Remove legacy incertae sedis

app/controllers/placements_controller.rb

@@ -15,16 +15,12 @@ def new
       Placement.new(
         name: @name, preferred: true, parent: @name.parent,
         publication: @name.assigned_in,
-        incertae_sedis: @name.incertae_sedis,
-        incertae_sedis_text: @name.incertae_sedis_text
       ).save!
     end
 
     unless @name.placement
       @placement.parent = @name.parent
       @placement.publication = @name.assigned_in
-      @placement.incertae_sedis = @name.incertae_sedis
-      @placement.incertae_sedis_text = @name.incertae_sedis_text
       @placement.preferred = true
     end
   end
@@ -108,7 +104,6 @@ def create_or_update(back_action)
           end
           @name.update!(
             parent: @placement.parent, assigned_in: @placement.publication,
-            incertae_sedis: nil, incertae_sedis_text: nil
           )
         end
       rescue
@@ -130,8 +125,8 @@ def prefer
       @name.placement.try(:update!, preferred: false)
       @placement.update!(preferred: true)
       @name.update!(
-        parent: @placement.parent, assigned_in: @placement.publication,
-        incertae_sedis: nil, incertae_sedis_text: nil
+        parent: @placement.parent,
+        assigned_in: @placement.publication
       )
       ok = true
     end

app/models/name.rb

@@ -28,6 +28,10 @@ class Name < ApplicationRecord
     :placements, -> { includes(:parent) },
     dependent: :destroy, inverse_of: :name
   )
+  delegate(
+    :incertae_sedis, :incertae_sedis?, :incertae_sedis_html,
+    :incertae_sedis_text, to: :placement, allow_nil: true
+  )
   has_many(
     :child_placements, -> { includes(:name) },
     class_name: 'Placement', foreign_key: 'parent_id', dependent: :destroy
@@ -115,7 +119,6 @@ class Name < ApplicationRecord
   has_rich_text(:description)
   has_rich_text(:notes)
   has_rich_text(:etymology_text)
-  has_rich_text(:incertae_sedis_text) # deprecated, but values still in DB
 
   validates(:name, presence: true, uniqueness: true)
   validates(
@@ -125,13 +128,6 @@ class Name < ApplicationRecord
       message: 'can only contain letters, dashes, dots, and apostrophe'
     }
   )
-  validates(:incertae_sedis, presence: true, allow_nil: true)
-  validates(
-    :incertae_sedis, absence: {
-      if: :parent,
-      message: 'cannot be declared if the parent taxon is set'
-    }
-  )
   validates(
     :nomenclatural_type_type,
     presence: {
@@ -1001,12 +997,6 @@ def type_name_alt_placement
     place if place != self
   end
 
-  def incertae_sedis_html
-    return '' unless incertae_sedis?
-
-    incertae_sedis.gsub(/(incertae sedis)/i, '<i>\\1</i>').html_safe
-  end
-
   def inferred_rank
     @inferred_rank ||=
       if rank?
@@ -1175,18 +1165,6 @@ def propose_lineage_name(rank)
     end
   end
 
-  def incertae_sedis_explain
-    (placement || self).incertae_sedis_text
-  end
-
-  def incertae_sedis
-    placement ? placement.incertae_sedis : self[:incertae_sedis]
-  end
-
-  def incertae_sedis?
-    incertae_sedis.present?
-  end
-
   def taxonomic_data?
     description? || notes? || parent || incertae_sedis? ||
       taxonomic_status? || !children.empty? || !alt_child_placements.empty?
@@ -1481,12 +1459,7 @@ def harmonize_register_and_status
   end
 
   def ensure_consistent_placement
-    placement_incertae_sedis =
-      if saved_change_to_incertae_sedis?
-        self[:incertae_sedis]
-      else
-        incertae_sedis
-      end
+    placement_incertae_sedis = incertae_sedis
 
     if parent_id.present? || placement_incertae_sedis.present?
       pp = placements.where(
@@ -1504,7 +1477,6 @@ def ensure_consistent_placement
             name_id: id,
             parent_id: parent_id,
             incertae_sedis: placement_incertae_sedis,
-            incertae_sedis_text: incertae_sedis_text,
             preferred: true
           ).save
       end

app/models/tutorial/batch.rb

@@ -348,6 +348,7 @@ def batch_step_01(params, user)
       default_pars = { status: 0, created_by: user }
       param_names.each do |par|
         new_par = {}
+        placement_par = nil
 
