdb337873ad6 Mon Sep 17 00:00:00 2001
From: Dasun Pubudumal <pubudumald@gmail.com>
Date: Tue, 19 Aug 2025 16:09:40 +0100
Subject: [PATCH 17/37] Refactor compatible_purposes method to use lazy
 enumeration for improved performance

---
 app/models/concerns/presenters/creation_behaviour.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/models/concerns/presenters/creation_behaviour.rb b/app/models/concerns/presenters/creation_behaviour.rb
index 6691f047a0..1b38f06723 100644
--- a/app/models/concerns/presenters/creation_behaviour.rb
+++ b/app/models/concerns/presenters/creation_behaviour.rb
@@ -62,7 +62,7 @@ def suggested_purpose_options
   end
 
   def compatible_purposes
-    Settings.purposes.children.lazy.select do |uuid, _purpose_settings|
+    Settings.purposes.lazy.select do |uuid, _purpose_settings|
       LabwareCreators.class_for(uuid).support_parent?(labware)
     end
   end

From f50a9bb9fe407a99592d68cd9b5fbf34f52d4fa1 Mon Sep 17 00:00:00 2001
From: Dasun Pubudumal <pubudumald@gmail.com>
Date: Tue, 19 Aug 2025 16:18:00 +0100
Subject: [PATCH 18/37] Refactor search_helper to remove unnecessary children
 method calls for accessing purposes

---
 app/helpers/search_helper.rb | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/app/helpers/search_helper.rb b/app/helpers/search_helper.rb
index 854f96f3a9..15f8dd83dd 100644
--- a/app/helpers/search_helper.rb
+++ b/app/helpers/search_helper.rb
@@ -2,20 +2,20 @@
 
 module SearchHelper # rubocop:todo Style/Documentation
   def stock_plate_uuids
-    Settings.purposes.children.select { |_uuid, config| config.input_plate }.keys
+    Settings.purposes.select { |_uuid, config| config.input_plate }.keys
   end
 
   def self.stock_plate_names
-    Settings.purposes.children.values.select(&:input_plate).map(&:name)
+    Settings.purposes.values.select(&:input_plate).map(&:name)
   end
 
   # Returns purpose names of stock plates using stock_plate flag instead of input_plate.
   def self.stock_plate_names_with_flag
-    Settings.purposes.children.values.select(&:stock_plate).map(&:name)
+    Settings.purposes.values.select(&:stock_plate).map(&:name)
   end
 
   def self.purpose_config_for_purpose_name(purpose_name)
-    Settings.purposes.children.values.find { |obj| obj[:name] == purpose_name }
+    Settings.purposes.values.find { |obj| obj[:name] == purpose_name }
   end
 
   def self.alternative_workline_reference_name(labware)
@@ -26,13 +26,12 @@ def self.alternative_workline_reference_name(labware)
   end
 
   def self.merger_plate_names
-    Settings.purposes.children.values.select(&:merger_plate).map(&:name)
+    Settings.purposes.values.select(&:merger_plate).map(&:name)
   end
 
   def purpose_options(type)
     Settings
       .purposes
-      .children
       .select { |_uuid, settings| settings[:asset_type] == type }
       .map { |uuid, settings| [settings[:name], uuid] }
   end

From b25ba844500244abfc7e3372aa994b24f9452424 Mon Sep 17 00:00:00 2001
From: Dasun Pubudumal <pubudumald@gmail.com>
Date: Wed, 20 Aug 2025 11:20:29 +0100
Subject: [PATCH 19/37] Changing test.yml

---
 app/helpers/search_helper.rb |  2 +-
 config/settings/test.yml     | 30 ++++++++++++++++++++++++++----
 2 files changed, 27 insertions(+), 5 deletions(-)

diff --git a/app/helpers/search_helper.rb b/app/helpers/search_helper.rb
index 15f8dd83dd..1f29ed085a 100644
--- a/app/helpers/search_helper.rb
+++ b/app/helpers/search_helper.rb
@@ -2,7 +2,7 @@
 
 module SearchHelper # rubocop:todo Style/Documentation
   def stock_plate_uuids
-    Settings.purposes.select { |_uuid, config| config.input_plate }.keys
+    Settings.purposes.select { |_uuid, config| config[:input_plate] }.keys
   end
 
   def self.stock_plate_names
diff --git a/config/settings/test.yml b/config/settings/test.yml
index 80293ca9ae..d7ac1efa59 100644
--- a/config/settings/test.yml
+++ b/config/settings/test.yml
@@ -1,15 +1,37 @@
 ---
 :searches: {}
-:transfer_templates: {}
+:transfer_templates:
+  'Custom pooling': custom-pooling
+  'Pool wells based on submission': custom-transfer-template
+  'Transfer between specific tubes': transfer-between-specific-tubes
+  'Transfer columns 1-12': transfer-1-12
+  'Transfer from tube to tube by submission': tube-to-tube-by-sub
+  'Transfer wells to MX library tubes by submission': transfer-to-mx-tubes-on-submission
+  'Whole plate to tube': whole-plate-to-tube
 :printers:
   limit: 5
   default_count: 2
 :purposes: {}
 :purpose_uuids: {}
 :robots: {}
-:default_pmb_templates: {}
-:default_sprint_templates: {}
-:default_printer_type_names: []
+:default_pmb_templates:
+  pmb_templates:
+    :plate_double: plate_6mm_double_code39
+    :plate_a: sqsc_96plate_label_template_code39
+    :tube_rack: sqsc_96plate_label_template_code39
+    :tube: tube_label_template_1d
+:default_sprint_templates:
+  sprint_templates:
+    :plate_double: plate_384.yml.erb
+    :plate_a: plate_96.yml.erb
+    :tube_rack: plate_96.yml.erb
+    :tube: tube_label_template_1d.yml.erb
+:default_printer_type_names:
+  printer_type_names:
+    :plate_double: 384 Well Plate Double
+    :plate_a: 96 Well Plate
+    :tube_rack: 96 Well Plate
+    :tube: 1D Tube
 :submission_templates: {}
 :qc_purposes: []
 :locations: {}

