Y24-268 - Create a presenter for automated submission for WGS branch on Adp Lig plate

app/models/concerns/presenters/statemachine/permissive_submission.rb

@@ -0,0 +1,94 @@
+# frozen_string_literal: true
+
+require_dependency 'presenters/statemachine'
+module Presenters::Statemachine
+ #
+ # Presenters::Statemachine::PermissiveSubmission can be included in a class to
+ # provide a state machine with the following behaviour:
+ # - When plates are 'passed', a combined default and submission sidebar will
+ # be displayed. This sidebar allows the user to build a submission for the
+ # plate, while still allowing child plates to be created.
+ # - When plates are 'pending', only the default sidebar will be displayed,
+ # allowing the user to create the child plates.
+ # - In all other states the default sidebar will be used.
+ # - In all states the library passing is not permitted.
+ #
+ # Typically this state machine should be used in conjunction with an input
+ # plate purpose. {file:docs/purposes_yaml_files.md See the purposes yaml configuration.}
+ # Purposes with input_plate set to true use the PlatePurpose::Input class in sequencescape.
+ # These plates show the following states:
+ # Pending: No submission made, or some wells with samples have no submissions
+ # Passed: Submissions made, and the plate is ready to proceed
+ # Cancelled/Failed: Seen when all requests out of the plate have these states.
+ #
+ # Other states: Typically not seen in standard scenarios.
+ module PermissiveSubmission
+ extend ActiveSupport::Concern
+ included do
+ include Shared
+
+ # The state machine for plates which has knock-on effects on the plates that can be created
+ state_machine :state, initial: :pending do
+ StateTransitions.inject(self)
+
+ # These are the states, which are really the only things we need ...
+ state :pending do
+ include StateAllowsChildCreation
+ include DoesNotAllowLibraryPassing
+ def sidebar_partial
+ 'default'
+ end
+ end
+
+ state :started do
+ include StateAllowsChildCreation
+ include DoesNotAllowLibraryPassing
+ end
+
+ state :processed_1 do
+ include StateAllowsChildCreation
+ include DoesNotAllowLibraryPassing
+ end
+
+ state :processed_2 do
+ include StateAllowsChildCreation
+ include DoesNotAllowLibraryPassing
+ end
+
+ state :processed_3 do
+ include StateAllowsChildCreation
+ include DoesNotAllowLibraryPassing
+ end
+
+ state :processed_4 do
+ include StateAllowsChildCreation
+ include DoesNotAllowLibraryPassing
+ end
+
+ state :passed do
+ include StateAllowsChildCreation
+ include DoesNotAllowLibraryPassing
+
+ def sidebar_partial
+ 'submission_default'
+ end
+ end
+
+ state :qc_complete, human_name: 'QC Complete' do
+ include StateAllowsChildCreation
+ include DoesNotAllowLibraryPassing
+ end
+
+ state :cancelled do
+ include StateDoesNotAllowChildCreation
+ include DoesNotAllowLibraryPassing
+ end
+
+ state :failed do
+ include StateDoesNotAllowChildCreation
+ include DoesNotAllowLibraryPassing
+ end
+ end
+ end
+ end
+end

app/models/concerns/presenters/submission_behaviour.rb

@@ -0,0 +1,45 @@
+# frozen_string_literal: true
+
+# Include in a presenter to add support for creating a submission
+module Presenters::SubmissionBehaviour
+ def each_submission_option
+ purpose_config.submission_options.each do |button_text, options|
+ submission_options = options.to_hash
+ submission_options[:asset_groups] = asset_groups
+ submission_options[:labware_barcode] = labware.labware_barcode.human
+ yield button_text, SequencescapeSubmission.new(submission_options)
+ end
+ end
+
+ def submissions
+ labware.direct_submissions
+ end
+
+ def pending_submissions?
+ submissions.any? { |submission| submission.building_in_progress?(ready_buffer: 20.seconds) }
+ end
+
+ # Determine whether the Choose Workflow buttons should be displayed
+ def allow_new_submission?
+ # No more than one submission of a type can be active at time for a given labware.
+ # Prevent new submissions if any are currently in progress, as the submission type
+ # is currently not available.
+ submissions_in_progress = pending_submissions? || active_submissions?
+ submissions_in_progress == false
+ end
+
+ private
+
+ def asset_groups
+ @asset_groups ||=
+ labware
+ .wells
+ .compact_blank
+ .group_by(&:order_group)
+ .map { |_, wells| { assets: wells.map(&:uuid), autodetect_studies: true, autodetect_projects: true } }
+ end
+
+ def active_submissions?
+ submissions.any?(&:ready?)
+ end
+end