         # Parents
         if par['parent']
@@ -356,12 +357,16 @@ def batch_step_01(params, user)
             parent = Name.new(default_pars.merge(name: par['parent'].name))
             parent.save!
           end
-          new_par[:parent] = parent
-          new_par[:incertae_sedis] = nil
+          placement_par = {
+            parent: parent,
+            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']
+          placement_par = {
+            parent: nil,
+            incertae_sedis: par['incertae_sedis'],
+            incertae_sedis_text: par['description']
+          }
         end
 
         # Nomenclatural types
@@ -384,7 +389,14 @@ def batch_step_01(params, user)
 
         name = Name.find_by_variants(par['name'])
         name.update!(new_par)
-        name.update_column(:incertae_sedis, nil) if par['incertae_sedis']
+        if placement_par
+          placement = name.placements.find_or_initialize_by(
+            parent: placement_par[:parent],
+            incertae_sedis: placement_par[:incertae_sedis]
+          )
+          name.placements.where.not(id: placement.id).update_all(preferred: false)
+          placement.update!(placement_par.merge(preferred: true))
+        end
       end
 
       # If all is good, go to next step

app/views/names/_taxonomy.html.erb

@@ -31,7 +31,7 @@
         <% if @name.incertae_sedis? %>
           <div class="border-left px-3">
             <b><%= @name.incertae_sedis_html %>:</b>
-            <%= @name.incertae_sedis_explain %>
+            <%= @name.incertae_sedis_text %>
           </div>
         <% elsif @name.parent %>
           <%= display_link(@name.parent, :name_html_correctness) %>

app/views/registers/table.html.erb

@@ -38,7 +38,7 @@
         <td>
           <% if name.incertae_sedis? %>
             <b><%= name.incertae_sedis_html %>:</b>
-            <%= name.incertae_sedis_explain %>
+            <%= name.incertae_sedis_text %>
           <% elsif !name.parent %>
             <u>Unknown</u>
           <% elsif @register.names.include? name %>

db/migrate/20260819100000_remove_incertae_sedis_from_names.rb

@@ -0,0 +1,18 @@
+# frozen_string_literal: true
+
+# Removes the legacy incertae sedis attributes now represented by placements.
+class RemoveIncertaeSedisFromNames < ActiveRecord::Migration[6.1]
+  def up
+    execute <<~SQL.squish
+      DELETE FROM action_text_rich_texts
+      WHERE record_type = 'Name'
+        AND name = 'incertae_sedis_text'
+    SQL
+
+    remove_column :names, :incertae_sedis, :string if column_exists?(:names, :incertae_sedis)
+  end
+
+  def down
+    raise ActiveRecord::IrreversibleMigration
+  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: 2026_08_08_100000) do
+ActiveRecord::Schema.define(version: 2026_08_19_100000) do
 
   # These are extensions that must be enabled in order to support this database
   enable_extension "fuzzystrmatch"
@@ -234,7 +234,6 @@
     t.datetime "irmng_at"
     t.text "col_json"
     t.datetime "col_at"
-    t.string "incertae_sedis"
     t.bigint "tutorial_id"
     t.bigint "genome_id"
     t.text "gbif_json"

test/fixtures/names.yml

@@ -64,6 +64,26 @@ bacillales:
   rank: order
   status: 15 # SeqCode
 
+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
+
+incertae_sedis:
+  name: Escherichia marmotae
+  rank: species
+  status: 15 # SeqCode
+
 type_genome_with_locations:
   name: Testimonas mappensis
   rank: species

test/fixtures/placements.yml

@@ -14,3 +14,8 @@ escherichia_coli:
   name: escherichia_coli
   parent: escherichia
   preferred: true
+
+incertae_sedis:
+  name: incertae_sedis
+  preferred: true
+  incertae_sedis: Incertae sedis (Bacteria)

test/models/name_test.rb

@@ -19,4 +19,12 @@ class NameTest < ActiveSupport::TestCase
     assert_includes name.errors[:register], 'must be a draft'
     assert_nil name.reload.register
   end
+
+  test 'incertae sedis HTML comes from the preferred placement' do
+    name = names(:incertae_sedis)
+
+    assert_equal(
+      '<i>Incertae sedis</i> (Bacteria)', name.incertae_sedis_html
+    )
+  end
 end