Merge pull request #1614 from sanger/develop

Release "DPL-1054 Add Vac tube barcode to the Aliquot tube labels", and dependency updates
sanger · Mar 6, 2024 · ab39dc1 · ab39dc1
2 parents a766371 + 8dc5d74
commit ab39dc1
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diff --git a/.release-version b/.release-version
@@ -1 +1 @@
-3.47.1
+3.48.0
diff --git a/Gemfile.lock b/Gemfile.lock
@@ -28,71 +28,71 @@ GIT
 GEM
   remote: https://rubygems.org/
   specs:
-    actioncable (7.1.3)
-      actionpack (= 7.1.3)
-      activesupport (= 7.1.3)
+    actioncable (7.1.3.2)
+      actionpack (= 7.1.3.2)
+      activesupport (= 7.1.3.2)
       nio4r (~> 2.0)
       websocket-driver (>= 0.6.1)
       zeitwerk (~> 2.6)
-    actionmailbox (7.1.3)
-      actionpack (= 7.1.3)
-      activejob (= 7.1.3)
-      activerecord (= 7.1.3)
-      activestorage (= 7.1.3)
-      activesupport (= 7.1.3)
+    actionmailbox (7.1.3.2)
+      actionpack (= 7.1.3.2)
+      activejob (= 7.1.3.2)
+      activerecord (= 7.1.3.2)
+      activestorage (= 7.1.3.2)
+      activesupport (= 7.1.3.2)
       mail (>= 2.7.1)
       net-imap
       net-pop
       net-smtp
-    actionmailer (7.1.3)
-      actionpack (= 7.1.3)
-      actionview (= 7.1.3)
-      activejob (= 7.1.3)
-      activesupport (= 7.1.3)
+    actionmailer (7.1.3.2)
+      actionpack (= 7.1.3.2)
+      actionview (= 7.1.3.2)
+      activejob (= 7.1.3.2)
+      activesupport (= 7.1.3.2)
       mail (~> 2.5, >= 2.5.4)
       net-imap
       net-pop
       net-smtp
       rails-dom-testing (~> 2.2)
-    actionpack (7.1.3)
-      actionview (= 7.1.3)
-      activesupport (= 7.1.3)
+    actionpack (7.1.3.2)
+      actionview (= 7.1.3.2)
+      activesupport (= 7.1.3.2)
       nokogiri (>= 1.8.5)
       racc
       rack (>= 2.2.4)
       rack-session (>= 1.0.1)
       rack-test (>= 0.6.3)
       rails-dom-testing (~> 2.2)
       rails-html-sanitizer (~> 1.6)
-    actiontext (7.1.3)
-      actionpack (= 7.1.3)
-      activerecord (= 7.1.3)
-      activestorage (= 7.1.3)
-      activesupport (= 7.1.3)
+    actiontext (7.1.3.2)
+      actionpack (= 7.1.3.2)
+      activerecord (= 7.1.3.2)
+      activestorage (= 7.1.3.2)
+      activesupport (= 7.1.3.2)
       globalid (>= 0.6.0)
       nokogiri (>= 1.8.5)
-    actionview (7.1.3)
-      activesupport (= 7.1.3)
+    actionview (7.1.3.2)
+      activesupport (= 7.1.3.2)
       builder (~> 3.1)
       erubi (~> 1.11)
       rails-dom-testing (~> 2.2)
       rails-html-sanitizer (~> 1.6)
-    activejob (7.1.3)
-      activesupport (= 7.1.3)
+    activejob (7.1.3.2)
+      activesupport (= 7.1.3.2)
       globalid (>= 0.3.6)
-    activemodel (7.1.3)
-      activesupport (= 7.1.3)
-    activerecord (7.1.3)
-      activemodel (= 7.1.3)
-      activesupport (= 7.1.3)
+    activemodel (7.1.3.2)
+      activesupport (= 7.1.3.2)
+    activerecord (7.1.3.2)
+      activemodel (= 7.1.3.2)
+      activesupport (= 7.1.3.2)
       timeout (>= 0.4.0)
-    activestorage (7.1.3)
-      actionpack (= 7.1.3)
-      activejob (= 7.1.3)
-      activerecord (= 7.1.3)
-      activesupport (= 7.1.3)
+    activestorage (7.1.3.2)
+      actionpack (= 7.1.3.2)
+      activejob (= 7.1.3.2)
+      activerecord (= 7.1.3.2)
+      activesupport (= 7.1.3.2)
       marcel (~> 1.0)
-    activesupport (7.1.3)
+    activesupport (7.1.3.2)
       base64
       bigdecimal
       concurrent-ruby (~> 1.0, >= 1.0.2)
@@ -130,6 +130,7 @@ GEM
     capybara-selenium (0.0.6)
       capybara
       selenium-webdriver
+    childprocess (5.0.0)
     coderay (1.1.3)
     concurrent-ruby (1.2.3)
     connection_pool (2.4.1)
@@ -140,8 +141,7 @@ GEM
     date (3.3.4)
     diff-lcs (1.5.1)
     docile (1.4.0)
-    drb (2.2.0)
-      ruby2_keywords
+    drb (2.2.1)
     erubi (1.12.0)
     exception_notification (4.5.0)
       actionmailer (>= 5.2, < 8)
@@ -211,9 +211,10 @@ GEM
       railties (>= 3.2.16)
     json (2.7.1)
     language_server-protocol (3.17.0.3)
-    launchy (2.5.2)
