Y25-682 - support '/' in plate purpose names

Gemfile.lock

@@ -236,7 +236,7 @@ GEM
     factory_bot_rails (6.5.1)
       factory_bot (~> 6.5)
       railties (>= 6.1.0)
-    faraday (2.14.0)
+    faraday (2.14.1)
       faraday-net_http (>= 2.0, < 3.5)
       json
       logger
@@ -338,8 +338,8 @@ GEM
     mutex_m (0.3.0)
     mysql2 (0.5.7)
       bigdecimal
-    net-http (0.7.0)
-      uri
+    net-http (0.9.1)
+      uri (>= 0.11.1)
     net-imap (0.5.9)
       date
       net-protocol

app/controllers/studies_controller.rb

@@ -253,18 +253,44 @@ def accession
     end
   end
 
+  # Accession all samples in the study.
+  #
+  # If the study does not have an accession number, adds an error to the study and returns.
+  # Otherwise, iterates through each sample in the study and attempts to accession it,
+  # unless the sample already has an accession number.
+  # If an Accession::Error occurs for a sample, adds the error message to the study's errors.
+  #
+  # NOTE: this does not check if the current user has permission to accession samples in this study
+  #
+  # @return [void]
   def accession_all_samples # rubocop:disable Metrics/AbcSize,Metrics/MethodLength
     @study = Study.find(params[:id])
     return accessioning_not_enabled_redirect unless accessioning_enabled?
 
     # TODO: Y26-026 - Enforce accessioning permissions
     # return accession_permission_denied_redirect unless permitted_to_accession?(@study)
 
-    @study.accession_all_samples(current_user)
+    unless @study.accession_number?
+      flash[:error] = 'Please accession the study before accessioning samples'
+      return redirect_to(study_path(@study))
+    end
+    unless @study.samples_accessionable?
+      flash[:error] = 'Study cannot accession samples, see Study Accessioning tab for details'
+      return redirect_to(study_path(@study))
+    end
+
+    @study.samples.find_each do |sample|
+      next if sample.accession_number?
+
+      begin
+        Accession.accession_sample(sample, current_user)
+      rescue Accession::Error => e
+        @study.errors.add(:base, e.message)
+      end
+    end
 
     if @study.errors.any?
-      error_messages = compile_accession_errors(@study.errors)
-      flash[:error] = error_messages
+      flash[:error] = compile_accession_errors(@study.errors)
     else
       flash[:notice] = 'All of the samples in this study have been sent for accessioning. ' \
                        'Please check back in 5 minutes to confirm that accessioning was successful.'

app/helpers/samples_helper.rb

@@ -4,7 +4,9 @@ module SamplesHelper
   # Indicate to the user that saving the sample will also accession it
   # This will not happen if the study has not been accessioned
   def save_text(sample)
-    return 'Save and Accession' if sample.should_be_accessioned?
+    if [accessioning_enabled?, sample.should_be_accessioned?, permitted_to_accession?(sample)].all?
+      return 'Save and Accession'
+    end
 
     'Save Sample'
   end

app/models/purpose.rb

@@ -44,7 +44,7 @@ class Purpose < ApplicationRecord
 
   before_validation :set_default_barcode_prefix
 
-  validates :name, format: { with: /\A\w[\s\w.-]+\w\z/i }, presence: true, uniqueness: { case_sensitive: false }
+  validates :name, format: { with: %r{\A\w[\s\w.\-/]+\w\z}i }, presence: true, uniqueness: { case_sensitive: false }
 
   # NOTE: We should validate against valid asset subclasses, but running into some issues with
   # subclass loading while seeding.

