Close #139

app/controllers/registers_controller.rb

@@ -154,6 +154,7 @@ def submit
     change_status(
       :submit, 'Register list successfully submitted for review', current_user
     )
+    add_automatic_correspondence('Register list submitted')
   end
 
   # GET /registers/r:abcd/return
@@ -190,6 +191,7 @@ def notify
     # the standard +change_status+ call used in all other status changes
     if @register.notify(current_user, register_notify_params, params[:doi])
       flash[:notice] = 'The list has been successfully submitted for validation'
+      add_automatic_correspondence('SeqCode Register notified')
       redirect_to(@register)
     else
       @register.title = par[:title]
@@ -300,12 +302,20 @@ def nomenclature_review
     @register.update_column(
       :nomenclature_review, !@register.nomenclature_review
     )
+    if @register.nomenclature_review
+      add_automatic_correspondence('Nomenclature review complete')
+    end
     redirect_back(fallback_location: @register)
   end
 
   # POST /registers/r:abc/genomics_review
   def genomics_review
-    @register.update_column(:genomics_review, !@register.genomics_review)
+    @register.update_column(
+      :genomics_review, !@register.genomics_review
+    )
+    if @register.genomics_review
+      add_automatic_correspondence('Genomics review complete')
+    end
     redirect_back(fallback_location: @register)
   end
 
@@ -364,6 +374,13 @@ def ensure_valid!
       @register&.validated?
     end
 
+    def add_automatic_correspondence(message)
+      RegisterCorrespondence.new(
+        message: message, notify: '0', automatic: true,
+        user: current_user, register: @register
+      ).save
+    end
+
     def change_status(fun, success_msg, *extra_opts)
       if @register.send(fun, *extra_opts)
         flash[:notice] = success_msg

app/models/register/status.rb

@@ -71,7 +71,8 @@ def submit(user)
         name.update!(par)
       end
       update_status_with_alert(
-        submitted: true, submitted_at: Time.now
+        submitted: true, submitted_at: Time.now,
+        genomics_review: false, nomenclature_review: false
       ) or return false
     end
     notify_status_change(:submit, user)

app/views/genomes/_genome.html.erb

@@ -148,7 +148,7 @@ end
 
     <% if @genome.source? %>
       <% def show_genome_sources(n = nil) %>
-        <% content_tag(:ul) do %>
+        <% content_tag(:ul, class: 'mb-1') do %>
           <% @genome.source_links.each_with_index.map do |link, k| %>
             <li>
               <%= link_to(link[0], target: '_blank', title: link[2]) do %>
@@ -171,7 +171,7 @@ end
           <% id = modal('Data sources') do %>
             <%= show_genome_sources %>
           <% end %>
-          <%= modal_button(id) do %>
+          <%= modal_button(id, class: 'btn btn-secondary') do %>
             See all sources
           <% end %>
         <% else %>

app/views/shared/_correspondence_message.html.erb

@@ -1,5 +1,7 @@
+<% automatic =
+      correspondence.respond_to?(:automatic) && correspondence.automatic %>
 <dt>
-  <%= fa_icon('comment') %>
+  <%= fa_icon(automatic ? 'robot' : 'comment') %>
   <%= link_to(correspondence.user) do %>
     <%= correspondence.user.username %>
     <% if correspondence.user.curator? %>
@@ -8,8 +10,11 @@
       </span>
     <% end %>
   <% end %>
+  <% if automatic %>
+    <span class="text-muted">(automatic message)</span>
+  <% end %>
   <span title="<%= correspondence.created_at %>">
-    <%= time_ago_in_words(correspondence.created_at) %> ago:
+    <%= time_ago_in_words(correspondence.created_at) %> ago
   </span>
 </dt>
 <dd><%= correspondence.message %></dd>

db/migrate/20240104203034_add_automatic_to_register_correspondence.rb

@@ -0,0 +1,5 @@
+class AddAutomaticToRegisterCorrespondence < ActiveRecord::Migration[6.1]
+  def change
+    add_column :register_correspondences, :automatic, :boolean, default: false
+  end
+end

db/migrate/20240104204413_add_automatic_to_name_correspondence.rb

@@ -0,0 +1,5 @@
+class AddAutomaticToNameCorrespondence < ActiveRecord::Migration[6.1]
+  def change
+    add_column :name_correspondences, :automatic, :boolean, default: false
+  end
+end

db/schema.rb

@@ -10,7 +10,7 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema.define(version: 2024_01_02_013502) do
+ActiveRecord::Schema.define(version: 2024_01_04_204413) do
 
   create_table "action_text_rich_texts", force: :cascade do |t|
     t.string "name", null: false
@@ -113,6 +113,7 @@
     t.integer "user_id", null: false
     t.datetime "created_at", precision: 6, null: false
     t.datetime "updated_at", precision: 6, null: false
+    t.boolean "automatic", default: false
     t.index ["name_id"], name: "index_name_correspondences_on_name_id"
     t.index ["user_id"], name: "index_name_correspondences_on_user_id"
   end
@@ -277,6 +278,7 @@
     t.integer "user_id", null: false
     t.datetime "created_at", precision: 6, null: false
     t.datetime "updated_at", precision: 6, null: false
+    t.boolean "automatic", default: false
     t.index ["register_id"], name: "index_register_correspondences_on_register_id"
     t.index ["user_id"], name: "index_register_correspondences_on_user_id"
   end