From 5258adcbf4a452052de2d87317fbf9a29d73a17c Mon Sep 17 00:00:00 2001
From: wy1 <wy1@sanger.ac.uk>
Date: Wed, 14 Aug 2024 16:00:36 +0100
Subject: [PATCH 01/14] add wip_list method to return wip file list

---
 lib/record_loader/application_record_loader.rb | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/lib/record_loader/application_record_loader.rb b/lib/record_loader/application_record_loader.rb
index b96a6a14e4..38d0cc5617 100644
--- a/lib/record_loader/application_record_loader.rb
+++ b/lib/record_loader/application_record_loader.rb
@@ -9,5 +9,13 @@ class ApplicationRecordLoader < RecordLoader::Base
     # Uses the standard RailsAdapter
     # @see https://rubydoc.info/github/sanger/record_loader/RecordLoader/Adapter
     adapter RecordLoader::Adapter::Rails.new
+  
+    def wip_list(directory)
+      wip_files = []
+      Find.find(directory) do |path|
+        files << path if path =~ /\wip\.yml$/
+      end
+      files
+    end
   end
 end

From cc4efbbe24b3039abccaa8ed6bc877912e5770d7 Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Wed, 21 Aug 2024 10:48:40 +0100
Subject: [PATCH 02/14] remove directory parameter in wip_list method

---
 lib/record_loader/application_record_loader.rb | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/lib/record_loader/application_record_loader.rb b/lib/record_loader/application_record_loader.rb
index 38d0cc5617..895de35cb8 100644
--- a/lib/record_loader/application_record_loader.rb
+++ b/lib/record_loader/application_record_loader.rb
@@ -1,4 +1,5 @@
 # frozen_string_literal: true
+require 'find' 
 
 # This file was automatically generated by `rails g record_loader`
 module RecordLoader
@@ -10,12 +11,13 @@ class ApplicationRecordLoader < RecordLoader::Base
     # @see https://rubydoc.info/github/sanger/record_loader/RecordLoader/Adapter
     adapter RecordLoader::Adapter::Rails.new
   
-    def wip_list(directory)
+    def wip_list
       wip_files = []
-      Find.find(directory) do |path|
-        files << path if path =~ /\wip\.yml$/
+      wip_files_path = Rails.root.join('config','default_records')
+      Find.find(wip_files_path) do |path|
+        wip_files << path if path =~ /\wip\.yml$/
       end
-      files
+      wip_files
     end
   end
 end

From 16f4d4ed8f2dfb4162316b38ab63b373ebba4158 Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Wed, 21 Aug 2024 11:02:08 +0100
Subject: [PATCH 03/14] fix the formatting

---
 lib/record_loader/application_record_loader.rb | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/lib/record_loader/application_record_loader.rb b/lib/record_loader/application_record_loader.rb
index 895de35cb8..a73ba5651f 100644
--- a/lib/record_loader/application_record_loader.rb
+++ b/lib/record_loader/application_record_loader.rb
@@ -1,5 +1,5 @@
 # frozen_string_literal: true
-require 'find' 
+require 'find'
 
 # This file was automatically generated by `rails g record_loader`
 module RecordLoader
@@ -10,13 +10,11 @@ class ApplicationRecordLoader < RecordLoader::Base
     # Uses the standard RailsAdapter
     # @see https://rubydoc.info/github/sanger/record_loader/RecordLoader/Adapter
     adapter RecordLoader::Adapter::Rails.new
-  
+
     def wip_list
       wip_files = []
-      wip_files_path = Rails.root.join('config','default_records')
-      Find.find(wip_files_path) do |path|
-        wip_files << path if path =~ /\wip\.yml$/
-      end
+      wip_files_path = Rails.root.join('config', 'default_records')
+      Find.find(wip_files_path) { |path| wip_files << path if path =~ /\wip\.yml$/ }
       wip_files
     end
   end