From a8b79101679fe5abb10e6bac7a83a1d56cae509b Mon Sep 17 00:00:00 2001
From: Dasun Pubudumal <pubudumald@gmail.com>
Date: Wed, 20 Aug 2025 11:29:55 +0100
Subject: [PATCH 20/37] Changing the metaprogramming logic to dynamically add
 mutator methods

---
 config/initializers/settings.rb | 27 ++++++++++++++++++++-------
 config/settings/test.yml        | 30 ++++--------------------------
 2 files changed, 24 insertions(+), 33 deletions(-)

diff --git a/config/initializers/settings.rb b/config/initializers/settings.rb
index 3ec2a80810..41309b47a2 100644
--- a/config/initializers/settings.rb
+++ b/config/initializers/settings.rb
@@ -20,14 +20,27 @@ module Settings
   # using metaprogramming. For example, when it will add purposes method for Settings, and
   # when it is invoked, it will use the CustomConfiguration class to send the value for it.
   CONFIGURATION_TYPES.each do |config|
-    # Accessor methods
-    self.class.send(:define_method, config, proc {
-      value = Settings.configuration.send(config)
-      value.respond_to?(:children) ? value.children : value
-    })
-    # Mutator methods
+    # Accessor
+    unless respond_to?(config)
+      self.class.send(:define_method, config, proc {
+        value = Settings.configuration.send(config)
+        value.respond_to?(:children) ? value.children : value
+      })
+    end
+    # Mutator
+    next if respond_to?("#{config}=")
+
     self.class.send(:define_method, "#{config}=", proc { |value|
-      Settings.configuration.send("#{config}=", value)
+      config_value = Settings.configuration.send(config)
+      if config_value.respond_to?(:children)
+        if config_value.children.is_a?(Hash) && value.is_a?(Hash)
+          config_value.children.replace(value)
+        else
+          Settings.configuration.send("#{config}=", value)
+        end
+      else
+        Settings.configuration.send("#{config}=", value)
+      end
     })
   end
 
diff --git a/config/settings/test.yml b/config/settings/test.yml
index d7ac1efa59..80293ca9ae 100644
--- a/config/settings/test.yml
+++ b/config/settings/test.yml
@@ -1,37 +1,15 @@
 ---
 :searches: {}
-:transfer_templates:
-  'Custom pooling': custom-pooling
-  'Pool wells based on submission': custom-transfer-template
-  'Transfer between specific tubes': transfer-between-specific-tubes
-  'Transfer columns 1-12': transfer-1-12
-  'Transfer from tube to tube by submission': tube-to-tube-by-sub
-  'Transfer wells to MX library tubes by submission': transfer-to-mx-tubes-on-submission
-  'Whole plate to tube': whole-plate-to-tube
+:transfer_templates: {}
 :printers:
   limit: 5
   default_count: 2
 :purposes: {}
 :purpose_uuids: {}
 :robots: {}
-:default_pmb_templates:
-  pmb_templates:
-    :plate_double: plate_6mm_double_code39
-    :plate_a: sqsc_96plate_label_template_code39
-    :tube_rack: sqsc_96plate_label_template_code39
-    :tube: tube_label_template_1d
-:default_sprint_templates:
-  sprint_templates:
-    :plate_double: plate_384.yml.erb
-    :plate_a: plate_96.yml.erb
-    :tube_rack: plate_96.yml.erb
-    :tube: tube_label_template_1d.yml.erb
-:default_printer_type_names:
-  printer_type_names:
-    :plate_double: 384 Well Plate Double
-    :plate_a: 96 Well Plate
-    :tube_rack: 96 Well Plate
-    :tube: 1D Tube
+:default_pmb_templates: {}
+:default_sprint_templates: {}
+:default_printer_type_names: []
 :submission_templates: {}
 :qc_purposes: []
 :locations: {}

From d01d39fd91256531c7bf1da831122356242e5181 Mon Sep 17 00:00:00 2001
From: Dasun Pubudumal <pubudumald@gmail.com>
Date: Wed, 20 Aug 2025 11:31:07 +0100
Subject: [PATCH 21/37] Changing the metaprogramming logic to dynamically add
 mutator methods

---
 config/initializers/settings.rb | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/config/initializers/settings.rb b/config/initializers/settings.rb
index 41309b47a2..0c133b9dea 100644
--- a/config/initializers/settings.rb
+++ b/config/initializers/settings.rb
@@ -30,11 +30,14 @@ module Settings
     # Mutator
     next if respond_to?("#{config}=")
 
