Batch tutorial: create placements directly

app/models/name.rb

@@ -24,7 +24,10 @@ class Name < ApplicationRecord
   alias :correspondences :name_correspondences
   has_many(:checks, dependent: :destroy)
   has_many(:check_users, -> { distinct }, through: :checks, source: :user)
-  has_many(:placements, -> { includes(:parent) }, dependent: :destroy)
+  has_many(
+    :placements, -> { includes(:parent) },
+    dependent: :destroy, inverse_of: :name
+  )
   has_many(
     :child_placements, -> { includes(:name) },
     class_name: 'Placement', foreign_key: 'parent_id', dependent: :destroy
@@ -39,7 +42,7 @@ class Name < ApplicationRecord
     :combinational_derivatives, class_name: 'Name', foreign_key: 'basonym_id',
     dependent: :nullify # Inverse of basonym
   )
-  has_many(:curations)
+  has_many(:curations, dependent: :destroy)
   has_many(:name_paratypes, dependent: :destroy)
   has_many(
     :paratype_publications, through: :name_paratypes, source: :publication
@@ -1478,9 +1481,16 @@ def harmonize_register_and_status
   end
 
   def ensure_consistent_placement
-    if parent_id.present? || incertae_sedis.present?
+    placement_incertae_sedis =
+      if saved_change_to_incertae_sedis?
+        self[:incertae_sedis]
+      else
+        incertae_sedis
+      end
+
+    if parent_id.present? || placement_incertae_sedis.present?
       pp = placements.where(
-        parent_id: parent_id, incertae_sedis: incertae_sedis
+        parent_id: parent_id, incertae_sedis: placement_incertae_sedis
       ).first
       if pp.present?
         if pp.preferred?
@@ -1491,8 +1501,11 @@ def ensure_consistent_placement
       else
         placements.update(preferred: false) &&
           Placement.new(
-            name_id: id, parent_id: parent_id, incertae_sedis: incertae_sedis,
-            incertae_sedis_text: incertae_sedis_text, preferred: true
+            name_id: id,
+            parent_id: parent_id,
+            incertae_sedis: placement_incertae_sedis,
+            incertae_sedis_text: incertae_sedis_text,
+            preferred: true
           ).save
       end
     else

app/models/tutorial/batch.rb

@@ -77,7 +77,19 @@ def param_names
   def ephemeral_names
     @ephemeral_names ||=
       param_names.map do |i|
-        Name.new(i)
+        name_attributes = i.except('parent', 'incertae_sedis')
+        placement_attributes = {
+          parent: i['parent'],
+          incertae_sedis: i['incertae_sedis'],
+          preferred: true
+        }
+        if i['incertae_sedis'].present?
+          placement_attributes[:incertae_sedis_text] = i['description']
+        end
+
+        Name.new(name_attributes).tap do |name|
+          name.placements.build(placement_attributes)
+        end
       rescue => e
         $stderr.puts e
         nil
@@ -113,15 +125,20 @@ def check_ephemeral_names(user)
     @check_ephemeral_names ||= :pending
     return ephemeral_names if @check_ephemeral_names == :done
 
-    name_names = ephemeral_names.map(&:name)
     ephemeral_names.each do |name|
+      placement = name.placements.first
+
       # Is the information complete?
       Tutorial::Batch.name_keys_base.each do |i|
+        next if i == :parent
+
         unless name.send(i).present?
           name.errors.add(i, :missing, message: 'is missing')
         end
       end
 
+      placement.validate # Populate placement.errors for the review step
+
       # Is the etymology present?
       unless name.etymology?
         name.errors.add(
@@ -139,8 +156,8 @@ def check_ephemeral_names(user)
       end
 
       # Is the parent already registered?
-      if name.parent && !name_exists?(name.parent.name)
-        name.errors.add(
+      if placement.parent && !name_exists?(placement.parent.name)
+        placement.errors.add(
           :parent, :does_not_exist,
           message: 'does not exist and is not proposed in this list'
         )
@@ -305,7 +322,8 @@ def batch_step_01(params, user)
         # Remove foreign keys in first pass
         par = par_ori.dup
         %w[
-          parent nomenclatural_type_entry nomenclatural_type_type
+          parent incertae_sedis
+          nomenclatural_type_entry nomenclatural_type_type
           nomenclatural_type_id nomenclatural_type
         ].each { |i| par.delete(i) }
 
@@ -333,12 +351,17 @@ def batch_step_01(params, user)
 