+    launchy (3.0.0)
       addressable (~> 2.8)
-    listen (3.8.0)
+      childprocess (~> 5.0)
+    listen (3.9.0)
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
     loofah (2.22.0)
@@ -225,7 +226,7 @@ GEM
       net-imap
       net-pop
       net-smtp
-    marcel (1.0.2)
+    marcel (1.0.4)
     matrix (0.4.2)
     method_source (1.0.0)
     mini_mime (1.1.5)
@@ -271,8 +272,8 @@ GEM
     puma (6.4.2)
       nio4r (~> 2.0)
     racc (1.7.3)
-    rack (3.0.9)
-    rack-mini-profiler (3.3.0)
+    rack (3.0.9.1)
+    rack-mini-profiler (3.3.1)
       rack (>= 1.2.0)
     rack-proxy (0.7.7)
       rack
@@ -283,20 +284,20 @@ GEM
     rackup (2.1.0)
       rack (>= 3)
       webrick (~> 1.8)
-    rails (7.1.3)
-      actioncable (= 7.1.3)
-      actionmailbox (= 7.1.3)
-      actionmailer (= 7.1.3)
-      actionpack (= 7.1.3)
-      actiontext (= 7.1.3)
-      actionview (= 7.1.3)
-      activejob (= 7.1.3)
-      activemodel (= 7.1.3)
-      activerecord (= 7.1.3)
-      activestorage (= 7.1.3)
-      activesupport (= 7.1.3)
+    rails (7.1.3.2)
+      actioncable (= 7.1.3.2)
+      actionmailbox (= 7.1.3.2)
+      actionmailer (= 7.1.3.2)
+      actionpack (= 7.1.3.2)
+      actiontext (= 7.1.3.2)
+      actionview (= 7.1.3.2)
+      activejob (= 7.1.3.2)
+      activemodel (= 7.1.3.2)
+      activerecord (= 7.1.3.2)
+      activestorage (= 7.1.3.2)
+      activesupport (= 7.1.3.2)
       bundler (>= 1.15.0)
-      railties (= 7.1.3)
+      railties (= 7.1.3.2)
     rails-controller-testing (1.0.5)
       actionpack (>= 5.0.1.rc1)
       actionview (>= 5.0.1.rc1)
@@ -308,9 +309,9 @@ GEM
     rails-html-sanitizer (1.6.0)
       loofah (~> 2.21)
       nokogiri (~> 1.14)
-    railties (7.1.3)
-      actionpack (= 7.1.3)
-      activesupport (= 7.1.3)
+    railties (7.1.3.2)
+      actionpack (= 7.1.3.2)
+      activesupport (= 7.1.3.2)
       irb
       rackup (>= 1.0.0)
       rake (>= 12.2)
@@ -324,7 +325,7 @@ GEM
     rdoc (6.6.2)
       psych (>= 4.0.0)
     regexp_parser (2.9.0)
-    reline (0.4.2)
+    reline (0.4.3)
       io-console (~> 0.5)
     rexml (3.2.6)
     rspec (3.13.0)
@@ -348,8 +349,8 @@ GEM
       rspec-expectations (~> 3.12)
       rspec-mocks (~> 3.12)
       rspec-support (~> 3.12)
-    rspec-support (3.13.0)
-    rubocop (1.60.2)
+    rspec-support (3.13.1)
+    rubocop (1.61.0)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
@@ -360,16 +361,16 @@ GEM
       rubocop-ast (>= 1.30.0, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 2.4.0, < 3.0)
-    rubocop-ast (1.30.0)
-      parser (>= 3.2.1.0)
+    rubocop-ast (1.31.1)
+      parser (>= 3.3.0.4)
     rubocop-performance (1.20.2)
       rubocop (>= 1.48.1, < 2.0)
       rubocop-ast (>= 1.30.0, < 2.0)
-    rubocop-rails (2.23.1)
+    rubocop-rails (2.24.0)
       activesupport (>= 4.2.0)
       rack (>= 1.1)
       rubocop (>= 1.33.0, < 2.0)
-      rubocop-ast (>= 1.30.0, < 2.0)
+      rubocop-ast (>= 1.31.1, < 2.0)
     ruby-progressbar (1.13.0)
     ruby-units (4.0.2)
     ruby2_keywords (0.0.5)
@@ -385,7 +386,7 @@ GEM
       sprockets-rails
       tilt
     select2-rails (4.0.13)
-    selenium-webdriver (4.17.0)
+    selenium-webdriver (4.18.1)
       base64 (~> 0.2)
       rexml (~> 3.2, >= 3.2.5)
       rubyzip (>= 1.2.2, < 3.0)
@@ -414,7 +415,7 @@ GEM
       sprockets (>= 3.0.0)
     state_machines (0.6.0)
     stringio (3.1.0)
-    thor (1.3.0)
+    thor (1.3.1)
     tilt (2.3.0)
     timeout (0.4.1)
     tzinfo (2.0.6)
@@ -427,7 +428,7 @@ GEM
       activemodel (>= 6.0.0)
       bindex (>= 0.4.0)
       railties (>= 6.0.0)
-    webmock (3.20.0)
+    webmock (3.23.0)
       addressable (>= 2.8.0)
       crack (>= 0.3.2)
       hashdiff (>= 0.4.0, < 2.0.0)
@@ -443,7 +444,7 @@ GEM
     websocket-extensions (0.1.5)
     xpath (3.2.0)
       nokogiri (~> 1.8)
-    yard (0.9.34)
+    yard (0.9.36)
     zeitwerk (2.6.13)
 
 PLATFORMS

diff --git a/README.md b/README.md
@@ -116,6 +116,15 @@ yarn prettier --check .