+    # rubocop:disable Lint/DuplicateBranch
     self.class.send(:define_method, "#{config}=", proc { |value|
       config_value = Settings.configuration.send(config)
       if config_value.respond_to?(:children)
         if config_value.children.is_a?(Hash) && value.is_a?(Hash)
           config_value.children.replace(value)
+        elsif config_value.children.is_a?(Array) && value.is_a?(Array)
+          config_value.children.replace(value)
         else
           Settings.configuration.send("#{config}=", value)
         end
@@ -42,6 +45,7 @@ module Settings
         Settings.configuration.send("#{config}=", value)
       end
     })
+    # rubocop:enable Lint/DuplicateBranch
   end
 
   # Delegates Settings.pipelines to the PipelinesLoader

From 27a16c525a6832f7b653a1fe843ede4ceb36af98 Mon Sep 17 00:00:00 2001
From: Dasun Pubudumal <pubudumald@gmail.com>
Date: Wed, 20 Aug 2025 13:36:40 +0100
Subject: [PATCH 22/37] Updating search helper

---
 app/helpers/search_helper.rb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/helpers/search_helper.rb b/app/helpers/search_helper.rb
index 1f29ed085a..eff47efcf2 100644
--- a/app/helpers/search_helper.rb
+++ b/app/helpers/search_helper.rb
@@ -6,12 +6,12 @@ def stock_plate_uuids
   end
 
   def self.stock_plate_names
-    Settings.purposes.values.select(&:input_plate).map(&:name)
+    Settings.purposes.values.select { |item| item[:input_plate] == true }.pluck(:name)
   end
 
   # Returns purpose names of stock plates using stock_plate flag instead of input_plate.
   def self.stock_plate_names_with_flag
-    Settings.purposes.values.select(&:stock_plate).map(&:name)
+    Settings.purposes.values.select { |item| item[:stock_plate] == true }.pluck(:name)
   end
 
   def self.purpose_config_for_purpose_name(purpose_name)

From 497b7189fcc129ede52ae3efae69bd1e4197916c Mon Sep 17 00:00:00 2001
From: Dasun Pubudumal <pubudumald@gmail.com>
Date: Wed, 20 Aug 2025 13:59:27 +0100
Subject: [PATCH 23/37] Trying to fix the donor pooling yaml frustratingly!!!

---
 .../config/poolings/donor_pooling.yml         | 192 +++++++++---------
 1 file changed, 96 insertions(+), 96 deletions(-)

diff --git a/spec/fixtures/config/poolings/donor_pooling.yml b/spec/fixtures/config/poolings/donor_pooling.yml
index ecc363fddb..b45d2a3855 100644
--- a/spec/fixtures/config/poolings/donor_pooling.yml
+++ b/spec/fixtures/config/poolings/donor_pooling.yml
@@ -3,99 +3,99 @@
 donor_pooling:
   # Maping between number of samples to number of pools.
   number_of_pools:
-    96: 8
-    95: 8
-    94: 8
-    93: 8
-    92: 8
-    91: 8
-    90: 8
-    89: 8
-    88: 8
-    87: 7
-    86: 7
-    85: 7
-    84: 7
-    83: 7
-    82: 7
-    81: 7
-    80: 7
-    79: 7
-    78: 7
-    77: 7
-    76: 6
-    75: 6
-    74: 6
-    73: 6
-    72: 6
-    71: 6
-    70: 6
-    69: 6
-    68: 6
-    67: 6
-    66: 6
-    65: 5
-    64: 5
-    63: 5
-    62: 5
-    61: 5
-    60: 5
-    59: 5
-    58: 5
-    57: 5
-    56: 5
-    55: 5
-    54: 5
-    53: 5
-    52: 4
-    51: 4
-    50: 4
-    49: 4
-    48: 4
-    47: 4
-    46: 4
-    45: 4
-    44: 4
-    43: 4
-    42: 4
-    41: 4
-    40: 4
-    39: 3
-    38: 3
-    37: 3
-    36: 3
-    35: 3
-    34: 3
-    33: 3
-    32: 3
-    31: 3
-    30: 3
-    29: 3
-    28: 3
-    27: 3
-    26: 2
-    25: 2
-    24: 2
-    23: 2
-    22: 2
-    21: 2
-    20: 1
-    19: 1
-    18: 1
-    17: 1
-    16: 1
-    15: 1
-    14: 1
-    13: 1
-    12: 1
-    11: 1
-    10: 1
-    9: 1
-    8: 1
-    7: 1
-    6: 1
-    5: 1
-    4: 1
-    3: 1
-    2: 1
-    1: 1
+    "96": 8,
+    "95": 8,
+    "94": 8,
+    "93": 8,
+    "92": 8,
+    "91": 8,
+    "90": 8,
+    "89": 8,
+    "88": 8,
+    "87": 7,
+    "86": 7,
+    "85": 7,
+    "84": 7,
+    "83": 7,
+    "82": 7,
+    "81": 7,
+    "80": 7,
+    "79": 7,
+    "78": 7,
+    "77": 7,
+    "76": 6,
+    "75": 6,
+    "74": 6,
+    "73": 6,
+    "72": 6,
+    "71": 6,
+    "70": 6,
+    "69": 6,
+    "68": 6,
+    "67": 6,
+    "66": 6,
+    "65": 5,
+    "64": 5,
+    "63": 5,
+    "62": 5,
+    "61": 5,
+    "60": 5,
+    "59": 5,
+    "58": 5,
+    "57": 5,
+    "56": 5,
+    "55": 5,
+    "54": 5,
+    "53": 5,
+    "52": 4,
+    "51": 4,
+    "50": 4,
+    "49": 4,
+    "48": 4,
+    "47": 4,
+    "46": 4,
+    "45": 4,
+    "44": 4,
+    "43": 4,
+    "42": 4,
+    "41": 4,
+    "40": 4,
+    "39": 3,
+    "38": 3,
+    "37": 3,
+    "36": 3,
+    "35": 3,
+    "34": 3,
+    "33": 3,
+    "32": 3,
+    "31": 3,
+    "30": 3,
+    "29": 3,
+    "28": 3,
+    "27": 3,
+    "26": 2,
+    "25": 2,
+    "24": 2,
+    "23": 2,
+    "22": 2,
+    "21": 2,
+    "20": 1,
+    "19": 1,
+    "18": 1,
+    "17": 1,
+    "16": 1,
+    "15": 1,
+    "14": 1,
+    "13": 1,
+    "12": 1,
+    "11": 1,
+    "10": 1,
+    "9": 1,
+    "8": 1,
+    "7": 1,
+    "6": 1,
+    "5": 1,
+    "4": 1,
+    "3": 1,
+    "2": 1,
+    "1": 1