app/models/sample.rb

@@ -553,7 +553,8 @@ def should_be_accessioned?
     false
   end
 
-  # NOTE: this does not check whether the current user is permitted to accession the sample
+  # NOTE: this does not check whether the current user is permitted to accession the sample,
+  # nor if accessioning is enabled, as these belong in a controller or library, rather than the model.
   def accession_and_handle_validation_errors
     event_user = current_user # the event_user for this sample must be set from the calling controller
     Accession.accession_sample(self, event_user, perform_now: true)

app/models/study.rb

@@ -583,31 +583,6 @@ def samples_accessionable?
     ].all?
   end
 
-  # Accession all samples in the study.
-  #
-  # If the study does not have an accession number, adds an error to the study and returns.
-  # Otherwise, iterates through each sample in the study and attempts to accession it,
-  # unless the sample already has an accession number.
-  # If an Accession::Error occurs for a sample, adds the error message to the study's errors.
-  #
-  # NOTE: this does not check if the current user has permission to accession samples in this study
-  #
-  # @return [void]
-  def accession_all_samples(event_user)
-    return errors.add(:base, 'Please accession the study before accessioning samples') unless accession_number?
-
-    unless samples_accessionable?
-      return errors.add(:base,
-                        'Study cannot accession samples, see Study Accessioning tab for details')
-    end
-
-    samples.find_each do |sample|
-      Accession.accession_sample(sample, event_user) unless sample.accession_number?
-    rescue Accession::Error => e
-      errors.add(:base, e.message)
-    end
-  end
-
   def abbreviation
     abbreviation = study_metadata.study_name_abbreviation
     abbreviation.presence || "#{id}STDY"

app/models/transfer_request.rb

@@ -71,6 +71,7 @@ class TransferRequest < ApplicationRecord # rubocop:todo Metrics/ClassLength
     # as being more concise as it has fewer states.
     state :pending, initial: true
     state :started
+    state :processed
     state :processed_1
     state :processed_2
     state :processed_3
@@ -85,6 +86,10 @@ class TransferRequest < ApplicationRecord # rubocop:todo Metrics/ClassLength
       transitions to: :started, from: [:pending], after: :on_started
     end
 
+    event :progress do
+      transitions to: :processed, from: [:started], after: :on_started
+    end
+
     event :process_1 do
       transitions to: :processed_1, from: [:pending], after: :on_started
     end
@@ -104,7 +109,7 @@ class TransferRequest < ApplicationRecord # rubocop:todo Metrics/ClassLength
     event :pass do
       # Jumping straight to passed moves through an implied started state.
       transitions to: :passed, from: :pending, after: :on_started
-      transitions to: :passed, from: %i[started failed processed_2 processed_3 processed_4]
+      transitions to: :passed, from: %i[started failed processed processed_2 processed_3 processed_4]
     end
 
     event :fail do

app/views/sdb/sample_manifests/_samples.html.erb

@@ -38,7 +38,7 @@
         <td><%= accession_status&.status&.capitalize %></td>
         <td><%= accession_status&.updated_at&.in_time_zone&.strftime('%Y-%m-%d %H:%M:%S %Z') %></td>
         <td>
-          <% if can?(:accession, sample) && configatron.accession_samples %>
+          <% if [accessioning_enabled?, sample.should_be_accessioned?, permitted_to_accession?(sample)].all? %>
             <%# Add link to perform sample accessioning %>
             <% if sample.current_accession_status %>
               <%# If status exists, offer retry %>

app/views/studies/information/_accession_statuses.html.erb

@@ -36,7 +36,7 @@
         <td><%= accession_status&.status&.capitalize %></td>
         <td><%= accession_status&.updated_at&.in_time_zone&.strftime('%Y-%m-%d %H:%M:%S %Z') %></td>
         <td>
-          <% if permitted_to_accession?(sample) & sample.should_be_accessioned? & accessioning_enabled? %>
+          <% if [accessioning_enabled?, sample.should_be_accessioned?, permitted_to_accession?(sample)].all? %>
             <%# Add link to perform sample accessioning %>
             <% if sample.current_accession_status %>
               <%# If status exists, offer retry %>