 yarn prettier --write .
 ```
 
+## Troubleshooting
+
+If during development changes do not seem to be taking effect, try:
+
+- Restart the application:
+- Destroy and recreate the Docker container `docker-compose down && GENERATE_CONFIG=false docker-compose up -d`
+- Rebuild the Docker image, particularly useful for changing dependencies
+- Clobber local resources `rails assets:clobber`
+
 ## Note about the remainder of this document
 
 The rest of the sections shown here were written for and apply to the native

diff --git a/app/assets/stylesheets/limber/pipeline-graph.scss b/app/assets/stylesheets/limber/pipeline-graph.scss
@@ -35,15 +35,15 @@
     height: calculate-graph-height();
     display: block;
     @extend .bg-dark;
-    @extend .text-white;
+    @extend .text-light;
   }
 
   #key {
     position: absolute;
     top: 10px;
     right: 10px;
     @extend .bg-dark;
-    @extend .text-white;
+    @extend .text-light;
     @extend .small;
 
     header {
@@ -62,7 +62,7 @@
       }
       #show-pipeline-groups:hover {
         @extend .icon-pipeline_single-light;
-        @extend .text-light:hover;
+        @extend .text-light, :hover;
       }
 
       #show-pipelines {
@@ -71,7 +71,7 @@
       }
       #show-pipelines:hover {
         @extend .icon-pipeline_stack-light;
-        @extend .text-light:hover;
+        @extend .text-light, :hover;
       }
 
       #pipelines-back {
@@ -83,7 +83,7 @@
         vertical-align: text-bottom;
       }
       #pipelines-back:hover {
-        @extend .text-light:hover;
+        @extend .text-light, :hover;
       }
     }
     ul {
@@ -97,7 +97,7 @@
         @extend .bg-dark;
       }
       li:hover {
-        @extend .text-light:hover;
+        @extend .text-light, :hover;
       }
     }
   }

diff --git a/app/sequencescape/sequencescape/api/v2/plate.rb b/app/sequencescape/sequencescape/api/v2/plate.rb
@@ -8,6 +8,7 @@ class Sequencescape::Api::V2::Plate < Sequencescape::Api::V2::Base
   include Sequencescape::Api::V2::Shared::HasRequests
   include Sequencescape::Api::V2::Shared::HasPurpose
   include Sequencescape::Api::V2::Shared::HasBarcode
+  include Sequencescape::Api::V2::Shared::HasWorklineIdentifier
 
   self.plate = true
   has_many :wells
@@ -97,22 +98,6 @@ def stock_plate
     stock_plates.order(id: :asc).last
   end
 
-  def workline_identifier
-    workline_reference&.barcode&.human
-  end
-
-  # This is the plate that will act as a reference in my workflow that will be
-  # printed in the label at the top_right field. It is the first stock by default,
-  # but in some cases we may want to display a different plate. To change the default
-  # selection from stock plate to other plate purpose, we have to modify the purposes.yml
-  # config file and add a workline_reference_identifier attribute with the purpose we want to select.
-  def workline_reference
-    alternative_workline_identifier_purpose = SearchHelper.alternative_workline_reference_name(self)
-    return stock_plate if alternative_workline_identifier_purpose.nil?
-
-    ancestors.where(purpose_name: alternative_workline_identifier_purpose).last
-  end
-
   def stock_plate?(purpose_names: SearchHelper.stock_plate_names)
     purpose_names.include?(purpose_name)
   end