Incertae sedis placement

app/assets/stylesheets/custom.scss

@@ -60,6 +60,26 @@ input[type=checkbox] {
   accent-color: theme-color-level(primary, 0);
 }
 
+.easy-autocomplete {
+  width: 100%;
+}
+
+.placement-form {
+  #incertae-sedis {
+    display: none;
+  }
+
+  &:has([name="placement[incertae_sedis]"][value="true"]:checked) {
+    #standard-placement {
+      display: none;
+    }
+
+    #incertae-sedis {
+      display: block;
+    }
+  }
+}
+
 #dashboard-actions, .btn {
   .fa, .fas, .far, .fal, .fad, .fab {
     min-width: 1.5em;
@@ -378,4 +398,3 @@ nav.navbar {
   [data-rank=g] { color: hsl(280deg, 80%, 30%); }
   [data-rank=s] { color: hsl(320deg, 80%, 30%); }
 }
-

app/controllers/names_controller.rb

@@ -52,19 +52,17 @@ class NamesController < ApplicationController
   before_action(:authenticate_can_edit_validated!, only: %i[update edit_links])
 
   # GET /names/autocomplete.json?q=Maco
-  # GET /names/autocomplete.json?q=Allo&rank=genus
-  # GET /names/autocomplete.json?q=Pseu&minimum_rank=class
+  # GET /names/autocomplete.json?q=Allo&ranks=genus
+  # GET /names/autocomplete.json?q=Pseu&ranks=domain,phylum,class
   def autocomplete
     name = params[:q].downcase
-    rank = params[:rank]&.downcase
-    minimum_rank = params[:minimum_rank]&.downcase
     @names =
       Name.where('LOWER(name) LIKE ?', "#{name}%")
           .or(Name.where('LOWER(name) LIKE ?', "% #{name}%"))
           .limit(20)
-    @names = @names.where(rank: rank) if rank
-    minimum_ranks = Name.ranks_at_or_above(minimum_rank)
-    @names = @names.where(rank: minimum_ranks) if minimum_ranks
+    if params.key?(:ranks)
+      @names = @names.where(rank: params[:ranks].downcase.split(','))
+    end
     @names = @names.where(redirect: nil)
   end
 

app/controllers/placements_controller.rb

@@ -46,10 +46,11 @@ def update
   def create_or_update(back_action)
     par = params.require(:placement).permit(
       :incertae_sedis, :incertae_sedis_text,
-      :parent, :preferred, :publication
+      :parent, :incertae_sedis_parent, :preferred, :publication
     )
     @placement.incertae_sedis = par[:incertae_sedis].presence
     @placement.incertae_sedis_text = par[:incertae_sedis_text]
+    par[:parent] = par[:incertae_sedis_parent] if @placement.incertae_sedis?
     if @name.placement
       @placement.preferred = par[:preferred] if current_user.curator?
     else
@@ -103,7 +104,8 @@ def create_or_update(back_action)
             old_placement.update!(preferred: false)
           end
           @name.update!(
-            parent: @placement.parent, assigned_in: @placement.publication,
+            parent: @placement.incertae_sedis? ? nil : @placement.parent,
+            assigned_in: @placement.publication,
           )
         end
       rescue
@@ -125,7 +127,7 @@ def prefer
       @name.placement.try(:update!, preferred: false)
       @placement.update!(preferred: true)
       @name.update!(
-        parent: @placement.parent,
+        parent: @placement.incertae_sedis? ? nil : @placement.parent,
         assigned_in: @placement.publication
       )
       ok = true

app/javascript/packs/application.js

@@ -29,4 +29,3 @@ import "packs/network";
 import "packs/styling";
 import "packs/copyable";
 import "channels/index.js";
-

app/javascript/packs/autocomplete.js

@@ -1,14 +1,14 @@
 
 $(document).on("turbolinks:load", function() {
   var eac_options = {
+    adjustWidth: false,
     url: function(phrase) {
       var data = $($(event)[0]["srcElement"]).data();
       var what = data["autocomplete"];
       var url = new URL(what + "/autocomplete.json", ROOT_PATH);
       url.searchParams.set("q", phrase);
-      if(data["rank"]) { url.searchParams.set("rank", data["rank"]); }
-      if(data["minimumRank"]) {
-        url.searchParams.set("minimum_rank", data["minimumRank"]);
+      if(data["ranks"] !== undefined) {
+        url.searchParams.set("ranks", data["ranks"].join(","));
       }
       return url.toString();
     },

app/models/name.rb

@@ -1018,9 +1018,7 @@ def lineage(with_self: false)
   def lineage_parent
     return parent if parent
 
