Merge branch 'y24-035-tnanoseq-update-configs-for-pipeline' into uat-…

…sequencescape-26th-jun-2024

app/uat_actions/uat_actions/plate_information.rb

@@ -20,6 +20,8 @@ def perform
     return false if plate.blank?
 
     report[:wells_with_aliquots] = wells_with_aliquots
+
+    report[:wells_with_active_requests_as_source] = wells_with_active_requests_as_source
     true
   end
 
@@ -37,4 +39,21 @@ def wells_with_aliquots
       end
       .join(', ')
   end
+
+  # For finding wells in a partial submission plate that are to go forward.
+  # i.e. wells will have active requests as source only if they are to progress.
+  def wells_with_active_requests_as_source
+    active_request_states = %w[pending started]
+
+    plate
+    .wells_in_column_order
+    .each_with_object([]) do |well, wells_with_active_requests_as_source|
+      # requests must have an active state
+      if well.requests_as_source.present? && well.requests_as_source.any? do |request|
+ active_request_states.include?(request.state) end
+        wells_with_active_requests_as_source << well.map_description
+      end
+    end
+    .join(', ')
+  end
 end

config/default_records/plate_purposes/005_limber_purposes.yml

@@ -59,3 +59,14 @@ RVI Cherrypick:
   cherrypickable_target: true
   type: PlatePurpose
   stock_plate: false
+
+# Targeted NanoSeq loop back point
+LTN AL Lib:
+  cherrypickable_target: false
+  type: PlatePurpose
+  stock_plate: false
+
+# Targeted NanoSeq plate for reISC
+LTN Lib PCR XP:
+  type: PlatePurpose
+  stock_plate: false

config/default_records/request_types/004_limber_high_throughput.yml

@@ -36,6 +36,7 @@ limber_reisc:
   request_class_name: Pulldown::Requests::ReIscLibraryRequest
   acceptable_purposes:
     - LB Lib PCR-XP
+    - LTN Lib PCR XP # for Targeted NanoSeq ReISC
   library_types:
     - Agilent Pulldown
     - Twist Pulldown

config/default_records/request_types/015_targeted_nanoseq_request_types.yml

@@ -0,0 +1,12 @@
+# Request types for Targeted NanoSeq ISC Prep
+---
+limber_targeted_nanoseq_isc_prep:
+  name: Limber Targeted NanoSeq ISC Prep
+  asset_type: Well
+  order: 1
+  request_class_name: CustomerRequest
+  for_multiplexing: false
+  billable: true
+  product_line_name: Short Read
+  acceptable_purposes:
+    - LTN AL Lib

config/default_records/submission_templates/002_targeted_nanoseq_submission_templates.yml

@@ -1,8 +1,14 @@
-# This submission template is associated with the Limber Targeted NanoSeq pipeline.
+# Submission templates associated with the Limber Targeted NanoSeq pipeline.
 ---
 Limber-Htp - Targeted NanoSeq:
   submission_class_name: "LinearSubmission"
   related_records:
     request_type_keys: ["limber_targeted_nanoseq"]
     product_line_name: Targeted-NanoSeq
     product_catalogue_name: Targeted-NanoSeq
+Limber-Htp - Targeted NanoSeq ISC Prep:
+  submission_class_name: "LinearSubmission"
+  related_records:
+    request_type_keys: ["limber_targeted_nanoseq_isc_prep"]
+    product_line_name: Targeted-NanoSeq
+    product_catalogue_name: Targeted-NanoSeq

spec/uat_actions/plate_information_spec.rb

@@ -4,15 +4,16 @@
 
 describe UatActions::PlateInformation do
   context 'when the plate has aliquots' do
-    let(:parameters) { { plate_barcode: 'SQPD-1' } }
+    let(:plate_barcode) { 'SQPD-1' }
+    let(:parameters) { { plate_barcode: plate_barcode } }
     let(:uat_action) { described_class.new(parameters) }
     let(:report) do
       # A report is a hash of key value pairs which get returned to the user.
       # It should include information such as barcodes and identifiers
-      { plate_barcode: 'SQPD-1', wells_with_aliquots: 'A1, B1, C1' }
+      { plate_barcode: plate_barcode, wells_with_aliquots: 'A1, B1, C1', wells_with_active_requests_as_source: '' }
     end
 
-    before { create :plate_with_untagged_wells, sample_count: 3, barcode: 'SQPD-1' }
+    before { create :plate_with_untagged_wells, sample_count: 3, barcode: plate_barcode }
 
     it 'can be performed' do
       expect(uat_action.perform).to be true
@@ -21,15 +22,16 @@
   end
 
   context 'when the plate is without aliquots' do
-    let(:parameters) { { plate_barcode: 'SQPD-2' } }
+    let(:plate_barcode) { 'SQPD-2' }
+    let(:parameters) { { plate_barcode: plate_barcode } }
     let(:uat_action) { described_class.new(parameters) }
     let(:report) do
       # A report is a hash of key value pairs which get returned to the user.
       # It should include information such as barcodes and identifiers
-      { plate_barcode: 'SQPD-2', wells_with_aliquots: '' }
+      { plate_barcode: plate_barcode, wells_with_aliquots: '', wells_with_active_requests_as_source: '' }
     end
 