         # Parents
         if par['parent']
-          new_par[:parent] = Name.find_by_variants(par['parent'].name)
-          unless new_par[:parent]
-            name = Name.new(default_pars.merge(name: par['parent'].name))
-            name.save!
-            new_par[:parent_id] = name.id
+          parent = Name.find_by_variants(par['parent'].name)
+          unless parent
+            parent = Name.new(default_pars.merge(name: par['parent'].name))
+            parent.save!
           end
+          new_par[:parent] = parent
+          new_par[:incertae_sedis] = nil
+        elsif par['incertae_sedis']
+          new_par[:parent] = nil
+          new_par[:incertae_sedis] = par['incertae_sedis']
+          new_par[:incertae_sedis_text] = par['description']
         end
 
         # Nomenclatural types
@@ -359,7 +382,9 @@ def batch_step_01(params, user)
           end
         end
 
-        Name.find_by_variants(par['name']).update!(new_par)
+        name = Name.find_by_variants(par['name'])
+        name.update!(new_par)
+        name.update_column(:incertae_sedis, nil) if par['incertae_sedis']
       end
 
       # If all is good, go to next step

app/views/tutorials/batch/_01.html.erb

@@ -9,6 +9,7 @@
   <div class="accordion" id="batch-names-accordion">
     <% @tutorial.check_ephemeral_names(current_user) %>
     <% @tutorial.ephemeral_names.each_with_index do |name, idx| %>
+      <% placement = name&.placements&.first %>
       <div class="card">
         <% id = "batch-names-#{idx}" %>
         <% if name.nil? || name&.name.nil? %>
@@ -32,13 +33,14 @@
             <button class="btn btn-link btn-block text-left" type="button"
                     data-toggle="collapse" data-target="#<%= id %>"
                     aria-expanded="false" aria-controls="<%= id %>">
-              <% if name.errors.any? %>
+              <% if name.errors.any? || placement.errors.any? %>
                 <%= fa_icon('exclamation-circle', class: 'text-danger') %>
               <% end %>
               <%= name.name_html %>
               <span class="text-muted">
                 - <%= name.rank %> of
-                  <%= name.parent.try(:name_html) || 'unknown' %>
+                  <%= placement.parent.try(:name_html) ||
+                      placement.incertae_sedis_html.presence || 'unknown' %>
               </span>
             </button>
           </h2>
@@ -66,11 +68,12 @@
               <% end %>
               <%= modal_button(id, as_anchor: true) do %>Record details<% end %>
 
-              <% if name.errors.any? %>
+              <% if name.errors.any? || placement.errors.any? %>
                 <div class="alert alert-danger">
                   <h4>Issues detected in preliminary check:</h4>
                   <ul>
-                    <% name.errors.full_messages.each do |error| %>
+                    <% (name.errors.full_messages +
+                        placement.errors.full_messages).each do |error| %>
                       <li><%= error %></li>
                     <% end %>
                   </ul>
@@ -166,4 +169,3 @@
   Please note that any errors saved will have to be individually resolved.
   This process may take up to a couple of minutes, please be patient.
 </p>
-

test/fixtures/names.yml

@@ -34,6 +34,21 @@ bacillus_subtilis:
   rank: species
   status: 20 # ICNP
 
+nanobdellaceae:
+  name: Nanobdellaceae
+  rank: family
+  status: 15 # SeqCode
+
+nanoclepta_minutus:
+  name: Nanoclepta minutus
+  rank: species
+  status: 15 # SeqCode
+
+luteria_ianthellae:
+  name: Luteria ianthellae
+  rank: species
+  status: 15 # SeqCode
+
 type_genome_with_locations:
   name: Testimonas mappensis
   rank: species

test/models/tutorial_test.rb

@@ -1,7 +1,153 @@
 require 'test_helper'
 