From e6b326ff3b767678abc21f53d305ddf188ac440a Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Wed, 21 Aug 2024 14:49:57 +0100
Subject: [PATCH 04/14] fix the format

---
 lib/record_loader/application_record_loader.rb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/record_loader/application_record_loader.rb b/lib/record_loader/application_record_loader.rb
index a73ba5651f..20e87ac89a 100644
--- a/lib/record_loader/application_record_loader.rb
+++ b/lib/record_loader/application_record_loader.rb
@@ -13,8 +13,8 @@ class ApplicationRecordLoader < RecordLoader::Base
 
     def wip_list
       wip_files = []
-      wip_files_path = Rails.root.join('config', 'default_records')
-      Find.find(wip_files_path) { |path| wip_files << path if path =~ /\wip\.yml$/ }
+      wip_files_path = Rails.root.join("config/default_records")
+      Find.find(wip_files_path) { |path| wip_files << path if /\wip\.yml$/.match?(path) }
       wip_files
     end
   end

From 401cfa541df612afc0b11034ff5ea0797baedf36 Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Wed, 21 Aug 2024 14:58:49 +0100
Subject: [PATCH 05/14] fix the format

---
 lib/record_loader/application_record_loader.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/record_loader/application_record_loader.rb b/lib/record_loader/application_record_loader.rb
index 20e87ac89a..32e909b8f8 100644
--- a/lib/record_loader/application_record_loader.rb
+++ b/lib/record_loader/application_record_loader.rb
@@ -13,7 +13,7 @@ class ApplicationRecordLoader < RecordLoader::Base
 
     def wip_list
       wip_files = []
-      wip_files_path = Rails.root.join("config/default_records")
+      wip_files_path = Rails.root.join('config/default_records')
       Find.find(wip_files_path) { |path| wip_files << path if /\wip\.yml$/.match?(path) }
       wip_files
     end

From d60b6bfd8fd6948910a50c8fe46db06acf24795d Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Wed, 21 Aug 2024 15:38:00 +0100
Subject: [PATCH 06/14] add deploy_wip_pipeline environment variable

---
 config/environments/development.rb | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/config/environments/development.rb b/config/environments/development.rb
index 03eb9d6529..3247fea461 100644
--- a/config/environments/development.rb
+++ b/config/environments/development.rb
@@ -71,6 +71,8 @@
     Bullet.bullet_logger = true
     Bullet.rails_logger = true
   end
+
+  config.deploy_wip_pipelines = true
 end
 
 Rack::MiniProfiler.config.position = 'right'

From e8d14fcb72efadfc2a6c24b44d88179478674a8e Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Thu, 22 Aug 2024 10:25:07 +0100
Subject: [PATCH 07/14] modify the wip_list to return file base name rather
 than file path

---
 lib/record_loader/application_record_loader.rb | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/lib/record_loader/application_record_loader.rb b/lib/record_loader/application_record_loader.rb
index 32e909b8f8..a6a8a03aee 100644
--- a/lib/record_loader/application_record_loader.rb
+++ b/lib/record_loader/application_record_loader.rb
@@ -14,7 +14,12 @@ class ApplicationRecordLoader < RecordLoader::Base
     def wip_list
       wip_files = []
       wip_files_path = Rails.root.join('config/default_records')
-      Find.find(wip_files_path) { |path| wip_files << path if /\wip\.yml$/.match?(path) }
+      Find.find(wip_files_path) do |path|
+        if path.match?(/\wip\.yml$/)
+          file_name = File.basename(path, '.wip.yml')
+          wip_files << file_name
+        end
+      end
       wip_files
     end
   end

From af301823bb5c79af3083fff81a4637030713caca Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Thu, 22 Aug 2024 13:25:15 +0100
Subject: [PATCH 08/14] add config wip flag option in wip_list method

