sanger · wendyyang · Sep 5, 2024 · Sep 9, 2024 · Sep 9, 2024 · Sep 9, 2024
diff --git a/app/models/plate_purpose.rb b/app/models/plate_purpose.rb
@@ -88,7 +88,11 @@ def pool_wells(wells) # rubocop:todo Metrics/MethodLength
   has_many :plates
 
   def self.stock_plate_purpose
-    PlatePurpose.create_with(stock_plate: true, cherrypickable_target: true).find_or_create_by!(name: 'Stock Plate')
+    PlatePurpose.create_with(
+      stock_plate: true,
+      cherrypickable_target: true,
+      type: 'PlatePurpose::Input'
+    ).find_or_create_by!(name: 'Stock Plate')
   end
 
   def size

diff --git a/app/models/tag_layout.rb b/app/models/tag_layout.rb
@@ -49,16 +49,15 @@ class TagLayout < ApplicationRecord
 
   # The plate we'll be laying out the tags into
   belongs_to :plate, optional: false
-
   validates :direction, inclusion: { in: DIRECTION_ALGORITHMS.keys }
   validates :walking_by, inclusion: { in: WALKING_ALGORITHMS.keys }
 
   validates :direction_algorithm, presence: true
   validates :walking_algorithm, presence: true
 
   # After creating the instance we can layout the tags into the wells.
-  after_create :layout_tags_into_wells, if: :valid?
 
+  after_create :layout_tags_into_wells, if: :valid?
   set_target_for_owner(:plate)
 
   delegate :direction, to: :direction_algorithm_module

diff --git a/config/default_records/plate_purposes/005_limber_purposes.yml b/config/default_records/plate_purposes/005_limber_purposes.yml
@@ -18,6 +18,8 @@ LTN Cherrypick: *limber_input_96
 LHR RT: *limber_input_96
 LTHR RT: *limber_input_96
 LTHR Cherrypick: *limber_input_96
+Stock Plate: *limber_input_96
+
 PF Cherrypicked:
   <<: *limber_input_96
   default_state: passed

diff --git a/config/default_records/request_types/005_limber_bespoke.yml b/config/default_records/request_types/005_limber_bespoke.yml
@@ -10,6 +10,7 @@ limber_pcr_bespoke:
   acceptable_purposes:
     - LBB Cherrypick
     - LBC Cherrypick
+    - Stock Plate
   library_types:
     - ChIP-Seq Auto
     - Chromium single cell HTO

diff --git a/db/seeds/0001_snp_plate_purposes.rb b/db/seeds/0001_snp_plate_purposes.rb
@@ -8,9 +8,6 @@
     cherrypickable_target: true
     stock_plate: false
     prefix: WD
-  - name: Stock Plate
-    stock_plate: true
-    cherrypickable_target: true
   - name: 40ng
   - name: Whole Genome Amplification
     cherrypickable_target: true

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

diff --git a/features/support/step_definitions/plate_steps.rb b/features/support/step_definitions/plate_steps.rb
@@ -121,6 +121,7 @@
 
 Given /^a "([^"]+)" plate called "([^"]+)" exists$/ do |name, plate_name|
   plate_purpose = PlatePurpose.find_by!(name: name)
+  # binding.pry
   plate_purpose.create!(name: plate_name)
 end
 

diff --git a/features/support/step_definitions/tag_layout_steps.rb b/features/support/step_definitions/tag_layout_steps.rb
@@ -54,12 +54,12 @@ def plate_view_of_oligos(label, mapping) # rubocop:todo Metrics/AbcSize
 
 def check_tag_layout(name, well_range, expected_wells_to_oligos) # rubocop:todo Metrics/MethodLength
   plate = Plate.find_by(name: name) or raise StandardError, "Cannot find plate #{name.inspect}"
+
   wells_to_oligos =
     plate
       .wells
       .filter_map do |w|
         next unless well_range.include?(w)
-
         [w.map.description, w.primary_aliquot.try(:tag).try(:oligo) || '']
       end
       .to_h

diff --git a/spec/support/download_helper.rb b/spec/support/download_helper.rb
@@ -14,7 +14,6 @@ def self.downloads
   end
 
   def self.downloaded_file(file, timeout: TIMEOUT)
-    # binding.pry
     wait_for_download(file, timeout)
     File.read(path_to(file))
   ensure