Merge pull request #567 from JamesGlover/issue560/gpl-712-as-a-user-w…

…hen-the-destination-plate-is-ready-i-would-like-to-scan-the-barcode-into-the-limber-pipeline-and-decide-whether-it-will-be-processed-as-a-384-or-96-well-plate

issue560/gpl 712 as a user when the destination plate is ready i would like to scan the barcode into the limber pipeline and decide whether it will be processed as a 384 or 96 well plate

.rubocop.yml

@@ -49,98 +49,36 @@ Metrics/BlockLength:
 Layout/LineLength:
   Max: 161
 
-
+Naming/VariableNumber:
+  CheckSymbols: false # Rubocop gets annoyed about our states. I'm disabling globally
+                      # as I'm honestly not that bothered.
 # Pending Cops
 # For more information: https://docs.rubocop.org/en/latest/versioning/
-Layout/EmptyLinesAroundAttributeAccessor:
-  Enabled: true
-Layout/SpaceAroundMethodCallOperator:
-  Enabled: true
-Lint/DeprecatedOpenSSLConstant:
-  Enabled: true
-Lint/RaiseException:
-  Enabled: true
-Lint/StructNewOverride:
-  Enabled: true
-Style/ExponentialNotation:
-  Enabled: true
-Style/HashEachMethods:
-  Enabled: true
-Style/HashTransformKeys:
-  Enabled: true
-Style/HashTransformValues:
-  Enabled: true
-Style/SlicingWithRange:
-  Enabled: true
-Lint/BinaryOperatorWithIdenticalOperands: # (new in 0.89)
-  Enabled: true
-Lint/DuplicateElsifCondition: # (new in 0.88)
-  Enabled: true
-Lint/DuplicateRequire: # (new in 0.90)
-  Enabled: true
-Lint/DuplicateRescueException: # (new in 0.89)
-  Enabled: true
-Lint/EmptyConditionalBody: # (new in 0.89)
-  Enabled: true
-Lint/EmptyFile: # (new in 0.90)
-  Enabled: true
-Lint/FloatComparison: # (new in 0.89)
-  Enabled: true
-Lint/MissingSuper: # (new in 0.89)
-  Enabled: true
-Lint/MixedRegexpCaptureTypes: # (new in 0.85)
+Lint/DuplicateBranch: # (new in 1.3)
   Enabled: true
-Lint/OutOfRangeRegexpRef: # (new in 0.89)
+Lint/DuplicateRegexpCharacterClassElement: # (new in 1.1)
   Enabled: true
-Lint/SelfAssignment: # (new in 0.89)
+Lint/EmptyBlock: # (new in 1.1)
   Enabled: true
-Lint/TopLevelReturnWithArgument: # (new in 0.89)
+Lint/EmptyClass: # (new in 1.3)
   Enabled: true
-Lint/TrailingCommaInAttributeDeclaration: # (new in 0.90)
+Lint/NoReturnInBeginEndBlocks: # (new in 1.2)
   Enabled: true
-Lint/UnreachableLoop: # (new in 0.89)
+Lint/ToEnumArguments: # (new in 1.1)
   Enabled: true
-Lint/UselessMethodDefinition: # (new in 0.90)
+Lint/UnmodifiedReduceAccumulator: # (new in 1.1)
   Enabled: true
-Style/AccessorGrouping: # (new in 0.87)
+Style/ArgumentsForwarding: # (new in 1.1)
   Enabled: true
-Style/ArrayCoercion: # (new in 0.88)
+Style/CollectionCompact: # (new in 1.2)
   Enabled: true
-Style/BisectedAttrAccessor: # (new in 0.87)
+Style/DocumentDynamicEvalDefinition: # (new in 1.1)
   Enabled: true
-Style/CaseLikeIf: # (new in 0.88)
+Style/NegatedIfElseCondition: # (new in 1.2)
   Enabled: true
-Style/CombinableLoops: # (new in 0.90)
+Style/NilLambda: # (new in 1.3)
   Enabled: true
-Style/ExplicitBlockArgument: # (new in 0.89)
-  Enabled: true
-Style/GlobalStdStream: # (new in 0.89)
-  Enabled: true
-Style/HashAsLastArrayItem: # (new in 0.88)
-  Enabled: true
-Style/HashLikeCase: # (new in 0.88)
-  Enabled: true
-Style/KeywordParametersOrder: # (new in 0.90)
-  Enabled: true
-Style/OptionalBooleanParameter: # (new in 0.89)
-  Enabled: true
-Style/RedundantAssignment: # (new in 0.87)
-  Enabled: true
-Style/RedundantFetchBlock: # (new in 0.86)
-  Enabled: true
-Style/RedundantFileExtensionInRequire: # (new in 0.88)
-  Enabled: true
-Style/RedundantRegexpCharacterClass: # (new in 0.85)
-  Enabled: true
-Style/RedundantRegexpEscape: # (new in 0.85)
-  Enabled: true
-Style/RedundantSelfAssignment: # (new in 0.90)
-  Enabled: true
-Style/SingleArgumentDig: # (new in 0.89)
-  Enabled: true
-Style/SoleNestedConditional: # (new in 0.89)
-  Enabled: true
-Style/StringConcatenation: # (new in 0.89)
+Style/SwapValues: # (new in 1.1)
   Enabled: true
 Rails/ActiveRecordCallbacksOrder: # (new in 2.7)
   Enabled: true
@@ -190,12 +128,3 @@ Performance/StringInclude: # (new in 1.7)
   Enabled: true
 Performance/Sum: # (new in 1.8)
   Enabled: true
-Layout/BeginEndAlignment: # (new in 0.91)
-  Enabled: true
-Lint/ConstantDefinitionInBlock: # (new in 0.91)
-  Enabled: true
-Lint/IdentityComparison: # (new in 0.91)
-  Enabled: true
-Lint/UselessTimes: # (new in 0.91)
-  Enabled: true
-