app/views/studies/information/_study_accession_checklist.html.erb

@@ -25,7 +25,7 @@
 
   <%= checklist_item(
         condition: !@study.study_metadata.strategy_not_applicable?,
-        good: "Study release strategy is #{Study::DATA_RELEASE_STRATEGY_OPEN.humanize} or #{Study::DATA_RELEASE_STRATEGY_MANAGED.humanize} #{tag.strong { "(#{@study.study_metadata.data_release_strategy.humanize})" }}".html_safe,
+        good: "Study release strategy is #{Study::DATA_RELEASE_STRATEGY_OPEN.humanize} or #{Study::DATA_RELEASE_STRATEGY_MANAGED.humanize} #{tag.strong { "(#{@study.study_metadata.data_release_strategy&.humanize})" }}".html_safe,
         bad: "Study release strategy is <strong>#{Study::DATA_RELEASE_STRATEGY_NOT_APPLICABLE.humanize}</strong>".html_safe,
         action: link_to('Change release strategy', edit_study_path(@study)),
         action_permission: can?(:edit, @study),
@@ -34,7 +34,7 @@
 
   <%= checklist_item(
         condition: !@study.study_metadata.never_release?,
-        good: "Study release timing is <strong>#{@study.study_metadata.data_release_timing.humanize}</strong>".html_safe,
+        good: "Study release timing is <strong>#{@study.study_metadata.data_release_timing&.humanize}</strong>".html_safe,
         bad: "Study release timing is <strong>#{Study::DATA_RELEASE_TIMING_NEVER.humanize}</strong>".html_safe,
         action: link_to('Change release settings', edit_study_path(@study)),
         action_permission: can?(:edit, @study),

config/default_records/request_types/018_limber_lcm_triomics_request_types.yml

@@ -24,3 +24,15 @@ limber_lcm_triomics_wgs:
     - LCMT DNA Adp Lig
   library_types:
     - LCMB
+limber_lcm_triomics_rnaseq:
+    name: LCM Triomics RNA-seq
+    asset_type: Well
+    order: 1
+    request_class_name: IlluminaHtp::Requests::StdLibraryRequest
+    for_multiplexing: false
+    billable: true
+    product_line_name: Short Read
+    acceptable_purposes:
+      - LCMT Lysate
+    library_types:
+      - Combined LCM RNA

config/default_records/submission_templates/014_lcm_triomics_submission_templates.yml

@@ -14,3 +14,10 @@ Limber-Htp - LCM Triomics WGS:
     request_type_keys: ["limber_lcm_triomics_wgs"]
     product_line_name: LCM Triomics
     product_catalogue_name: LCM Triomics
+
+Limber-Htp - LCM Triomics RNA-seq:
+  submission_class_name: "LinearSubmission"
+  related_records:
+    request_type_keys: ["limber_lcm_triomics_rnaseq"]
+    product_line_name: LCM Triomics
+    product_catalogue_name: LCM Triomics