From 831e592be09108ec2c6ffa8f16a92e182b2969ac Mon Sep 17 00:00:00 2001
From: Dasun Pubudumal <pubudumald@gmail.com>
Date: Wed, 20 Aug 2025 15:19:31 +0100
Subject: [PATCH 24/37] Fixing yet another config issue.

---
 .../presenters/submission_behaviour.rb        |   2 +-
 .../labware_creators/multi_stamp_tubes.rb     |   2 +-
 app/models/presenters/presenter.rb            |   2 +-
 app/models/presenters/tube_presenter.rb       |   4 +-
 .../config/poolings/donor_pooling.yml         | 192 +++++++++---------
 5 files changed, 101 insertions(+), 101 deletions(-)

diff --git a/app/models/concerns/presenters/submission_behaviour.rb b/app/models/concerns/presenters/submission_behaviour.rb
index 3940061d43..954bd9702e 100644
--- a/app/models/concerns/presenters/submission_behaviour.rb
+++ b/app/models/concerns/presenters/submission_behaviour.rb
@@ -3,7 +3,7 @@
 # Include in a presenter to add support for creating a submission
 module Presenters::SubmissionBehaviour
   def each_submission_option
-    purpose_config.submission_options.each do |button_text, options|
+    purpose_config[:submission_options].each do |button_text, options|
       submission_options = options.to_hash
       submission_options[:asset_groups] = asset_groups
       submission_options[:labware_barcode] = labware.labware_barcode.human
diff --git a/app/models/labware_creators/multi_stamp_tubes.rb b/app/models/labware_creators/multi_stamp_tubes.rb
index 6c4d00958d..a0b18bb612 100644
--- a/app/models/labware_creators/multi_stamp_tubes.rb
+++ b/app/models/labware_creators/multi_stamp_tubes.rb
@@ -125,7 +125,7 @@ def request_hash(transfer)
     # Returns: a hash containing the submission parameters
     # Adds: errors if there is more than one submission specified
     def configured_params
-      submission_options_from_config = purpose_config.submission_options
+      submission_options_from_config = purpose_config[:submission_options]
 
       # if there's more than one appropriate submission, we can't know which one to choose,
       # so don't create one.
diff --git a/app/models/presenters/presenter.rb b/app/models/presenters/presenter.rb
index 2fe917878d..c78d4362a9 100644
--- a/app/models/presenters/presenter.rb
+++ b/app/models/presenters/presenter.rb
@@ -57,7 +57,7 @@ def content_title
   end
 
   def default_printer
-    @default_printer ||= Settings.printers[purpose_config.default_printer_type]
+    @default_printer ||= Settings.printers[purpose_config[:default_printer_type]]
   end
 
   def default_label_count
diff --git a/app/models/presenters/tube_presenter.rb b/app/models/presenters/tube_presenter.rb
index 40d9b24598..a73a519feb 100644
--- a/app/models/presenters/tube_presenter.rb
+++ b/app/models/presenters/tube_presenter.rb
@@ -46,9 +46,9 @@ def custom_metadata_fields
     end
 
     def sequencescape_submission
-      return nil if purpose_config.submission.empty?
+      return nil if purpose_config[:submission].empty?
 