---
 lib/record_loader/application_record_loader.rb | 18 +++++++++++-------
 1 file changed, 11 insertions(+), 7 deletions(-)

diff --git a/lib/record_loader/application_record_loader.rb b/lib/record_loader/application_record_loader.rb
index a6a8a03aee..a2d5694233 100644
--- a/lib/record_loader/application_record_loader.rb
+++ b/lib/record_loader/application_record_loader.rb
@@ -12,15 +12,19 @@ class ApplicationRecordLoader < RecordLoader::Base
     adapter RecordLoader::Adapter::Rails.new
 
     def wip_list
-      wip_files = []
-      wip_files_path = Rails.root.join('config/default_records')
-      Find.find(wip_files_path) do |path|
-        if path.match?(/\wip\.yml$/)
-          file_name = File.basename(path, '.wip.yml')
-          wip_files << file_name
+      if Rails.application.config.deploy_wip_pipelines
+        wip_files = []
+        wip_files_path = Rails.root.join('config/default_records')
+        Find.find(wip_files_path) do |path|
+          if path.match?(/\wip\.yml$/)
+            file_name = File.basename(path, '.wip.yml')
+            wip_files << file_name
+          end
         end
+        wip_files
+      else
+        []
       end
-      wip_files
     end
   end
 end

From ffca885ed3ad55922f59bea1551313016da79a08 Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Thu, 22 Aug 2024 13:35:08 +0100
Subject: [PATCH 09/14] fix formating

---
 .../application_record_loader.rb              | 20 +++++++++----------
 1 file changed, 9 insertions(+), 11 deletions(-)

diff --git a/lib/record_loader/application_record_loader.rb b/lib/record_loader/application_record_loader.rb
index a2d5694233..c393467176 100644
--- a/lib/record_loader/application_record_loader.rb
+++ b/lib/record_loader/application_record_loader.rb
@@ -12,19 +12,17 @@ class ApplicationRecordLoader < RecordLoader::Base
     adapter RecordLoader::Adapter::Rails.new
 
     def wip_list
-      if Rails.application.config.deploy_wip_pipelines
-        wip_files = []
-        wip_files_path = Rails.root.join('config/default_records')
-        Find.find(wip_files_path) do |path|
-          if path.match?(/\wip\.yml$/)
-            file_name = File.basename(path, '.wip.yml')
-            wip_files << file_name
-          end
+      return [] unless Rails.application.config.deploy_wip_pipelines
+
+      wip_files = []
+      wip_files_path = Rails.root.join('config/default_records')
+      Find.find(wip_files_path) do |path|
+        if path.match?(/\wip\.yml$/)
+          file_name = File.basename(path, '.wip.yml')
+          wip_files << file_name
         end
-        wip_files
-      else
-        []
       end
+      wip_files
     end
   end
 end

From 69ce5037326c264fb8c9d5a7fab1be4657070cd4 Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Thu, 22 Aug 2024 14:05:56 +0100
Subject: [PATCH 10/14] adding to handle if flag not set

---
 lib/record_loader/application_record_loader.rb | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/lib/record_loader/application_record_loader.rb b/lib/record_loader/application_record_loader.rb
index c393467176..cbd066a8e3 100644
--- a/lib/record_loader/application_record_loader.rb
+++ b/lib/record_loader/application_record_loader.rb
@@ -12,7 +12,15 @@ class ApplicationRecordLoader < RecordLoader::Base
     adapter RecordLoader::Adapter::Rails.new
 
     def wip_list
-      return [] unless Rails.application.config.deploy_wip_pipelines
+      deploy_wip_pipelines =
+        (
+          if Rails.application.config.respond_to?(:deploy_wip_pipelines)
+            Rails.application.config.deploy_wip_pipelines
+          else
+            false
+          end
+        )
+      return [] unless deploy_wip_pipelines
 
       wip_files = []
       wip_files_path = Rails.root.join('config/default_records')

