Merge branch 'develop' into dpl-829-pbmc-plate-tube-rack-bed-verifica…

…tion

Gemfile.lock

@@ -28,67 +28,67 @@ GIT
 GEM
   remote: https://rubygems.org/
   specs:
-    actioncable (7.0.4)
-      actionpack (= 7.0.4)
-      activesupport (= 7.0.4)
+    actioncable (7.0.7.2)
+      actionpack (= 7.0.7.2)
+      activesupport (= 7.0.7.2)
       nio4r (~> 2.0)
       websocket-driver (>= 0.6.1)
-    actionmailbox (7.0.4)
-      actionpack (= 7.0.4)
-      activejob (= 7.0.4)
-      activerecord (= 7.0.4)
-      activestorage (= 7.0.4)
-      activesupport (= 7.0.4)
+    actionmailbox (7.0.7.2)
+      actionpack (= 7.0.7.2)
+      activejob (= 7.0.7.2)
+      activerecord (= 7.0.7.2)
+      activestorage (= 7.0.7.2)
+      activesupport (= 7.0.7.2)
       mail (>= 2.7.1)
       net-imap
       net-pop
       net-smtp
-    actionmailer (7.0.4)
-      actionpack (= 7.0.4)
-      actionview (= 7.0.4)
-      activejob (= 7.0.4)
-      activesupport (= 7.0.4)
+    actionmailer (7.0.7.2)
+      actionpack (= 7.0.7.2)
+      actionview (= 7.0.7.2)
+      activejob (= 7.0.7.2)
+      activesupport (= 7.0.7.2)
       mail (~> 2.5, >= 2.5.4)
       net-imap
       net-pop
       net-smtp
       rails-dom-testing (~> 2.0)
-    actionpack (7.0.4)
-      actionview (= 7.0.4)
-      activesupport (= 7.0.4)
-      rack (~> 2.0, >= 2.2.0)
+    actionpack (7.0.7.2)
+      actionview (= 7.0.7.2)
+      activesupport (= 7.0.7.2)
+      rack (~> 2.0, >= 2.2.4)
       rack-test (>= 0.6.3)
       rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.0, >= 1.2.0)
-    actiontext (7.0.4)
-      actionpack (= 7.0.4)
-      activerecord (= 7.0.4)
-      activestorage (= 7.0.4)
-      activesupport (= 7.0.4)
+    actiontext (7.0.7.2)
+      actionpack (= 7.0.7.2)
+      activerecord (= 7.0.7.2)
+      activestorage (= 7.0.7.2)
+      activesupport (= 7.0.7.2)
       globalid (>= 0.6.0)
       nokogiri (>= 1.8.5)
-    actionview (7.0.4)
-      activesupport (= 7.0.4)
+    actionview (7.0.7.2)
+      activesupport (= 7.0.7.2)
       builder (~> 3.1)
       erubi (~> 1.4)
       rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.1, >= 1.2.0)
-    activejob (7.0.4)
-      activesupport (= 7.0.4)
+    activejob (7.0.7.2)
+      activesupport (= 7.0.7.2)
       globalid (>= 0.3.6)
-    activemodel (7.0.4)
-      activesupport (= 7.0.4)
-    activerecord (7.0.4)
-      activemodel (= 7.0.4)
-      activesupport (= 7.0.4)
-    activestorage (7.0.4)
-      actionpack (= 7.0.4)
-      activejob (= 7.0.4)
-      activerecord (= 7.0.4)
-      activesupport (= 7.0.4)
+    activemodel (7.0.7.2)
+      activesupport (= 7.0.7.2)
+    activerecord (7.0.7.2)
+      activemodel (= 7.0.7.2)
+      activesupport (= 7.0.7.2)
+    activestorage (7.0.7.2)
+      actionpack (= 7.0.7.2)
+      activejob (= 7.0.7.2)
+      activerecord (= 7.0.7.2)
+      activesupport (= 7.0.7.2)
       marcel (~> 1.0)
       mini_mime (>= 1.1.0)
-    activesupport (7.0.4)
+    activesupport (7.0.7.2)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 1.6, < 2)
       minitest (>= 5.1)
@@ -125,6 +125,7 @@ GEM
     crack (0.4.5)
       rexml
     crass (1.0.6)
+    date (3.3.3)
     diff-lcs (1.5.0)
     docile (1.4.0)
     erubi (1.12.0)
@@ -161,8 +162,8 @@ GEM
       faraday (~> 1.0)
     ffi (1.15.5)
     formatador (1.1.0)
-    globalid (1.0.1)
-      activesupport (>= 5.0)
+    globalid (1.2.1)
+      activesupport (>= 6.1)
     guard (2.18.0)
       formatador (>= 0.2.4)
       listen (>= 2.7, < 4.0)
@@ -179,7 +180,7 @@ GEM
       rspec (>= 2.99.0, < 4.0)
     hashdiff (1.0.1)
     hashie (5.0.0)
-    i18n (1.13.0)
+    i18n (1.14.1)
       concurrent-ruby (~> 1.0)