-      s = SequencescapeSubmission.new(purpose_config.submission.to_hash.merge(assets: [labware.uuid]))
+      s = SequencescapeSubmission.new(purpose_config[:submission].to_hash.merge(assets: [labware.uuid]))
       yield s if block_given?
       s
     end
diff --git a/spec/fixtures/config/poolings/donor_pooling.yml b/spec/fixtures/config/poolings/donor_pooling.yml
index b45d2a3855..b7a5818d86 100644
--- a/spec/fixtures/config/poolings/donor_pooling.yml
+++ b/spec/fixtures/config/poolings/donor_pooling.yml
@@ -3,99 +3,99 @@
 donor_pooling:
   # Maping between number of samples to number of pools.
   number_of_pools:
-    "96": 8,
-    "95": 8,
-    "94": 8,
-    "93": 8,
-    "92": 8,
-    "91": 8,
-    "90": 8,
-    "89": 8,
-    "88": 8,
-    "87": 7,
-    "86": 7,
-    "85": 7,
-    "84": 7,
-    "83": 7,
-    "82": 7,
-    "81": 7,
-    "80": 7,
-    "79": 7,
-    "78": 7,
-    "77": 7,
-    "76": 6,
-    "75": 6,
-    "74": 6,
-    "73": 6,
-    "72": 6,
-    "71": 6,
-    "70": 6,
-    "69": 6,
-    "68": 6,
-    "67": 6,
-    "66": 6,
-    "65": 5,
-    "64": 5,
-    "63": 5,
-    "62": 5,
-    "61": 5,
-    "60": 5,
-    "59": 5,
-    "58": 5,
-    "57": 5,
-    "56": 5,
-    "55": 5,
-    "54": 5,
-    "53": 5,
-    "52": 4,
-    "51": 4,
-    "50": 4,
-    "49": 4,
-    "48": 4,
-    "47": 4,
-    "46": 4,
-    "45": 4,
-    "44": 4,
-    "43": 4,
-    "42": 4,
-    "41": 4,
-    "40": 4,
-    "39": 3,
-    "38": 3,
-    "37": 3,
-    "36": 3,
-    "35": 3,
-    "34": 3,
-    "33": 3,
-    "32": 3,
-    "31": 3,
-    "30": 3,
-    "29": 3,
-    "28": 3,
-    "27": 3,
-    "26": 2,
-    "25": 2,
-    "24": 2,
-    "23": 2,
-    "22": 2,
-    "21": 2,
-    "20": 1,
-    "19": 1,
-    "18": 1,
-    "17": 1,
-    "16": 1,
-    "15": 1,
-    "14": 1,
-    "13": 1,
-    "12": 1,
-    "11": 1,
-    "10": 1,
-    "9": 1,
-    "8": 1,
-    "7": 1,
-    "6": 1,
-    "5": 1,
-    "4": 1,
-    "3": 1,
-    "2": 1,
-    "1": 1
+    '96': 8,
+    '95': 8,
+    '94': 8,
+    '93': 8,
+    '92': 8,
+    '91': 8,
+    '90': 8,
+    '89': 8,
+    '88': 8,
+    '87': 7,
+    '86': 7,
+    '85': 7,
+    '84': 7,
+    '83': 7,
+    '82': 7,
+    '81': 7,
+    '80': 7,
+    '79': 7,
+    '78': 7,
+    '77': 7,
+    '76': 6,
+    '75': 6,
+    '74': 6,
+    '73': 6,
+    '72': 6,
+    '71': 6,
+    '70': 6,
+    '69': 6,
+    '68': 6,
+    '67': 6,
+    '66': 6,
+    '65': 5,
+    '64': 5,
+    '63': 5,
+    '62': 5,
+    '61': 5,
+    '60': 5,
+    '59': 5,
+    '58': 5,
+    '57': 5,
+    '56': 5,
+    '55': 5,
+    '54': 5,
+    '53': 5,
+    '52': 4,
+    '51': 4,
+    '50': 4,
+    '49': 4,
+    '48': 4,
+    '47': 4,
+    '46': 4,
+    '45': 4,
+    '44': 4,
+    '43': 4,
+    '42': 4,
+    '41': 4,
+    '40': 4,
+    '39': 3,
+    '38': 3,
+    '37': 3,
+    '36': 3,
+    '35': 3,
+    '34': 3,
+    '33': 3,
+    '32': 3,
+    '31': 3,
+    '30': 3,
+    '29': 3,
+    '28': 3,
+    '27': 3,
+    '26': 2,
+    '25': 2,
+    '24': 2,
+    '23': 2,
+    '22': 2,
+    '21': 2,
+    '20': 1,
+    '19': 1,
+    '18': 1,
+    '17': 1,
+    '16': 1,
+    '15': 1,
+    '14': 1,
+    '13': 1,
+    '12': 1,
+    '11': 1,
+    '10': 1,
+    '9': 1,
+    '8': 1,
+    '7': 1,
+    '6': 1,
+    '5': 1,
+    '4': 1,
+    '3': 1,
+    '2': 1,
+    '1': 1

From 77b16ff401de9efe9a0db58655b4bd60b183a557 Mon Sep 17 00:00:00 2001
From: Dasun Pubudumal <pubudumald@gmail.com>
Date: Thu, 21 Aug 2025 09:11:15 +0100
Subject: [PATCH 25/37] Fixing yet another config issue.