Gemfile

@@ -19,7 +19,9 @@ gem 'hashie'
 gem 'json_api_client', github: 'sanger/json_api_client', branch: 'merge_upstream'
 
 # Older Sequencescape API
-gem 'sequencescape-client-api', require: 'sequencescape'
+gem 'sequencescape-client-api', '~> 0.5.0.pre.rc1', require: 'sequencescape'
+# Speed up json encoding/decoding with oj
+gem 'oj'
 
 gem 'pmb-client', '0.1.0', github: 'sanger/pmb-client'
 gem 'sprint_client'

Gemfile.lock

@@ -194,8 +194,9 @@ GEM
     notiffany (0.1.3)
       nenv (~> 0.1)
       shellany (~> 0.0)
-    parallel (1.19.2)
-    parser (2.7.1.5)
+    oj (3.10.16)
+    parallel (1.20.0)
+    parser (2.7.2.0)
       ast (~> 2.4.1)
     popper_js (1.16.0)
     pry (0.13.1)
@@ -250,7 +251,7 @@ GEM
     rb-fsevent (0.10.4)
     rb-inotify (0.10.1)
       ffi (~> 1.0)
-    regexp_parser (1.8.1)
+    regexp_parser (1.8.2)
     rexml (3.2.4)
     rspec (3.9.0)
       rspec-core (~> 3.9.0)
@@ -274,16 +275,16 @@ GEM
       rspec-mocks (~> 3.9)
       rspec-support (~> 3.9)
     rspec-support (3.9.3)
-    rubocop (0.92.0)
+    rubocop (1.3.0)
       parallel (~> 1.10)
       parser (>= 2.7.1.5)
       rainbow (>= 2.2.2, < 4.0)
-      regexp_parser (>= 1.7)
+      regexp_parser (>= 1.8)
       rexml
-      rubocop-ast (>= 0.5.0)
+      rubocop-ast (>= 1.1.1)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 1.4.0, < 2.0)
-    rubocop-ast (0.7.1)
+    rubocop-ast (1.1.1)
       parser (>= 2.7.1.5)
     rubocop-performance (1.8.1)
       rubocop (>= 0.87.0)
@@ -309,11 +310,11 @@ GEM
       childprocess (>= 0.5, < 4.0)
       rubyzip (>= 1.2.2)
     semantic_range (2.3.0)
-    sequencescape-client-api (0.4.3)
+    sequencescape-client-api (0.5.0.pre.rc1)
       activemodel (>= 5.0.0)
       activesupport (>= 5.0.0)
       i18n
-      yajl-ruby (>= 1.4.1)
+      multi_json
     shellany (0.0.1)
     simplecov (0.19.1)
       docile (~> 1.1)
@@ -374,7 +375,6 @@ GEM
     websocket-extensions (0.1.5)
     xpath (3.2.0)
       nokogiri (~> 1.8)
-    yajl-ruby (1.4.1)
     yard (0.9.25)
 
