Prenotification stub

Author: lmrodriguezr

app/controllers/registers_controller.rb

@@ -3,8 +3,9 @@ class RegistersController < ApplicationController
     :set_register,
     only: %i[
       show table list certificate_image cite edit update destroy tree
-      submit return return_commit endorse notify notify_commit
-      validate editorial_checks publish publish_commit new_correspondence
+      submit return return_commit endorse prenotify prenotify_commit
+      notify notify_commit validate
+      editorial_checks publish publish_commit new_correspondence
       internal_notes nomenclature_review genomics_review snooze_curation
       observe unobserve merge merge_commit sample_map
       reviewer_token reviewer_token_create reviewer_token_delete
@@ -36,11 +37,12 @@ class RegistersController < ApplicationController
   before_action(
     :authenticate_can_edit!,
     only: %i[
-      edit update destroy submit notify notify_commit merge merge_commit
-      reviewer_token_create reviewer_token_delete
+      edit update destroy submit prenotify prenotify_commit notify notify_commit
+      merge merge_commit reviewer_token_create reviewer_token_delete
     ]
   )
   before_action(:authenticate_user!, only: %i[observe unobserve])
+  before_action(:check_pending_genomes!, only: %i[notify notify_commit])
 
   # GET /registers or /registers.json
   def index(status = :validated)
@@ -200,6 +202,16 @@ def endorse
     )
   end
 
+  # GET /registers/r:abc/prenotify
+  def prenotify
+    @genomes = @register.names.map(&:type_genome).compact.select(&:pending?)
+    redirect_to(notify_register_path(@register)) if @genomes.empty?
+  end
+
+  # POST /registers/r:abc/prenotify
+  def prenotify_commit
+  end
+
   # GET /registers/r:abc/notify
   def notify
     @register.title ||= @register.propose_title
@@ -527,6 +539,12 @@ def ensure_valid!
       @register&.validated?
     end
 
+    def check_pending_genomes!
+      if @register.pending_genomes?
+        redirect_to(prenotify_register_path(@register))
+      end
+    end
+
     def add_automatic_correspondence(message)
       RegisterCorrespondence.new(
         message: message, notify: '0', automatic: true,

app/models/register.rb

@@ -416,6 +416,10 @@ def wikispecies_issues?
     names.any? { |n| n.wikispecies_issues.any? }
   end
 
+  def pending_genomes?
+    names.any? { |n| n.type_genome.try(:pending?) }
+  end
+
   private
 
   def assign_accession

app/views/registers/notify.html.erb

@@ -29,6 +29,7 @@
       html: { multipart: true }
     ) do |f| %>
   <br/>
+
   <h2>Register List</h2>
   <%= render(partial: 'edit_title_abstract', locals: { f: f }) %>
 

app/views/registers/prenotify.html.erb

@@ -0,0 +1,52 @@
+<h1>
+  Notification of Effective Publication
+</h1>
+<hr/>
+
+<p class="lead">
+  Before reporting the effective publication associated to this register list,
+  you must report the accession numbers of all pending genomes serving as
+  nomenclatural types in the list.
+</p>
+
+<%= simple_form_for(
+      @register, url: prenotify_register_url(@register), method: :post
+    ) do |f| %>
+  <br/>
+
+  <h2>Pending genomes</h2>
+  <table class="table table-hover table-responsive">
+    <thead>
+      <tr>
+        <th scope=col>Name</th>
+        <th scope=col>Temporary designation</th>
+        <th scope=col>Database</th>
+        <th scope=col>Accession</th>
+      </tr>
+    </thead>
+    <tbody>
+      <% @genomes.each do |genome| %>
+        <tr>
+          <td><%= display_link(genome.name) %></td>
+          <td><%= genome.accession %></td>
+          <td></td>
+          <td></td>
+        </tr>
+      <% end %>
+    </tbody>
+  </table>
+  <%=
+    f.input(
+      :publication_pdf, label: 'Publication PDF', required: true,
+      hint: 'Published manuscript in PDF: the preferred PDF is the final ' \
+            'typeset version, but the author accepted manuscript version ' \
+            'is also acceptable'
+    )
+  %>
+
+  <br/>
+  <%= f.button(:submit, 'Submit list for validation') %>
+  <%= link_to('Cancel', @register, class: 'btn btn-secondary') %>
+  <br/><br/>
+<% end %>
+

config/routes.rb

@@ -157,6 +157,8 @@
       post :endorse
       get  :notify
       post :notify, action: :notify_commit
+      get  :prenotify
+      post :prenotify, action: :prenotify_commit
       post :validate
       get  :editorial_checks
       get  :publish