---
 app/models/concerns/presenters/creation_behaviour.rb | 2 +-
 app/models/presenters/plate_presenter.rb             | 2 +-
 config/settings/test.yml                             | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/app/models/concerns/presenters/creation_behaviour.rb b/app/models/concerns/presenters/creation_behaviour.rb
index 1b38f06723..52161cbe80 100644
--- a/app/models/concerns/presenters/creation_behaviour.rb
+++ b/app/models/concerns/presenters/creation_behaviour.rb
@@ -23,7 +23,7 @@ def compatible_tube_rack_purposes
 
   # Eventually this will end up on our labware_creators/creations module
   def purposes_of_type(type)
-    compatible_purposes.select { |_uuid, purpose| purpose.asset_type == type }
+    compatible_purposes.select { |_uuid, purpose| purpose[:asset_type] == type }
   end
 
   def construct_buttons(scope)
diff --git a/app/models/presenters/plate_presenter.rb b/app/models/presenters/plate_presenter.rb
index 7ae03673d0..e68593984d 100644
--- a/app/models/presenters/plate_presenter.rb
+++ b/app/models/presenters/plate_presenter.rb
@@ -110,7 +110,7 @@ def csv_file_links
       links =
         purpose_config
           .fetch(:file_links, [])
-          .select { |link| can_be_enabled?(link&.states) }
+          .select { |link| can_be_enabled?(link & [:states]) }
           .map do |link|
           [
             link.name,
diff --git a/config/settings/test.yml b/config/settings/test.yml
index 80293ca9ae..b84ce4173b 100644
--- a/config/settings/test.yml
+++ b/config/settings/test.yml
@@ -9,7 +9,7 @@
 :robots: {}
 :default_pmb_templates: {}
 :default_sprint_templates: {}
-:default_printer_type_names: []
+:default_printer_type_names: {}
 :submission_templates: {}
 :qc_purposes: []
 :locations: {}

From d17c47eaca57b84b52557ccb33ce8d6f343c43de Mon Sep 17 00:00:00 2001
From: Dasun Pubudumal <pubudumald@gmail.com>
Date: Thu, 21 Aug 2025 09:26:44 +0100
Subject: [PATCH 26/37] Fixing yet another config issue.

---
 app/models/presenters/tube_presenter.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/models/presenters/tube_presenter.rb b/app/models/presenters/tube_presenter.rb
index a73a519feb..5a37ada3d0 100644
--- a/app/models/presenters/tube_presenter.rb
+++ b/app/models/presenters/tube_presenter.rb
@@ -72,7 +72,7 @@ def transfer_volumes?
     def csv_file_links
       purpose_config
         .fetch(:file_links, [])
-        .select { |link| can_be_enabled?(link&.states) }
+        .select { |link| can_be_enabled?(link & [:states]) }
         .map do |link|
           format_extension = link.format || 'csv'
           [

From acf5e2ecc9ffd03619f25931fff8da96cd639ac0 Mon Sep 17 00:00:00 2001
From: Dasun Pubudumal <pubudumald@gmail.com>
Date: Thu, 21 Aug 2025 09:32:56 +0100
Subject: [PATCH 27/37] Fixing yet another config issue.

---
 app/models/presenters/tube_presenter.rb | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/app/models/presenters/tube_presenter.rb b/app/models/presenters/tube_presenter.rb
index 5a37ada3d0..0727d2e909 100644
--- a/app/models/presenters/tube_presenter.rb
+++ b/app/models/presenters/tube_presenter.rb
@@ -72,15 +72,15 @@ def transfer_volumes?
     def csv_file_links
       purpose_config
         .fetch(:file_links, [])
-        .select { |link| can_be_enabled?(link & [:states]) }
+        .select { |link| can_be_enabled?(link[:states]) }
         .map do |link|
-          format_extension = link.format || 'csv'
+          format_extension = link[:format] || 'csv'
           [
-            link.name,
+            link[:name],
             [
               :limber_tube,
               :tubes_export,
-              { id: link.id, limber_tube_id: human_barcode, format: format_extension, **link.params || {} }
+              { id: link[:id], limber_tube_id: human_barcode, format: format_extension, **link[:params] || {} }
             ]
           ]
         end

From 90c0e170d4a28fff00d858a28cc52f57b20a6618 Mon Sep 17 00:00:00 2001
From: Dasun Pubudumal <pubudumald@gmail.com>
Date: Thu, 21 Aug 2025 09:33:18 +0100
Subject: [PATCH 28/37] Fixing yet another config issue.

---
 app/models/presenters/plate_presenter.rb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/models/presenters/plate_presenter.rb b/app/models/presenters/plate_presenter.rb
index e68593984d..74e5bfcd3d 100644
--- a/app/models/presenters/plate_presenter.rb
+++ b/app/models/presenters/plate_presenter.rb
@@ -113,11 +113,11 @@ def csv_file_links
           .select { |link| can_be_enabled?(link & [:states]) }
           .map do |link|
           [
-            link.name,
+            link[:name],
             [
               :limber_plate,
               :export,
-              { id: link.id, limber_plate_id: human_barcode, format: :csv, **link.params || {} }
+              { id: link[:id], limber_plate_id: human_barcode, format: :csv, **link[:params] || {} }
             ]
           ]
         end

From 20c1e74f6fc56c341b04839b1cbd7bbad13f1b98 Mon Sep 17 00:00:00 2001
From: Dasun Pubudumal <pubudumald@gmail.com>
Date: Thu, 21 Aug 2025 09:51:34 +0100
Subject: [PATCH 29/37] Fixing yet another config issue.

