Triomic epic

app/controllers/concerns/sequencescape_submission_behaviour.rb

@@ -21,6 +21,7 @@ def sequencescape_submission_parameters
     params
       .expect(sequencescape_submission: [
                 :template_uuid,
+                :supplied_project_uuid,
                 :labware_barcode, {
                   request_options: {}, assets: [], asset_groups: {}, extra_barcodes: []
                 }

app/controllers/plates_controller.rb

@@ -5,6 +5,20 @@
 # fail_wells => Updates the state of individual wells when failing
 # Note: Finds plates via the v2 api
 class PlatesController < LabwareController
+  # AJAX endpoint to search for a Project by id using Sequencescape API
+  def find_project_by_id
+    project_id = params[:project_id]
+    begin
+      project = Sequencescape::Api::V2::Project.find!(project_id)
+      # Ensure we return both id and uuid for clarity
+      render json: { found: true,
+                     project: { id: project.first.id, uuid: project.first.uuid, name: project.first.name } }
+    rescue JsonApiClient::Errors::NotFound
+      render json: { found: false, error: 'Project not found' }, status: :not_found
+    rescue StandardError => e
+      render json: { found: false, error: e.message }, status: :internal_server_error
+    end
+  end
   before_action :check_for_current_user!, only: %i[update fail_wells] # rubocop:todo Rails/LexicallyScopedActionFilter
 
   def fail_wells # rubocop:todo Metrics/AbcSize

app/frontend/entrypoints/pages/choose_workflow.js

@@ -1,3 +1,116 @@
 import { disableEnterKeySubmit } from '@/javascript/lib/disable_enter_key_submit.js'
 
 disableEnterKeySubmit('#choose_workflow_card', '#submission_forms')
+
+const globalInput = document.getElementById('project_cost_code_global')
+const resultDiv = document.getElementById('project_search_result')
+
+if (globalInput && resultDiv) {
+  let foundProjectId = null
+  let validatedProjectCode = null
+
+  const injectProjectFields = function (form, projectCode, projectUuid) {
+    const hiddenProjectCode = form.querySelector('.project-cost-code-hidden')
+    const hiddenProjectUuid = form.querySelector('.supplied-project-uuid-hidden')
+
+    if (hiddenProjectCode) {
+      hiddenProjectCode.value = projectCode
+    }
+
+    if (hiddenProjectUuid) {
+      hiddenProjectUuid.value = projectUuid || ''
+    }
+  }
+
+  const showError = function (message) {
+    foundProjectId = null
+    validatedProjectCode = null
+    resultDiv.innerHTML = `<div class="alert alert-danger">${message}</div>`
+    globalInput.classList.add('is-invalid')
+  }
+
+  const showSuccess = function (project) {
+    resultDiv.textContent = `Project found: ${project.name || project.uuid}`
+    globalInput.classList.remove('is-invalid')
+  }
+
+  const lookupProject = async function (projectCode) {
+    resultDiv.textContent = 'Searching...'
+    globalInput.classList.remove('is-invalid')
+
+    try {
+      const response = await fetch(`/plates/find_project_by_id?project_id=${encodeURIComponent(projectCode)}`)
+      const data = await response.json()
+
+      if (!response.ok || !data.found) {
+        throw new Error(data.error || 'Project not found')
+      }
+
+      foundProjectId = data.project.uuid
+      validatedProjectCode = projectCode
+      showSuccess(data.project)
+      return true
+    } catch (error) {
+      showError(error.message || 'Project not found')
+      return false
+    }
+  }
+
+  const triggerLookup = async function ({ requireValue = false } = {}) {
+    const projectCode = globalInput.value.trim()
+
+    if (!projectCode) {
+      if (requireValue) showError('Project / Cost Code is required')
+      return
+    }
+    if (validatedProjectCode === projectCode && foundProjectId) return
+    await lookupProject(projectCode)
+  }
+
+  globalInput.addEventListener('input', function () {
+    foundProjectId = null
+    validatedProjectCode = null
+    resultDiv.textContent = ''
+    globalInput.classList.remove('is-invalid')
+  })
+
+  globalInput.addEventListener('keydown', async function (event) {
+    if (event.key !== 'Enter') return
+    event.preventDefault()
+    await triggerLookup({ requireValue: true })
+  })
+
+  globalInput.addEventListener('blur', function () {
+    triggerLookup()
+  })
+
+  document.querySelectorAll('#submission_forms form').forEach(function (form) {
+    form.addEventListener('submit', async function (event) {
+      const projectCode = globalInput.value.trim()
+
+      if (!projectCode) {
+        event.preventDefault()
+        showError('Project / Cost Code is required')
+        globalInput.focus()
+        return
+      }
+
+      if (validatedProjectCode === projectCode && foundProjectId) {
+        injectProjectFields(form, projectCode, foundProjectId)
+        return
+      }
+
+      event.preventDefault()
+
+      const projectFound = await lookupProject(projectCode)
+
+      if (!projectFound) {
+        globalInput.focus()
+        return
+      }
+
+      injectProjectFields(form, projectCode, foundProjectId)
+      form.submit()
+    })
+  })
+}