     inline_svg (1.8.0)
       activesupport (>= 3.0)
@@ -197,33 +198,36 @@ GEM
     listen (3.8.0)
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
-    loofah (2.21.3)
+    loofah (2.21.4)
       crass (~> 1.0.2)
       nokogiri (>= 1.12.0)
     lumberjack (1.2.8)
-    mail (2.7.1)
+    mail (2.8.1)
       mini_mime (>= 0.1.1)
+      net-imap
+      net-pop
+      net-smtp
     marcel (1.0.2)
     matrix (0.4.2)
     method_source (1.0.0)
-    mini_mime (1.1.2)
-    mini_portile2 (2.8.2)
-    minitest (5.18.0)
+    mini_mime (1.1.5)
+    mini_portile2 (2.8.5)
+    minitest (5.20.0)
     msgpack (1.5.1)
     multi_json (1.15.0)
     multipart-post (2.2.3)
     nenv (0.3.0)
-    net-imap (0.3.1)
+    net-imap (0.4.2)
+      date
       net-protocol
     net-pop (0.1.2)
       net-protocol
-    net-protocol (0.1.3)
+    net-protocol (0.2.1)
       timeout
-    net-smtp (0.3.3)
+    net-smtp (0.4.0)
       net-protocol
-      timeout
     nio4r (2.5.9)
-    nokogiri (1.15.2)
+    nokogiri (1.15.4)
       mini_portile2 (~> 2.8.2)
       racc (~> 1.4)
     notiffany (0.1.3)
@@ -242,42 +246,44 @@ GEM
       byebug (~> 11.0)
       pry (>= 0.13, < 0.15)
     public_suffix (5.0.0)
-    puma (6.0.0)
+    puma (6.3.1)
       nio4r (~> 2.0)
-    racc (1.6.0)
-    rack (2.2.4)
+    racc (1.7.1)
+    rack (2.2.8)
     rack-mini-profiler (3.0.0)
       rack (>= 1.2.0)
     rack-proxy (0.7.4)
       rack
-    rack-test (2.0.2)
+    rack-test (2.1.0)
       rack (>= 1.3)
-    rails (7.0.4)
-      actioncable (= 7.0.4)
-      actionmailbox (= 7.0.4)
-      actionmailer (= 7.0.4)
-      actionpack (= 7.0.4)
-      actiontext (= 7.0.4)
-      actionview (= 7.0.4)
-      activejob (= 7.0.4)
-      activemodel (= 7.0.4)
-      activerecord (= 7.0.4)
-      activestorage (= 7.0.4)
-      activesupport (= 7.0.4)
+    rails (7.0.7.2)
+      actioncable (= 7.0.7.2)
+      actionmailbox (= 7.0.7.2)
+      actionmailer (= 7.0.7.2)
+      actionpack (= 7.0.7.2)
+      actiontext (= 7.0.7.2)
+      actionview (= 7.0.7.2)
+      activejob (= 7.0.7.2)
+      activemodel (= 7.0.7.2)
+      activerecord (= 7.0.7.2)
+      activestorage (= 7.0.7.2)
+      activesupport (= 7.0.7.2)
       bundler (>= 1.15.0)
-      railties (= 7.0.4)
+      railties (= 7.0.7.2)
     rails-controller-testing (1.0.5)
       actionpack (>= 5.0.1.rc1)
       actionview (>= 5.0.1.rc1)
       activesupport (>= 5.0.1.rc1)
-    rails-dom-testing (2.0.3)
-      activesupport (>= 4.2.0)
+    rails-dom-testing (2.2.0)
+      activesupport (>= 5.0.0)
+      minitest
       nokogiri (>= 1.6)
-    rails-html-sanitizer (1.4.3)
-      loofah (~> 2.3)
-    railties (7.0.4)
-      actionpack (= 7.0.4)
-      activesupport (= 7.0.4)
+    rails-html-sanitizer (1.6.0)
+      loofah (~> 2.21)
+      nokogiri (~> 1.14)
+    railties (7.0.7.2)
+      actionpack (= 7.0.7.2)
+      activesupport (= 7.0.7.2)
       method_source
       rake (>= 12.2)
       thor (~> 1.0)
@@ -373,10 +379,10 @@ GEM
       activesupport (>= 5.2)
       sprockets (>= 3.0.0)
     state_machines (0.5.0)
-    thor (1.2.1)
+    thor (1.3.0)
     tilt (2.0.11)
-    timeout (0.3.0)
-    tzinfo (2.0.5)
+    timeout (0.4.0)
+    tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
     uglifier (4.2.0)
       execjs (>= 0.3.0, < 3)
@@ -397,14 +403,14 @@ GEM
       semantic_range (>= 2.3.0)
     webrick (1.7.0)
     websocket (1.2.9)
-    websocket-driver (0.7.5)
+    websocket-driver (0.7.6)
       websocket-extensions (>= 0.1.0)
     websocket-extensions (0.1.5)
     xpath (3.2.0)
       nokogiri (~> 1.8)
     yard (0.9.28)
       webrick (~> 1.7.0)
-    zeitwerk (2.6.8)
+    zeitwerk (2.6.12)
 