From 22d04b43b62a430555c3f94a117cf1aaff36664b Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Thu, 22 Aug 2024 14:39:11 +0100
Subject: [PATCH 11/14] refactor wip method

---
 lib/record_loader/application_record_loader.rb | 9 +--------
 1 file changed, 1 insertion(+), 8 deletions(-)

diff --git a/lib/record_loader/application_record_loader.rb b/lib/record_loader/application_record_loader.rb
index cbd066a8e3..9d7aa2a1a0 100644
--- a/lib/record_loader/application_record_loader.rb
+++ b/lib/record_loader/application_record_loader.rb
@@ -12,14 +12,7 @@ class ApplicationRecordLoader < RecordLoader::Base
     adapter RecordLoader::Adapter::Rails.new
 
     def wip_list
-      deploy_wip_pipelines =
-        (
-          if Rails.application.config.respond_to?(:deploy_wip_pipelines)
-            Rails.application.config.deploy_wip_pipelines
-          else
-            false
-          end
-        )
+      deploy_wip_pipelines = Rails.application.config.try(:deploy_wip_pipelines) || false
       return [] unless deploy_wip_pipelines
 
       wip_files = []

From df8acfb0cd41a56af4bb78df1fa4dbfc3115c49e Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Fri, 23 Aug 2024 18:39:51 +0100
Subject: [PATCH 12/14] add test for wip_list method

---
 config/environments/development.rb            |  1 +
 .../application_record_loader.rb              |  3 +-
 .../application_record_loader_spec.rb         | 41 +++++++++++++++++++
 3 files changed, 44 insertions(+), 1 deletion(-)
 create mode 100644 spec/lib/record_loader/application_record_loader_spec.rb

diff --git a/config/environments/development.rb b/config/environments/development.rb
index 3247fea461..d633043d05 100644
--- a/config/environments/development.rb
+++ b/config/environments/development.rb
@@ -72,6 +72,7 @@
     Bullet.rails_logger = true
   end
 
+  # load WIP features flag
   config.deploy_wip_pipelines = true
 end
 
diff --git a/lib/record_loader/application_record_loader.rb b/lib/record_loader/application_record_loader.rb
index 9d7aa2a1a0..51cc250102 100644
--- a/lib/record_loader/application_record_loader.rb
+++ b/lib/record_loader/application_record_loader.rb
@@ -12,11 +12,12 @@ class ApplicationRecordLoader < RecordLoader::Base
     adapter RecordLoader::Adapter::Rails.new
 
     def wip_list
+      # return a list of WIP files name as features if deploy_wip_pipelines is set to true, or return empty list
       deploy_wip_pipelines = Rails.application.config.try(:deploy_wip_pipelines) || false
       return [] unless deploy_wip_pipelines
 
       wip_files = []
-      wip_files_path = Rails.root.join('config/default_records')
+      wip_files_path = @path
       Find.find(wip_files_path) do |path|
         if path.match?(/\wip\.yml$/)
           file_name = File.basename(path, '.wip.yml')
diff --git a/spec/lib/record_loader/application_record_loader_spec.rb b/spec/lib/record_loader/application_record_loader_spec.rb
new file mode 100644
index 0000000000..8f55825505
--- /dev/null
+++ b/spec/lib/record_loader/application_record_loader_spec.rb
@@ -0,0 +1,41 @@
+# frozen_string_literal: true
+
+require 'rails_helper'
+require 'record_loader/application_record_loader'
+
+RSpec.describe RecordLoader::ApplicationRecordLoader, :loader, type: :model do
+  def a_new_record_loader
+    described_class.new(directory: test_directory)
+  end
+
+  subject(:record_loader) { a_new_record_loader }
+
+  let(:test_directory) { Rails.root.join('spec/data/record_loader/application_record_loader') }
+
+  context 'when deploy_wip_pipelines is false' do
+    before { allow(Rails.application.config).to receive(:deploy_wip_pipelines).and_return(false) }
+
+    it 'returns an empty array' do
+      expect(record_loader.wip_list).to eq([])
+    end
+  end
+
+  context 'when deploy_wip_pipelines is true' do
+    before do
+      allow(Rails.application.config).to receive(:deploy_wip_pipelines).and_return(true)
+      allow(Find).to receive(:find).with(test_directory).and_yield("#{test_directory}/example.wip.yml")
+    end
+
+    it 'returns a list of WIP features' do
+      expect(record_loader.wip_list).to eq(['example'])
+    end
+  end
+
+  context 'when deploy_wip_pipelines is not set' do
+    before { allow(Rails.application.config).to receive(:deploy_wip_pipelines).and_return(nil) }
+
+    it 'returns an empty array' do
+      expect(record_loader.wip_list).to eq([])
+    end
+  end
+end