-    if incertae_sedis? && incertae_sedis =~ /Incertae sedis \((.+)\)/
-      self.class.find_by_variants($1)
-    end
+    placement.parent if incertae_sedis?
   end
 
   def type_name_alt_placement
@@ -1486,11 +1484,9 @@ def harmonize_register_and_status
   end
 
   def ensure_consistent_placement
-    placement_incertae_sedis = incertae_sedis
-
-    if parent_id.present? || placement_incertae_sedis.present?
+    if parent_id.present?
       pp = placements.where(
-        parent_id: parent_id, incertae_sedis: placement_incertae_sedis
+        parent_id: parent_id, incertae_sedis: false
       ).first
       if pp.present?
         if pp.preferred?
@@ -1503,10 +1499,12 @@ def ensure_consistent_placement
           Placement.new(
             name_id: id,
             parent_id: parent_id,
-            incertae_sedis: placement_incertae_sedis,
+            incertae_sedis: false,
             preferred: true
           ).save
       end
+    elsif placements.where(preferred: true, incertae_sedis: true).exists?
+      true
     else
       # Conservatively preserve as alternative placement
       placements.update(preferred: false)

app/models/name/quality_checks.rb

@@ -112,15 +112,17 @@ class QcWarning
       inconsistent_parent_rank: {
         message: ->(_w, n) {
           <<~MSG
-            The parent rank (#{n.parent.inferred_rank}) is inconsistent 
+            The parent rank (#{n.placement.parent.inferred_rank}) is inconsistent 
             with the rank of this name (#{n.inferred_rank})
           MSG
         },
         area:    :nomenclature,
         rules:   %w[7a 7b],
-        scope:   ->(_w, n) { n.rank? && n.parent&.rank? },
+        scope:   ->(_w, n) {
+          n.rank? && n.placement&.parent&.rank?
+        },
         failure: ->(_w, n) {
-          n.class.ranks.index(n.rank) != n.class.ranks.index(n.parent.rank) + 1
+          !n.placement.allowed_parent_ranks.include?(n.placement.parent.rank)
         }
       }.merge(@@link_to_edit_parent),
       # - Rules 7c and 7d are implied by the structure of the SeqCode Registry
@@ -141,7 +143,10 @@ class QcWarning
         link_to: ->(_w, n) { [:edit_parent, n] },
         recommendations: %w[7],
         scope:   ->(_w, n) { n.rank? && !n.top_rank? },
-        failure: ->(_w, n) { !n.incertae_sedis? && !n.parent.present? }
+        failure: ->(_w, n) {
+          parent = n.incertae_sedis? ? n.placement.parent : n.parent
+          !parent.present?
+        }
       },
 
       # Section 3. Naming of Taxa

app/models/placement.rb

@@ -5,16 +5,12 @@ class Placement < ApplicationRecord
   )
   belongs_to(:publication, optional: true)
   validates(:name, presence: true)
-  validates(:parent, presence: true, unless: :incertae_sedis?)
+  validates(:parent, presence: true)
 
   has_rich_text(:incertae_sedis_text)
   validates(:incertae_sedis_text, presence: true, if: :incertae_sedis?)
-  validates(:incertae_sedis, presence: true, allow_nil: true)
   validates(
-    :incertae_sedis, absence: {
-      if: :parent,
-      message: 'cannot be declared if the parent taxon is set'
-    }
+    :incertae_sedis, inclusion: { in: [true, false] }
   )
   validates(:preferred, uniqueness: { scope: :name_id, if: :preferred? })
 
@@ -23,7 +19,20 @@ class Placement < ApplicationRecord
   def incertae_sedis_html
     return '' unless incertae_sedis?
 