spec/controllers/studies_controller_spec.rb

@@ -192,6 +192,48 @@
     end
 
     context 'when the accessioning succeeds' do
+      it 'accessions all samples in the study' do
+        study.samples.each do |sample|
+          expect(sample.reload.sample_metadata.sample_ebi_accession_number).to eq('EGA00001000240')
+        end
+      end
+
+      it 'redirects to the accession-statuses tab of the study page' do
+        expect(subject).to redirect_to(study_path(study, anchor: 'accession-statuses'))
+      end
+
+      it 'does not set a flash error message' do
+        expect(flash[:error]).to be_nil
+      end
+
+      it 'does not set a flash warning message' do
+        expect(flash[:warning]).to be_nil
+      end
+
+      it 'sets a flash notice message' do
+        expect(flash[:notice]).to eq(
+          'All of the samples in this study have been sent for accessioning. ' \
+          'Please check back in 5 minutes to confirm that accessioning was successful.'
+        )
+      end
+
+      it 'does not set a flash info message' do
+        expect(flash[:info]).to be_nil
+      end
+    end
+
+    context 'when a sample already has an accession number' do
+      # add a 6th already accessioned sample to the study
+      let(:samples) { create_list(:sample_for_accessioning, number_of_samples) + create_list(:accessioned_sample, 1) }
+      let(:study) { create(:open_study, accession_number: 'ENA123', samples: samples) }
+
+      it 'does not attempt to accession accessioned samples' do
+        # confirm that only 5 calls were made to the accession client, not 6
+        expect(Accession::Submission.client)
+          .to have_received(:submit_and_fetch_accession_number)
+          .exactly(number_of_samples).times
+      end
+
       it 'redirects to the accession-statuses tab of the study page' do
         expect(subject).to redirect_to(study_path(study, anchor: 'accession-statuses'))
       end
@@ -308,6 +350,63 @@
           end
         end
       end
+
+      context 'when the study does not have an accession number' do
+        let(:study) { create(:managed_study, samples:) }
+
+        it 'does not attempt to accession samples' do
+          expect(Accession::Submission.client).not_to have_received(:submit_and_fetch_accession_number)
+        end
+
+        it 'redirects to the study page' do
+          expect(subject).to redirect_to(study_path(study))
+        end
+
+        it 'does not set a flash warning message' do
+          expect(flash[:warning]).to be_nil
+        end
+
+        it 'does not set a flash notice message' do
+          expect(flash[:notice]).to be_nil
+        end
+
+        it 'sets a flash error message' do
+          expect(flash[:error]).to eq('Please accession the study before accessioning samples')
+        end
+
+        it 'does not set a flash info message' do
+          expect(flash[:info]).to be_nil
+        end
+      end
+
+      context 'when a study is not longer accessionable' do
+        let(:study_metadata) { create(:study_metadata_for_accessioning, study_ebi_accession_number: 'EGA123') }
+        let(:study) { create(:study, study_metadata:, samples:) }
+
+        it 'does not attempt to accession samples' do
+          expect(Accession::Submission.client).not_to have_received(:submit_and_fetch_accession_number)
+        end
+
+        it 'redirects to the study page' do
+          expect(subject).to redirect_to(study_path(study))
+        end
+
+        it 'does not set a flash warning message' do
+          expect(flash[:warning]).to be_nil
+        end
+
+        it 'does not set a flash notice message' do
+          expect(flash[:notice]).to be_nil
+        end
+
+        it 'sets a flash error message' do
+          expect(flash[:error]).to eq('Study cannot accession samples, see Study Accessioning tab for details')
+        end
+
+        it 'does not set a flash info message' do
+          expect(flash[:info]).to be_nil
+        end
+      end
     end
   end
 end

spec/helpers/samples_helper_spec.rb

@@ -0,0 +1,41 @@
+# frozen_string_literal: true
+
+require 'rails_helper'
+
+RSpec.describe SamplesHelper, type: :helper do
+  subject { helper.save_text(sample) }
+
+  let(:sample) { create(:sample) }
+
+  let(:accessioning_enabled) { true }
+  let(:should_be_accessioned) { true }
+  let(:permitted) { true }
+
+  before do
+    allow(helper).to receive(:accessioning_enabled?).and_return(accessioning_enabled)
+    allow(helper).to receive(:permitted_to_accession?).with(sample).and_return(permitted)
+    allow(sample).to receive(:should_be_accessioned?).and_return(should_be_accessioned)
+  end
+
+  context 'when accessioning is enabled, sample should be accessioned, and user is permitted' do
+    it { is_expected.to eq('Save and Accession') }
+  end
+
+  context 'when accessioning is disabled' do
+    let(:accessioning_enabled) { false }
+
+    it { is_expected.to eq('Save Sample') }
+  end
+
+  context 'when sample should not be accessioned' do
+    let(:should_be_accessioned) { false }
+
+    it { is_expected.to eq('Save Sample') }
+  end
+
+  context 'when user is not permitted to accession' do
+    let(:permitted) { false }
+
+    it { is_expected.to eq('Save Sample') }
+  end
+end