app/frontend/entrypoints/pages/choose_workflow.spec.js

@@ -0,0 +1,148 @@
+describe('choose_workflow submission form project fields', () => {
+  const waitForCondition = async (predicate, timeoutMs = 1000, intervalMs = 10) => {
+    const start = Date.now()
+
+    while (Date.now() - start < timeoutMs) {
+      if (predicate()) return
+      await new Promise((resolve) => setTimeout(resolve, intervalMs))
+    }
+
+    throw new Error('Timed out waiting for async workflow update')
+  }
+
+  beforeEach(() => {
+    document.body.innerHTML = `
+      <div id="choose_workflow_card">
+        <input id="project_cost_code_global" type="text" />
+        <div id="project_search_result"></div>
+        <div id="submission_forms">
+          <form>
+            <input type="hidden" class="project-cost-code-hidden" />
+            <input type="hidden" class="supplied-project-uuid-hidden" />
+          </form>
+        </div>
+      </div>
+    `
+  })
+
+  afterEach(() => {
+    vi.unstubAllGlobals()
+  })
+
+  it('sets hidden project fields when the form is submitted', async () => {
+    vi.resetModules()
+
+    const projectInput = document.getElementById('project_cost_code_global')
+    const resultDiv = document.getElementById('project_search_result')
+    const form = document.querySelector('#submission_forms form')
+    const hiddenProjectCode = form.querySelector('.project-cost-code-hidden')
+    const hiddenProjectUuid = form.querySelector('.supplied-project-uuid-hidden')
+
+    vi.stubGlobal(
+      'fetch',
+      vi.fn().mockResolvedValue({
+        ok: true,
+        json: vi.fn().mockResolvedValue({
+          found: true,
+          project: { uuid: 'project-uuid-123', name: 'Example Project' },
+        }),
+      }),
+    )
+
+    await import('./choose_workflow.js')
+
+    projectInput.value = '12345'
+    projectInput.dispatchEvent(new KeyboardEvent('keydown', { key: 'Enter', bubbles: true }))
+    await waitForCondition(() => resultDiv.textContent === 'Project found: Example Project')
+
+    form.dispatchEvent(new Event('submit', { bubbles: true, cancelable: true }))
+
+    expect(hiddenProjectCode.value).toBe('12345')
+    expect(hiddenProjectUuid.value).toBe('project-uuid-123')
+  })
+
+  it('validates and submits the form when project is entered without pressing enter first', async () => {
+    vi.resetModules()
+
+    const projectInput = document.getElementById('project_cost_code_global')
+    const resultDiv = document.getElementById('project_search_result')
+    const form = document.querySelector('#submission_forms form')
+    const hiddenProjectCode = form.querySelector('.project-cost-code-hidden')
+    const hiddenProjectUuid = form.querySelector('.supplied-project-uuid-hidden')
+
+    form.submit = vi.fn()
+
+    vi.stubGlobal(
+      'fetch',
+      vi.fn().mockResolvedValue({
+        ok: true,
+        json: vi.fn().mockResolvedValue({
+          found: true,
+          project: { uuid: 'project-uuid-456', name: 'Validated Project' },
+        }),
+      }),
+    )
+
+    await import('./choose_workflow.js')
+
+    projectInput.value = '67890'
+    form.dispatchEvent(new Event('submit', { bubbles: true, cancelable: true }))
+
+    await waitForCondition(() => resultDiv.textContent === 'Project found: Validated Project')
+    await waitForCondition(() => form.submit.mock.calls.length === 1)
+
+    expect(hiddenProjectCode.value).toBe('67890')
+    expect(hiddenProjectUuid.value).toBe('project-uuid-456')
+  })
+
+  it('sets project uuid hidden field to empty string when no project is found', async () => {
+    vi.resetModules()
+
+    const projectInput = document.getElementById('project_cost_code_global')
+    const resultDiv = document.getElementById('project_search_result')
+    const form = document.querySelector('#submission_forms form')
+    const hiddenProjectCode = form.querySelector('.project-cost-code-hidden')
+    const hiddenProjectUuid = form.querySelector('.supplied-project-uuid-hidden')
+
+    vi.stubGlobal(
+      'fetch',
+      vi.fn().mockResolvedValue({
+        ok: false,
+        json: vi.fn().mockResolvedValue({
+          found: false,
+          error: 'Project not found',
+        }),
+      }),
+    )
+
+    await import('./choose_workflow.js')
+
+    projectInput.value = '99999'
+    projectInput.dispatchEvent(new KeyboardEvent('keydown', { key: 'Enter', bubbles: true }))
+    await waitForCondition(() => resultDiv.textContent === 'Project not found')
+
+    form.dispatchEvent(new Event('submit', { bubbles: true, cancelable: true }))
+
+    expect(hiddenProjectCode.value).toBe('')
+    expect(hiddenProjectUuid.value).toBe('')
+  })
+
+  it('shows an error and does not submit when project code is blank', async () => {
+    vi.resetModules()
+
+    const projectInput = document.getElementById('project_cost_code_global')
+    const resultDiv = document.getElementById('project_search_result')
+    const form = document.querySelector('#submission_forms form')
+
+    form.submit = vi.fn()
+
+    await import('./choose_workflow.js')
+
+    projectInput.value = '   '
+    form.dispatchEvent(new Event('submit', { bubbles: true, cancelable: true }))
+
+    expect(resultDiv.textContent).toContain('Project / Cost Code is required')
+    expect(projectInput.classList.contains('is-invalid')).toBe(true)
+    expect(form.submit).not.toHaveBeenCalled()
+  })
+})