 class TutorialTest < ActiveSupport::TestCase
-  # test "the truth" do
-  #   assert true
-  # end
+  test 'batch parses a name' do
+    tutorial = upload_batch_spreadsheet('SCR_UploadBatch-Nanoclepta.xlsx')
+    name = tutorial.ephemeral_names.first
+    placement = name.placements.first
+
+    assert_equal 1, tutorial.step
+    assert_empty tutorial.value(:genomes)
+    assert_equal 1, tutorial.value(:names).size
+    assert_equal 'Nanoclepta', tutorial.value(:names).first['name']
+    assert_equal 'Nanobdellaceae', tutorial.value(:names).first['parent']
+    assert_nil name.parent
+    assert_nil name[:incertae_sedis]
+    assert_same name, placement.name
+    assert_equal 'Nanobdellaceae', placement.parent.name
+    assert_nil placement.incertae_sedis
+    assert_empty placement.incertae_sedis_text.to_plain_text
+  end
+
+  test 'batch parses an incertae sedis name' do
+    tutorial = upload_batch_spreadsheet(
+      'SCR_UploadBatch-Luteria-Incertae_sedis.xlsx'
+    )
+    name = tutorial.ephemeral_names.first
+    placement = name.placements.first
+
+    assert_equal 1, tutorial.step
+    assert_empty tutorial.value(:genomes)
+    assert_equal 1, tutorial.value(:names).size
+    assert_equal 'Luteria', tutorial.value(:names).first['name']
+    assert_equal(
+      'incertae sedis (Bacteria)', tutorial.value(:names).first['parent']
+    )
+    assert_nil name.parent
+    assert_nil name[:incertae_sedis]
+    assert_nil placement.parent
+    assert_equal 'incertae sedis (Bacteria)', placement.incertae_sedis
+    assert_equal(
+      tutorial.value(:names).first['description'],
+      placement.incertae_sedis_text.to_plain_text
+    )
+  end
+
+  test 'batch creates a parent placement' do
+    tutorial = upload_batch_spreadsheet('SCR_UploadBatch-Nanoclepta.xlsx')
+    parent = names(:nanobdellaceae)
+
+    assert tutorial.batch_step_01({}, users(:contributor))
+
+    name = Name.find_by!(name: 'Nanoclepta')
+    placement = name.placement
+
+    assert_not_nil placement
+    assert_predicate placement, :preferred?
+    assert_equal parent, placement.parent
+    assert_equal parent, name.parent
+    assert_nil placement.incertae_sedis
+  end
+
+  test 'batch updates a claimable name with a preferred placement' do
+    parent = names(:nanobdellaceae)
+    name = Name.create!(
+      name: 'Nanoclepta', rank: 'genus', status: 5,
+      created_by: users(:contributor), parent: parent
+    )
+    placement = name.placement
+    tutorial = upload_batch_spreadsheet('SCR_UploadBatch-Nanoclepta.xlsx')
+
+    assert_no_difference('Placement.count') do
+      assert tutorial.batch_step_01({}, users(:contributor))
+    end
+
+    assert_equal placement, name.reload.placement
+    assert_equal parent, name.parent
+  end
+
+  test 'batch replaces a claimable name preferred placement' do
+    old_parent = Name.create!(
+      name: 'Nanoarchaeaceae', rank: 'family', status: 15
+    )
+    name = Name.create!(
+      name: 'Nanoclepta', rank: 'genus', status: 5,
+      created_by: users(:contributor), parent: old_parent
+    )
+    old_placement = name.placement
+    tutorial = upload_batch_spreadsheet('SCR_UploadBatch-Nanoclepta.xlsx')
+
+    assert_difference('Placement.count', 1) do
+      assert tutorial.batch_step_01({}, users(:contributor))
+    end
+
+    name = Name.find(name.id)
+    assert_equal names(:nanobdellaceae), name.placement.parent
+    assert_not old_placement.reload.preferred?
+    assert_includes name.alt_placements, old_placement
+  end
+
+  test 'batch creates an incertae sedis placement' do
+    tutorial = upload_batch_spreadsheet(
+      'SCR_UploadBatch-Luteria-Incertae_sedis.xlsx'
+    )
+    explanation = tutorial.value(:names).first['description']
+
+    assert tutorial.batch_step_01({}, users(:contributor))
+
+    name = Name.find_by!(name: 'Luteria')
+    placement = name.placement
+
+    assert_not_nil placement
+    assert_predicate placement, :preferred?
+    assert_nil placement.parent
+    assert_nil name.parent
+    assert_equal 'incertae sedis (Bacteria)', placement.incertae_sedis
+    assert_equal explanation, placement.incertae_sedis_text.to_plain_text
+    assert_nil name[:incertae_sedis]
+  end
+
+  test 'batch replaces a claimable name placement with incertae sedis' do
+    old_parent = names(:escherichia)
+    name = Name.create!(
+      name: 'Luteria', rank: 'genus', status: 5,
+      created_by: users(:contributor), parent: old_parent
+    )
+    old_placement = name.placement
+    tutorial = upload_batch_spreadsheet(
+      'SCR_UploadBatch-Luteria-Incertae_sedis.xlsx'
+    )
+
+    assert_difference('Placement.count', 1) do
+      assert tutorial.batch_step_01({}, users(:contributor))
+    end
+
+    name = Name.find(name.id)
+    assert_equal 'incertae sedis (Bacteria)', name.placement.incertae_sedis
+    assert_not_predicate old_placement.reload, :preferred?
+    assert_includes name.alt_placements, old_placement
+    assert_nil name[:incertae_sedis]
+  end
+
+  private
+
+  def upload_batch_spreadsheet(filename)
+    tutorial = Tutorial.create!(
+      pipeline: 'batch', user: users(:contributor), step: 0, ongoing: true
+    )
+    File.open(Rails.root.join('test/fixtures/files', filename)) do |file|
+      assert tutorial.batch_step_00({ file: file }, users(:contributor))
+    end
+    tutorial
+  end
 end