---
 app/models/presenters/plate_presenter.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/models/presenters/plate_presenter.rb b/app/models/presenters/plate_presenter.rb
index 74e5bfcd3d..6bad80f164 100644
--- a/app/models/presenters/plate_presenter.rb
+++ b/app/models/presenters/plate_presenter.rb
@@ -110,7 +110,7 @@ def csv_file_links
       links =
         purpose_config
           .fetch(:file_links, [])
-          .select { |link| can_be_enabled?(link & [:states]) }
+          .select { |link| can_be_enabled?(link[:states]) }
           .map do |link|
           [
             link[:name],

From 1fe05e65a34b32ebc2c3f6eb29e0e4103f4ba565 Mon Sep 17 00:00:00 2001
From: Dasun Pubudumal <pubudumald@gmail.com>
Date: Thu, 21 Aug 2025 16:16:15 +0100
Subject: [PATCH 30/37] Fixing yet another config issue.

---
 app/models/concerns/presenters/robot_controlled.rb     |  3 +--
 .../stamped_plate_adding_randomised_controls.rb        | 10 +++++-----
 2 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/app/models/concerns/presenters/robot_controlled.rb b/app/models/concerns/presenters/robot_controlled.rb
index 5ac31bb738..72036022fc 100644
--- a/app/models/concerns/presenters/robot_controlled.rb
+++ b/app/models/concerns/presenters/robot_controlled.rb
@@ -17,8 +17,7 @@ def suitable_robots
     end
 
     def suitable_for_labware?(config)
-      config
-        .beds
+      config[:beds]
         .detect { |_bed, bed_config| bed_config.purpose == purpose_name && bed_config.states.include?(labware.state) }
         .present?
     end
diff --git a/app/models/labware_creators/stamped_plate_adding_randomised_controls.rb b/app/models/labware_creators/stamped_plate_adding_randomised_controls.rb
index 0f85990334..428c0bb42d 100644
--- a/app/models/labware_creators/stamped_plate_adding_randomised_controls.rb
+++ b/app/models/labware_creators/stamped_plate_adding_randomised_controls.rb
@@ -79,9 +79,9 @@ def generate_control_locations_from_purpose_config
       control_locations = []
       list_of_controls.count.times do |control_index|
         control = list_of_controls[control_index]
-        if control.fixed_location?
+        if control[:fixed_location].present?
           # use the location specified in the purpose config for this control
-          control_locations.push(control.fixed_location)
+          control_locations.push(control[:fixed_location])
         else
           # sample a random parent well and fetch its location (child not created yet)
           control_locations.push(parent.wells.sample.position['name'])
@@ -92,13 +92,13 @@ def generate_control_locations_from_purpose_config
 
     def check_control_rules_from_config(control_locations)
       list_of_rules.each do |rule|
-        case rule.type
+        case rule[:type]
         when 'not'
           # locations must not match this combination of wells (order is important)
-          return false if control_locations == rule.value
+          return false if control_locations == rule[:value]
         when 'well_exclusions'
           # locations must not be in this list well locations (exclusions)
-          return false if control_locations.any? { |location| rule.value.include?(location) }
+          return false if control_locations.any? { |location| rule[:value].include?(location) }
         else
           # check for unrecognised rule type
           raise StandardError, "Unrecognised control locations rule type from purpose config #{rule.type}"

From 5ad1a96dabf623a71c9fa298825951f790702b2d Mon Sep 17 00:00:00 2001
From: Dasun Pubudumal <pubudumald@gmail.com>
Date: Tue, 26 Aug 2025 14:07:29 +0100
Subject: [PATCH 31/37] Fixing yet another config issue.

---
 config/initializers/settings.rb | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/config/initializers/settings.rb b/config/initializers/settings.rb
index 0c133b9dea..1d7ce35395 100644
--- a/config/initializers/settings.rb
+++ b/config/initializers/settings.rb
@@ -69,6 +69,8 @@ def self.load_yaml
     config_data.with_indifferent_access
   end
 
+  # Returns an instance of CustomConfiguration that provides access to the
+  # configuration data loaded from the YAML file.
   def self.configuration
     @configuration ||= CustomConfiguration.new(load_yaml)
   end

From d6150bcbb57f1d8f643b71dc3836811597c2b15b Mon Sep 17 00:00:00 2001
From: Dasun Pubudumal <pubudumald@gmail.com>
Date: Wed, 27 Aug 2025 09:00:09 +0100
Subject: [PATCH 32/37] Trying CI out again

---
 config/initializers/settings.rb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/config/initializers/settings.rb b/config/initializers/settings.rb
index 1d7ce35395..a331427cc5 100644
--- a/config/initializers/settings.rb
+++ b/config/initializers/settings.rb
@@ -69,6 +69,7 @@ def self.load_yaml
     config_data.with_indifferent_access
   end
 
+
   # Returns an instance of CustomConfiguration that provides access to the
   # configuration data loaded from the YAML file.
   def self.configuration

From 0eab969e74df0fd4f0c24739cb2626e2ebfd1445 Mon Sep 17 00:00:00 2001
From: Dasun Pubudumal <pubudumald@gmail.com>
Date: Wed, 27 Aug 2025 09:15:08 +0100
Subject: [PATCH 33/37] Fix prettier