-    incertae_sedis.gsub(/(incertae sedis)/i, '<i>\\1</i>').html_safe
+    ActionController::Base.helpers.safe_join(
+      ['<i>incertae sedis</i>'.html_safe, (" (#{parent.name})" if parent)].compact
+    )
+  end
+
+  def allowed_parent_ranks(incertae_sedis: incertae_sedis?)
+    rank_index = name&.rank_index
+    return [] unless rank_index && rank_index.positive?
+
+    if incertae_sedis
+      Name.ranks.take(rank_index - 1)
+    else
+      [Name.ranks[rank_index - 1]]
+    end
   end
 
   def downwards?
@@ -36,6 +45,6 @@ def downwards?
   private
 
   def harmonize_name_parent
-    name.update(parent: parent) if preferred
+    name.update(parent: incertae_sedis? ? nil : parent) if preferred
   end
 end

app/models/tutorial/batch.rb

@@ -54,9 +54,11 @@ def param_names
 
           # Deal with foreign keys
           if j['parent'] &&
-               j['parent'] =~ /^incertae sedis( \((Archaea|Bacteria)\))?/
-            j['incertae_sedis'] = j['parent']
-            j['parent'] = nil
+               match = j['parent'].match(
+                 /^incertae sedis( \((Archaea|Bacteria)\))?/
+               )
+            j['incertae_sedis'] = true
+            j['parent'] = match[2]
           end
           j['parent'] &&= Name.new(name: j['parent'])
           if j['nomenclatural_type_type'].to_s.downcase == 'name' &&
@@ -80,7 +82,7 @@ def ephemeral_names
         name_attributes = i.except('parent', 'incertae_sedis')
         placement_attributes = {
           parent: i['parent'],
-          incertae_sedis: i['incertae_sedis'],
+          incertae_sedis: i['incertae_sedis'] || false,
           preferred: true
         }
         if i['incertae_sedis'].present?
@@ -348,7 +350,6 @@ 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']
@@ -357,16 +358,14 @@ def batch_step_01(params, user)
             parent = Name.new(default_pars.merge(name: par['parent'].name))
             parent.save!
           end
-          placement_par = {
-            parent: parent,
-            incertae_sedis: nil
-          }
-        elsif par['incertae_sedis']
-          placement_par = {
-            parent: nil,
-            incertae_sedis: par['incertae_sedis'],
-            incertae_sedis_text: par['description']
-          }
+          name = Name.find_by_variants(par['name'])
+          placement = name.placements.find_or_initialize_by(parent: parent)
+          name.placements.where(preferred: true).where.not(id: placement.id)
+              .find_each { |current| current.update!(preferred: false) }
+          placement.update!(
+            incertae_sedis: par['incertae_sedis'] || false,
+            incertae_sedis_text: par['description'], preferred: true
+          )
         end
 
         # Nomenclatural types
@@ -387,16 +386,7 @@ def batch_step_01(params, user)
           end
         end
 
-        name = Name.find_by_variants(par['name'])
-        name.update!(new_par)
-        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
+        Name.find_by_variants(par['name']).update!(new_par)
       end
 
       # If all is good, go to next step

app/views/dev/autocomplete.html.erb

@@ -26,7 +26,7 @@
       <label for="autocomplete-phylum">Phylum only</label>
       <input id="autocomplete-phylum" class="form-control" type="text"
              value="Pseu" data-behavior="autocomplete"
-             data-autocomplete="names" data-rank="phylum">
+             data-autocomplete="names" data-ranks='["phylum"]'>
     </div>
   </div>
 
@@ -35,15 +35,17 @@
       <label for="autocomplete-class-or-above">Class or above</label>
       <input id="autocomplete-class-or-above" class="form-control" type="text"
              value="Bac" data-behavior="autocomplete"
-             data-autocomplete="names" data-minimum-rank="class">
+             data-autocomplete="names"
+             data-ranks='<%= Name.ranks_at_or_above('class').to_json %>'>
       <small class="form-text text-muted">Domain, phylum, or class.</small>
     </div>
 
     <div class="form-group">
       <label for="autocomplete-genus-or-above">Genus or above</label>
       <input id="autocomplete-genus-or-above" class="form-control" type="text"
              value="Escher" data-behavior="autocomplete"
-             data-autocomplete="names" data-minimum-rank="genus">
+             data-autocomplete="names"
+             data-ranks='<%= Name.ranks_at_or_above('genus').to_json %>'>
       <small class="form-text text-muted">
         Domain through genus; excludes species and subspecies.
       </small>