app/models/presenters/permissive_submission_plate_presenter.rb

@@ -0,0 +1,43 @@
+# frozen_string_literal: true
+
+module Presenters
+ #
+ # The PermissiveSubmissionPlatePresenter is used when a pipeline needs to
+ # branch, but also needs to allow plates to be created in advance. Currently
+ # this is only used for the EMSeq pipeline's split to the WGS branch (and it
+ # is hoped that other use cases will be avoided in future). It presents the
+ # user with a selection of workflows, and allows them to generate
+ # corresponding Sequencescape submissions. Once these submissions are passed,
+ # the plate behaves like a standard stock plate. Otherwise it includes aspects
+ # of the PermissivePresenter and allows plates to be created even when the
+ # plate is pending.
+ #
+ # Submission options are defined by the submission_options config in the
+ # purposes/*.yml file. Structure is:
+ # <button text>:
+ # template_name: <submission template name>
+ # request_options:
+ # <request_option_key>: <request_option_value>
+ # ...
+ class PermissiveSubmissionPlatePresenter < PlatePresenter
+ include Presenters::Statemachine::PermissiveSubmission
+ include Presenters::SubmissionBehaviour
+
+ validates_with Validators::SuboptimalValidator
+ validates_with Validators::ActiveRequestValidator
+
+ self.allow_well_failure_in_states = []
+
+ # Stock style class causes well state to inherit from plate state.
+ self.style_class = 'stock'
+
+ self.summary_items = {
+ 'Barcode' => :barcode,
+ 'Number of wells' => :number_of_wells,
+ 'Plate type' => :purpose_name,
+ 'Current plate state' => :state,
+ 'Input plate barcode' => :input_barcode,
+ 'Created on' => :created_on
+ }
+ end
+end

app/models/presenters/submission_plate_presenter.rb

@@ -17,8 +17,12 @@ module Presenters
  class SubmissionPlatePresenter < PlatePresenter
  include Presenters::Statemachine::Submission
  include Presenters::Statemachine::DoesNotAllowLibraryPassing
+ include Presenters::SubmissionBehaviour
  include Presenters::StateChangeless
 
+ self.allow_well_failure_in_states = []
+
+ # Stock style class causes well state to inherit from plate state.
  self.style_class = 'stock'
 
  self.summary_items = {
@@ -29,35 +33,5 @@ class SubmissionPlatePresenter < PlatePresenter
  'Input plate barcode' => :input_barcode,
  'Created on' => :created_on
  }
-
- self.allow_well_failure_in_states = []
-
- def each_submission_option
- purpose_config.submission_options.each do |button_text, options|
- submission_options = options.to_hash
- submission_options[:asset_groups] = asset_groups
- submission_options[:labware_barcode] = labware.labware_barcode.human
- yield button_text, SequencescapeSubmission.new(submission_options)
- end
- end
-
- def pending_submissions?
- submissions.any? { |submission| submission.building_in_progress?(ready_buffer: 20.seconds) }
- end
-
- def submissions
- labware.direct_submissions
- end
-
- private
-
- def asset_groups
- @asset_groups ||=
- labware
- .wells
- .compact_blank
- .group_by(&:order_group)
- .map { |_, wells| { assets: wells.map(&:uuid), autodetect_studies: true, autodetect_projects: true } }
- end
  end
 end

app/views/plates/_choose_workflow.html.erb

@@ -1,10 +1,9 @@
 <%= vite_javascript_tag 'entrypoints/pages/choose_workflow.js', defer: true %>
 <%= card title:'Choose workflow', id: 'choose_workflow_card', css_class: 'suggested-actions logged_in_only' do %>
  <p class="lead">
- This plate can be processed via multiple workflows and there are currently
- no active workflows associated with the plate. Please select a workflow.
- This will build the necessary submissions in Sequencescape, and will allow
- you to proceed.
+ A new workflow can be created for this plate. Please choose a workflow to
+ continue. This will build the necessary submissions in Sequencescape,
+ allowing you to proceed.
  </p>
 
  <div id="submission_forms">

app/views/plates/_pending_submissions.html.erb

@@ -1,8 +1,9 @@
-<% if presenter.submissions.present? %>
+<%# presenter.submissions returns a JsonApiClient::Query::Builder at this point #%>
+<% if presenter.submissions.present? and presenter.submissions.size > 0 %>
  <%= card title:'Submissions', css_class: 'suggested-actions', without_block: true do %>
  <% if presenter.pending_submissions? %>
  <div class="card-body">
- <p class="lead">There are currently submissions being built, This page will refresh in
+ <p class="lead">There are currently submissions being built, the page will refresh in
  <span id="refresh_time" data-reload-time="5">5</span> seconds.</p>
  </div>
  <% end %>

app/views/plates/show.html.erb

@@ -16,5 +16,5 @@
  <% end %>
  <% end %>
 
- <%= render "plates/sidebars/#{@presenter.sidebar_partial}", presenter: @presenter %>
+ <%= render "plates/sidebars/container", presenter: @presenter %>
 <% end %>

app/views/plates/sidebars/_container.html.erb

@@ -0,0 +1,4 @@
+<%= sidebar do %>
+ <%= render 'logged_out_warning' %>
+ <%= render "plates/sidebars/#{@presenter.sidebar_partial}", presenter: @presenter %>
+<% end %>