 PLATFORMS
   ruby

app/sequencescape/sequencescape/api/v2/well.rb

@@ -35,6 +35,10 @@ def latest_live_cell_count
     latest_qc(key: 'live_cell_count', units: 'cells/ml')
   end
 
+  def latest_cell_viability
+    latest_qc(key: 'viability', units: '%')
+  end
+
   def latest_qc(key:, units:)
     qc_results.to_a # Convert to array to resolve any api queries. Otherwise select fails to work.
       .select { |qc| qc.key.casecmp(key).zero? }

app/views/exports/pbmc_bank_tubes_content_report.csv.erb

@@ -0,0 +1,81 @@
+<%# This is a report of the contents of the tubes in the PBMC Bank plate %>
+<%# Based on app/views/exports/hamilton_lrc_pbmc_bank_to_lrc_bank_seq_and_spare.csv.erb %>
+<%= CSV.generate_line ['Workflow', @workflow], row_sep: '' %>
+
+<%=
+  CSV.generate_line [
+                      'Well name',
+                      'Donor ID',
+                      'Stock barcode',
+                      'FluidX barcode',
+                      'Extraction and freeze date',
+                      'Sequencing or contingency',
+                      'Cell count (cells/ml)',
+                      'Viability (%)',
+                      'Volume (µl)',
+                      'Study name',
+                      'Collection site'
+                    ],
+                    row_sep: ''
+%>
+<%
+  rows_array = []
+  @plate.wells_in_columns.each do |source_well|
+    # skip if well empty (not all wells have samples in them)
+    next if source_well.empty?
+
+    # skip if well not in passed state
+    next unless source_well.passed?
+
+    # skip if no downstream tubes for this well (not set up children in Limber yet)
+    next if source_well.downstream_tubes.empty?
+
+    child_tube_v1 = source_well.downstream_tubes.last
+    child_tube_v2 =
+      Sequencescape::Api::V2.tube_with_custom_includes(
+        'custom_metadatum_collection',
+        nil,
+        barcode: child_tube_v1.labware_barcode.machine
+      )
+
+    next unless child_tube_v2 && child_tube_v2.custom_metadatum_collection
+
+    # get tube metadata from child_tube
+    metadata = child_tube_v2.custom_metadatum_collection.metadata
+
+    next unless metadata
+
+    tube_rack_barcode = metadata['tube_rack_barcode']
+    tube_rack_position = metadata['tube_rack_position']
+
+    next unless tube_rack_barcode && tube_rack_position
+
+    sample_uuid = source_well.aliquots.first.sample.uuid
+    source_well_posn = source_well.position['name']
+
+    sample_metadata = source_well.aliquots.first.sample.sample_metadata
+
+    # donor_id is sourced from the sample metadata provided by Sequencescape
+    donor_id = sample_metadata.respond_to?(:donor_id) ? sample_metadata.donor_id : nils
+    child_tube_purpose = child_tube_v2.purpose.name
+    destination = ((child_tube_purpose == 'LRC Blood Seq') ? 'Sequencing' : 'Contingency')
+    volume = 135
+
+    rows_array << [
+      source_well.name, # Well name
+      donor_id, # Donor ID
+      @ancestor_tubes[sample_uuid].labware_barcode.human, # LRC Blood Vac purpose barcode
+      child_tube_v2.barcode, # FluidX barcode
+      child_tube_v2.created_at, # Extraction and freeze date
+      destination, # Sequencing or contingency
+      source_well.latest_live_cell_count.value, # Cell count
+      source_well.latest_cell_viability.value, # Viability
+      volume, # Volume
+      source_well.aliquots.first.study.name, # Study name
+      source_well.aliquots.first.sample.sample_metadata&.collected_by # Collection site
+    ]
+  end
+%>
+<% rows_array.sort_by{ |a| WellHelpers.well_coordinate(a[0]) }.each do |row| %>
+<%= CSV.generate_line row, row_sep: '' %>
+<% end %>

config/exports/exports.yml

@@ -164,3 +164,12 @@ hamilton_lrc_blood_bank_to_lrc_pbmc_bank:
     - wells.transfer_requests_as_target.source_asset
   ancestor_tube_purpose: LRC Blood Vac
   ancestor_purpose: LRC Blood Bank
+pbmc_bank_tubes_content_report:
+  csv: pbmc_bank_tubes_content_report
+  workflow: scRNA Core PBMC Bank
+  plate_includes:
+    - wells.downstream_tubes
+    - wells.aliquots
+    - wells.aliquots.sample
+    - wells.aliquots.sample.sample_metadata
+  ancestor_tube_purpose: LRC Blood Vac

config/purposes/scrna_core_cell_extraction.wip.yml

@@ -81,6 +81,8 @@ LRC PBMC Bank:
       id: hamilton_lrc_blood_bank_to_lrc_pbmc_bank
     - name: 'Download Hamilton LRC PBMC Bank plate to LRC Bank Seq and Spare tubes CSV'
       id: hamilton_lrc_pbmc_bank_to_lrc_bank_seq_and_spare
+    - name: 'Download PBMC Bank Tubes Content Report'
+      id: pbmc_bank_tubes_content_report
   :qc_thresholds:
     viability:
       units: '%'