-    before { create :plate_with_empty_wells, well_count: 3, barcode: 'SQPD-2' }
+    before { create :plate_with_empty_wells, well_count: 3, barcode: plate_barcode }
 
     it 'can be performed' do
       expect(uat_action.perform).to be true
@@ -52,6 +54,117 @@
     end
   end
 
+  # This test is for the scenario where the plate has a partial submission on it.
+  # We expect to return the wells that have been submitted (have active requests as source)
+  context 'when the plate has a partial submission' do
+    let(:plate_barcode) { 'SQPD-3' }
+    let(:parameters) { { plate_barcode: plate_barcode } }
+    let(:uat_action) { described_class.new(parameters) }
+    let(:submission) { create :submission }
+    let(:request_type) { create :library_creation_request_type }
+    let(:report) do
+      { plate_barcode: plate_barcode, wells_with_aliquots: 'A1, B1, C1',
+wells_with_active_requests_as_source: 'A1, C1' }
+    end
+
+    before do
+      plate = create :plate_with_untagged_wells, sample_count: 3, barcode: plate_barcode
+
+      plate_wells = plate.wells.with_contents
+
+      req1 = create :library_creation_request, asset: plate_wells.first, submission: submission,
+request_type: request_type, state: 'started'
+      plate_wells.first.requests_as_source << req1
+
+      req2 = create :library_creation_request, asset: plate_wells.last, submission: submission,
+request_type: request_type, state: 'started'
+      plate_wells.last.requests_as_source << req2
+    end
+
+    it 'can be performed' do
+      expect(uat_action.perform).to be true
+      expect(uat_action.report).to eq report
+    end
+  end
+
+  # This test is for a scenario where there there is a previous (now closed) submission on the wells ONLY
+  # i.e. only want wells with ACTIVE requests as source so this should not return any wells
+  context 'when the plate has a closed submission' do
+    let(:plate_barcode) { 'SQPD-4' }
+    let(:parameters) { { plate_barcode: plate_barcode } }
+    let(:uat_action) { described_class.new(parameters) }
+    let(:submission) { create :submission }
+    let(:request_type) { create :library_creation_request_type }
+    let(:report) do
+      { plate_barcode: plate_barcode, wells_with_aliquots: 'A1, B1, C1', wells_with_active_requests_as_source: '' }
+    end
+
+    before do
+      plate = create :plate_with_untagged_wells, sample_count: 3, barcode: plate_barcode
+
+      plate_wells = plate.wells.with_contents
+
+      req1 = create :library_creation_request, asset: plate_wells.first, submission: submission,
+request_type: request_type, state: 'passed'
+      plate_wells.first.requests_as_source << req1
+
+      req2 = create :library_creation_request, asset: plate_wells.last, submission: submission,
+request_type: request_type, state: 'passed'
+      plate_wells.last.requests_as_source << req2
+    end
+
+    it 'can be performed' do
+      expect(uat_action.perform).to be true
+      expect(uat_action.report).to eq report
+    end
+  end
+
+  # This test is for the scenario where we have both an old submission and a new submission on the plate (different
+  # subsets of wells) - we expect to only return the wells with the new (active) submission
+  context 'when the plate has both active and closed submissions' do
+    let(:plate_barcode) { 'SQPD-4' }
+    let(:parameters) { { plate_barcode: plate_barcode } }
+    let(:uat_action) { described_class.new(parameters) }
+    let(:submission) { create :submission }
+    let(:submission2) { create :submission }
+    let(:request_type) { create :library_creation_request_type }
+    let(:report) do
+      { plate_barcode: plate_barcode, wells_with_aliquots: 'A1, B1, C1',
+wells_with_active_requests_as_source: 'A1, C1' }
+    end
+
+    before do
+      plate = create :plate_with_untagged_wells, sample_count: 3, barcode: plate_barcode
+
+      plate_wells = plate.wells.with_contents
+
+      req1 = create :library_creation_request, asset: plate_wells.first, submission: submission,
+request_type: request_type, state: 'passed'
+      plate_wells.first.requests_as_source << req1
+
+      req2 = create :library_creation_request, asset: plate_wells.second, submission: submission,
+request_type: request_type, state: 'passed'
+      plate_wells.second.requests_as_source << req2
+
+      req3 = create :library_creation_request, asset: plate_wells.last, submission: submission,
+request_type: request_type, state: 'passed'
+      plate_wells.last.requests_as_source << req3
+
+      req4 = create :library_creation_request, asset: plate_wells.first, submission: submission2,
+request_type: request_type, state: 'started'
+      plate_wells.first.requests_as_source << req4
+
+      req5 = create :library_creation_request, asset: plate_wells.last, submission: submission2,
+request_type: request_type, state: 'started'
+      plate_wells.last.requests_as_source << req5
+    end
+
+    it 'can be performed' do
+      expect(uat_action.perform).to be true
+      expect(uat_action.report).to eq report
+    end
+  end
+
   it 'returns a default' do
     expect(described_class.default).to be_a described_class
   end