From 68e710e1e044d916cecb5490ccc3a5305a8644ae Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Fri, 23 Aug 2024 20:06:18 +0100
Subject: [PATCH 13/14] add test config & test file

---
 config/environments/test.rb                   |  3 ++
 .../application_record_loader/example.wip.yml | 40 +++++++++++++++++++
 2 files changed, 43 insertions(+)
 create mode 100644 spec/data/record_loader/application_record_loader/example.wip.yml

diff --git a/config/environments/test.rb b/config/environments/test.rb
index 1cd73956ed..b118bfe8c2 100644
--- a/config/environments/test.rb
+++ b/config/environments/test.rb
@@ -50,4 +50,7 @@
 
   # Raises error for missing translations.
   # config.action_view.raise_on_missing_translations = true
+
+  # load WIP features flag
+  config.deploy_wip_pipelines = true
 end
diff --git a/spec/data/record_loader/application_record_loader/example.wip.yml b/spec/data/record_loader/application_record_loader/example.wip.yml
new file mode 100644
index 0000000000..e4fc108981
--- /dev/null
+++ b/spec/data/record_loader/application_record_loader/example.wip.yml
@@ -0,0 +1,40 @@
+# Submission templates for the aggregation and library prep parts of the scRNA Core pipeline.
+---
+Limber-Htp - scRNA Core Aggregation:
+  submission_class_name: "LinearSubmission"
+  related_records:
+    request_type_keys: ["limber_scrna_core_aggregation"]
+    product_line_name: Short Read
+    product_catalogue_name: scRNA Core
+Limber-Htp - scRNA Core Library Prep:
+  submission_class_name: "LinearSubmission"
+  related_records:
+    request_type_keys: ["limber_scrna_core_library_prep"]
+    product_line_name: Short Read
+    product_catalogue_name: scRNA Core
+Limber-Htp - scRNA Core Library Prep - Pool:
+  submission_class_name: "LinearSubmission"
+  related_records:
+    request_type_keys: ["limber_scrna_core_library_prep", "limber_multiplexing"]
+    product_line_name: Short Read
+    product_catalogue_name: scRNA Core
+Limber-Htp - scRNA Core Library Prep - NovaSeqX paired end sequencing:
+  submission_class_name: "LinearSubmission"
+  related_records:
+    request_type_keys:
+      ["limber_scrna_core_library_prep", "limber_multiplexing", "illumina_htp_novaseqx_paired_end_sequencing"]
+    product_line_name: Short Read
+    product_catalogue_name: scRNA Core
+Limber-Htp - scRNA Core Library Prep - NovaSeq 6000 paired end sequencing:
+  submission_class_name: "LinearSubmission"
+  related_records:
+    request_type_keys:
+      ["limber_scrna_core_library_prep", "limber_multiplexing", "illumina_htp_novaseq_6000_paired_end_sequencing"]
+    product_line_name: Short Read
+    product_catalogue_name: scRNA Core
+Limber-Htp - scRNA Core Library Prep - MiSeq sequencing:
+  submission_class_name: "LinearSubmission"
+  related_records:
+    request_type_keys: ["limber_scrna_core_library_prep", "limber_multiplexing", "illumina_b_miseq_sequencing"]
+    product_line_name: Short Read
+    product_catalogue_name: scRNA Core