---
 config/initializers/settings.rb | 1 -
 1 file changed, 1 deletion(-)

diff --git a/config/initializers/settings.rb b/config/initializers/settings.rb
index a331427cc5..1d7ce35395 100644
--- a/config/initializers/settings.rb
+++ b/config/initializers/settings.rb
@@ -69,7 +69,6 @@ def self.load_yaml
     config_data.with_indifferent_access
   end
 
-
   # Returns an instance of CustomConfiguration that provides access to the
   # configuration data loaded from the YAML file.
   def self.configuration

From 1adecd11352090152f9c17d52a632f8caf535f41 Mon Sep 17 00:00:00 2001
From: Dasun Pubudumal <pubudumald@gmail.com>
Date: Wed, 27 Aug 2025 09:16:19 +0100
Subject: [PATCH 34/37] Fixing yet another config issue

---
 app/models/concerns/presenters/robot_controlled.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/models/concerns/presenters/robot_controlled.rb b/app/models/concerns/presenters/robot_controlled.rb
index 72036022fc..f636d29ea2 100644
--- a/app/models/concerns/presenters/robot_controlled.rb
+++ b/app/models/concerns/presenters/robot_controlled.rb
@@ -18,7 +18,7 @@ def suitable_robots
 
     def suitable_for_labware?(config)
       config[:beds]
-        .detect { |_bed, bed_config| bed_config.purpose == purpose_name && bed_config.states.include?(labware.state) }
+        .detect { |_bed, bed_config| bed_config[:purpose] == purpose_name && bed_config[:states].include?(labware.state) }
         .present?
     end
 

From 07634e98e4ae09f5f3686b148b21b555e36e3edb Mon Sep 17 00:00:00 2001
From: Dasun Pubudumal <pubudumald@gmail.com>
Date: Wed, 27 Aug 2025 09:17:03 +0100
Subject: [PATCH 35/37] Fixing a linting issue

---
 app/models/concerns/presenters/robot_controlled.rb | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/app/models/concerns/presenters/robot_controlled.rb b/app/models/concerns/presenters/robot_controlled.rb
index f636d29ea2..98e9b25d61 100644
--- a/app/models/concerns/presenters/robot_controlled.rb
+++ b/app/models/concerns/presenters/robot_controlled.rb
@@ -18,7 +18,9 @@ def suitable_robots
 
     def suitable_for_labware?(config)
       config[:beds]
-        .detect { |_bed, bed_config| bed_config[:purpose] == purpose_name && bed_config[:states].include?(labware.state) }
+        .detect do |_bed, bed_config|
+          bed_config[:purpose] == purpose_name && bed_config[:states].include?(labware.state)
+        end
         .present?
     end
 

From 9de6f715ce1b3365e9ce130b75ef34716890d83c Mon Sep 17 00:00:00 2001
From: Dasun Pubudumal <pubudumald@gmail.com>
Date: Wed, 27 Aug 2025 09:26:58 +0100
Subject: [PATCH 36/37] Fixing yet another config issue

---
 app/models/presenters/tube_rack_presenter.rb | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/app/models/presenters/tube_rack_presenter.rb b/app/models/presenters/tube_rack_presenter.rb
index d11d4ac325..4229738d1f 100644
--- a/app/models/presenters/tube_rack_presenter.rb
+++ b/app/models/presenters/tube_rack_presenter.rb
@@ -42,9 +42,10 @@ def tube_failing_applicable?
     def csv_file_links
       purpose_config
         .fetch(:file_links, [])
-        .select { |link| can_be_enabled?(link&.states) }
+        .select { |link| can_be_enabled?(link[:states]) }
         .map do |link|
-          [link.name, [:limber_tube_rack, :tube_racks_export, { id: link.id, limber_tube_rack_id: uuid, format: :csv }]]
+          [link[:name],
+           [:limber_tube_rack, :tube_racks_export, { id: link[:id], limber_tube_rack_id: uuid, format: :csv }]]
         end
     end
 

From c0104e1a807593b7f565acf3b282ea91537ee34e Mon Sep 17 00:00:00 2001
From: Dasun Pubudumal <pubudumald@gmail.com>
Date: Wed, 27 Aug 2025 09:53:18 +0100
Subject: [PATCH 37/37] Fixing yet another config issue

---
 app/models/labware_creators/merged_plate.rb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/models/labware_creators/merged_plate.rb b/app/models/labware_creators/merged_plate.rb
index 61776dda96..622fb0d0cc 100644
--- a/app/models/labware_creators/merged_plate.rb
+++ b/app/models/labware_creators/merged_plate.rb
@@ -29,7 +29,7 @@ def labware_wells
     # @return [Array] Purpose name strings.
     #
     def expected_source_purposes
-      Settings.purposes.dig(@purpose_uuid, :merged_plate).source_purposes
+      Settings.purposes.dig(@purpose_uuid, :merged_plate)[:source_purposes]
     end
 
     #
@@ -38,7 +38,7 @@ def expected_source_purposes
     # @return [String] Some descriptive text.
     #
     def help_text
-      Settings.purposes.dig(@purpose_uuid, :merged_plate).help_text
+      Settings.purposes.dig(@purpose_uuid, :merged_plate)[:help_text]
     end
 
     def barcodes=(barcodes)