app/frontend/stylesheets/limber/_labware-mixins.scss

@@ -8,6 +8,7 @@
     background: none;
   }
   .started,
+  .processed,
   .process_1,
   .process_2 {
     background-color: $info;

app/frontend/stylesheets/limber/screen.scss

@@ -380,6 +380,7 @@ dl#samples-information {
     @extend .list-group-item-warning;
   }
   li.state-started,
+  li.state-processed,
   li.state-process_1,
   li.state-process_2 {
     @extend .list-group-item-info;
@@ -413,6 +414,7 @@ dl#samples-information {
   @extend.bg-warning;
 }
 .state-badge.started,
+.state-badge.processed,
 .state-badge.process_1,
 .state-badge.process_2 {
   @extend.bg-info;

app/integrations/sequencescape/api/v2/submission_template.rb

@@ -2,4 +2,7 @@
 
 # submission template resource
 class Sequencescape::Api::V2::SubmissionTemplate < Sequencescape::Api::V2::Base
+  def self.find_by(uuid:)
+    where(uuid:).first
+  end
 end

app/models/concerns/presenters/collect_project_behaviour.rb

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+# Include in a presenter which needs to collect a project from the user before allowing submission creation
+module Presenters::CollectProjectBehaviour
+  def collect_project?
+    return false if purpose_config[:presenter_class].is_a?(String)
+
+    purpose_config.dig(:presenter_class, :args, :collect_project) || false
+  end
+end

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

@@ -23,6 +23,15 @@ module Permissive # rubocop:todo Style/Documentation
           include DoesNotAllowLibraryPassing
         end
 
+        state :processed do
+          include StateAllowsChildCreation
+          include DoesNotAllowLibraryPassing
+
+          def sidebar_partial
+            'default'
+          end
+        end
+
         state :processed_1 do
           include StateAllowsChildCreation
           include DoesNotAllowLibraryPassing

app/models/presenters/pcr_permissive_presenter.rb

@@ -0,0 +1,17 @@
+# frozen_string_literal: true
+
+module Presenters
+  #
+  # Combines PCR rendering (tagged aliquots) with permissive plate creation behavior
+  #
+  class PcrPermissivePresenter < StandardPresenter
+    include Presenters::Statemachine::Permissive
+
+    # Use the tagged aliquot partial from PcrPresenter
+    self.aliquot_partial = 'tagged_aliquot'
+
+    # Include the same validators as PermissivePresenter
+    validates_with Validators::SuboptimalValidator
+    validates_with Validators::ActiveRequestValidator
+  end
+end

app/models/presenters/permissive_submission_plate_presenter.rb

@@ -22,6 +22,7 @@ module Presenters
   class PermissiveSubmissionPlatePresenter < PlatePresenter
     include Presenters::Statemachine::PermissiveSubmission
     include Presenters::SubmissionBehaviour
+    include Presenters::CollectProjectBehaviour
 
     validates_with Validators::SuboptimalValidator
     validates_with Validators::ActiveRequestValidator

app/models/presenters/plate_presenter.rb

@@ -190,6 +190,10 @@ def display_manual_transfer_button?
       can_be_enabled?(purpose_config.dig(:manual_transfer, :states))
     end
 
+    def disable_button_for_submission?(_submission)
+      false
+    end
+
     private
 
     def libraries_passable?