 PLATFORMS
@@ -395,6 +395,7 @@ DEPENDENCIES
   jquery-ui-rails
   json_api_client!
   launchy
+  oj
   pmb-client (= 0.1.0)!
   pry
   pry-byebug
@@ -411,7 +412,7 @@ DEPENDENCIES
   sanger_barcode_format!
   sass-rails
   select2-rails
-  sequencescape-client-api
+  sequencescape-client-api (~> 0.5.0.pre.rc1)
   simplecov
   simplecov-json
   sprint_client

Guardfile

@@ -17,7 +17,7 @@
 #
 # and, you'll have to watch "config/Guardfile" instead of "Guardfile"
 
-# Note: The cmd option is now required due to the increasing number of ways
+# NOTE: The cmd option is now required due to the increasing number of ways
 #       rspec may be run, below are examples of the most common uses.
 #  * bundler: 'bundle exec rspec'
 #  * bundler binstubs: 'bin/rspec'

app/assets/stylesheets/limber/screen.scss

@@ -60,6 +60,17 @@ header.limber-header {
   }
 }
 
+.submission-list {
+  @extend .list-group;
+  @extend .list-group-flush;
+
+  li {
+    @extend .list-group-item;
+    @extend .justify-content-between;
+    @extend .d-flex;
+  }
+}
+
 button#btnGroupInboxes, button#btnGroupRobots {
   @extend .btn;
   @extend .btn-primary;
@@ -127,7 +138,7 @@ nav.inbox-list, nav.robots-list {
   }
 }
 
-.work-completion-button, .robots-button, .create-plate-button, .create-tube-button, .csv-link {
+.work-completion-button, .robots-button, .create-plate-button, .create-tube-button, .csv-link, .create-submission-button {
   @extend .btn;
   @extend .btn-lg;
   @extend .btn-block;
@@ -138,7 +149,7 @@ nav.inbox-list, nav.robots-list {
   .work-completion-button, .create-plate-button, .create-tube-button { @extend .btn-secondary;}
 }
 .suggested-actions {
-  .work-completion-button, .create-plate-button, .create-tube-button { @extend .btn-success;}
+  .work-completion-button, .create-plate-button, .create-tube-button, .create-submission-button { @extend .btn-success;}
 }
 .robots-button {
   @extend .btn-primary;

app/controllers/concerns/sequencescape_submission_behaviour.rb

@@ -0,0 +1,25 @@
+# frozen_string_literal: true
+
+# Module SequencescapeSubmissionBehaviour provides the ability to
+# generate submissions to controllers
+#
+# @author Genome Research Ltd.
+#
+module SequencescapeSubmissionBehaviour
+  # Builds a submission using the supplied params[:sequencescape_submission]
+  def create_submission
+    ss = SequencescapeSubmission.new(sequencescape_submission_parameters)
+    if ss.save
+      flash[:notice] ||= []
+      flash[:notice] << 'Your submissions have been made and should be built shortly.'
+    else
+      flash[:alert] = truncate_flash(ss.errors.full_messages)
+    end
+  end
+
+  def sequencescape_submission_parameters
+    params
+      .require(:sequencescape_submission).permit(:template_uuid, request_options: {}, assets: [], asset_groups: {})
+      .merge(api: api, user: current_user_uuid)
+  end
+end