From 9949dec9036c6ee30dfe45053b5ec34acfef5455 Mon Sep 17 00:00:00 2001
From: Wendy Yang <wy1@sanger.ac.uk>
Date: Tue, 27 Aug 2024 16:24:45 +0100
Subject: [PATCH 14/14] simplify test file & add comments

---
 .../application_record_loader.rb              |  2 +
 .../application_record_loader/example.wip.yml | 42 ++-----------------
 2 files changed, 5 insertions(+), 39 deletions(-)

diff --git a/lib/record_loader/application_record_loader.rb b/lib/record_loader/application_record_loader.rb
index 51cc250102..961a9c07c6 100644
--- a/lib/record_loader/application_record_loader.rb
+++ b/lib/record_loader/application_record_loader.rb
@@ -17,6 +17,8 @@ def wip_list
       return [] unless deploy_wip_pipelines
 
       wip_files = []
+      # @path returns 'config/default_records' directory
+      # see https://github.com/sanger/record_loader/blob/master/lib/record_loader/base.rb
       wip_files_path = @path
       Find.find(wip_files_path) do |path|
         if path.match?(/\wip\.yml$/)
diff --git a/spec/data/record_loader/application_record_loader/example.wip.yml b/spec/data/record_loader/application_record_loader/example.wip.yml
index e4fc108981..51074a83b0 100644
--- a/spec/data/record_loader/application_record_loader/example.wip.yml
+++ b/spec/data/record_loader/application_record_loader/example.wip.yml
@@ -1,40 +1,4 @@
-# Submission templates for the aggregation and library prep parts of the scRNA Core pipeline.
+# Test record loader records
 ---
-Limber-Htp - scRNA Core Aggregation:
-  submission_class_name: "LinearSubmission"
-  related_records:
-    request_type_keys: ["limber_scrna_core_aggregation"]
-    product_line_name: Short Read
-    product_catalogue_name: scRNA Core
-Limber-Htp - scRNA Core Library Prep:
-  submission_class_name: "LinearSubmission"
-  related_records:
-    request_type_keys: ["limber_scrna_core_library_prep"]
-    product_line_name: Short Read
-    product_catalogue_name: scRNA Core
-Limber-Htp - scRNA Core Library Prep - Pool:
-  submission_class_name: "LinearSubmission"
-  related_records:
-    request_type_keys: ["limber_scrna_core_library_prep", "limber_multiplexing"]
-    product_line_name: Short Read
-    product_catalogue_name: scRNA Core
-Limber-Htp - scRNA Core Library Prep - NovaSeqX paired end sequencing:
-  submission_class_name: "LinearSubmission"
-  related_records:
-    request_type_keys:
-      ["limber_scrna_core_library_prep", "limber_multiplexing", "illumina_htp_novaseqx_paired_end_sequencing"]
-    product_line_name: Short Read
-    product_catalogue_name: scRNA Core
-Limber-Htp - scRNA Core Library Prep - NovaSeq 6000 paired end sequencing:
-  submission_class_name: "LinearSubmission"
-  related_records:
-    request_type_keys:
-      ["limber_scrna_core_library_prep", "limber_multiplexing", "illumina_htp_novaseq_6000_paired_end_sequencing"]
-    product_line_name: Short Read
-    product_catalogue_name: scRNA Core
-Limber-Htp - scRNA Core Library Prep - MiSeq sequencing:
-  submission_class_name: "LinearSubmission"
-  related_records:
-    request_type_keys: ["limber_scrna_core_library_prep", "limber_multiplexing", "illumina_b_miseq_sequencing"]
-    product_line_name: Short Read
-    product_catalogue_name: scRNA Core
+Test Record:
+  test_attribute: "A Value"