app/controllers/concerns/work_completion_behaviour.rb

@@ -6,32 +6,31 @@
 # @author Genome Research Ltd.
 #
 module WorkCompletionBehaviour
+  extend ActiveSupport::Concern
+
+  included do
+    include SequencescapeSubmissionBehaviour
+  end
   # Create a work completion for the given limber_plate_id
   # and redirect to the plate page.
   # Work completions mark library creation requests as completed
   # and hook them up to the correct wells.
-  # rubocop:todo Metrics/MethodLength
-  def create # rubocop:todo Metrics/AbcSize
-    messages = Hash.new { |message_store, category| message_store[category] = [] }
+  def create
     api.work_completion.create!(
       # Our pools keys are our submission uuids.
       submissions: labware.in_progress_submission_uuids,
       target: labware.uuid,
       user: current_user_uuid
     )
-    messages[:notice] << 'Requests have been passed'
 
-    if params[:sequencescape_submission]
-      ss = SequencescapeSubmission.new(sequencescape_submission_parameters)
-      if ss.save
-        messages[:notice] << 'Your submissions have been made and should be built shortly.'
-      else
-        messages[:alert] = truncate_flash(ss.errors.full_messages)
-      end
-    end
-    redirect_to labware, messages
+    # We assign the message in an array as create_submission may wish to add
+    # its own feedback.
+    flash[:notice] = ['Requests have been passed']
+
+    create_submission if params[:sequencescape_submission]
+
+    redirect_to labware
   end
-  # rubocop:enable Metrics/MethodLength
 
   def sequencescape_submission_parameters
     params

app/controllers/exports_controller.rb

@@ -12,8 +12,7 @@ class ExportsController < ApplicationController
   WELL_QC_SAMPLE_INCLUDES = 'wells.qc_results,wells.aliquots.sample.sample_metadata'
   WELL_SRC_ASSET_INCLUDES = 'wells.transfer_requests_as_target.source_asset'
 
-  CSVDetail = Struct.new(:csv, :plate_includes, :workflow, :ancestor_purpose) do
-  end
+  CSVDetail = Struct.new(:csv, :plate_includes, :workflow, :ancestor_purpose)
 
   CSV_DETAILS = {
     'concentrations_ngul' =>

app/controllers/labware_controller.rb

@@ -27,7 +27,7 @@ def show # rubocop:todo Metrics/AbcSize
         render @presenter.csv
         response.headers['Content-Disposition'] = "attachment; filename=#{@presenter.filename(params['offset'])}" if @presenter.filename
       end
-      format.json {}
+      format.json
     end
   end
 

app/controllers/sequencescape_submissions_controller.rb

@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+# Handles generation of submissions in Sequencescape
+class SequencescapeSubmissionsController < ApplicationController
+  include SequencescapeSubmissionBehaviour
+
+  before_action :check_for_current_user!
+
+  def create
+    create_submission
+    redirect_back fallback_location: :root
+  end
+end

app/helpers/page_helper.rb

@@ -62,8 +62,7 @@ def state_badge(state)
   # <span class="badge badge-primary">10</span>
   def count_badge(count, badge_id = nil)
     state = case count
-            when nil then 'secondary'
-            when 0 then 'secondary'
+            when nil, 0 then 'secondary'
             else 'primary'
             end
     tag.span(count || '...', class: "badge badge-pill badge-#{state}", id: badge_id)

app/javascript/packs/application.js

@@ -17,3 +17,4 @@ require('custom-tagged-plate')
 // Load simple javscripts
 // Tag animations rotates the displayed tag Id in wells with multiple tags
 require('plain-javascript/tag-animations')
+require('plain-javascript/page-reloader')