New wiki source page for names

app/controllers/names_controller.rb

@@ -3,7 +3,7 @@ class NamesController < ApplicationController
   before_action(
     :set_name,
     only: %i[
-      show edit update destroy network
+      show edit update destroy network wiki
       proposed_in not_validly_proposed_in emended_in assigned_in
       corrigendum_in corrigendum_orphan corrigendum
       edit_description edit_rank edit_notes edit_etymology edit_links edit_type
@@ -15,10 +15,10 @@ class NamesController < ApplicationController
   before_action(
     :authenticate_can_edit!,
     only: %i[
-      edit update destroy
+      edit destroy
       proposed_in not_validly_proposed_in emended_in assigned_in
       corrigendum_in corrigendum_orphan corrigendum
-      edit_description edit_rank edit_notes edit_etymology edit_links edit_type
+      edit_description edit_rank edit_notes edit_etymology edit_type
       autofill_etymology edit_parent
     ]
   )
@@ -35,6 +35,7 @@ class NamesController < ApplicationController
     ]
   )
   before_action(:authenticate_user!, only: %i[observe unobserve observing])
+  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
@@ -223,6 +224,11 @@ def network
     end
   end
 
+  # GET /names/1/wiki
+  def wiki
+    @crumbs = [['Names', names_path], [@name.name_html, @name], 'Wiki source']
+  end
+
   # GET /names/new
   def new
     @name = Name.new
@@ -505,29 +511,42 @@ def set_tutorial
     def authenticate_owner_or_curator!
       unless current_user.try(:curator?) || @name.user?(current_user)
         flash[:alert] = 'User is not the owner of the name'
-        redirect_to(root_path)
+        redirect_to(@name)
+      end
+    end
+
+    def authenticate_can_edit_validated!
+      unless @name.can_edit_validated?(current_user)
+        flash[:alert] = 'User cannot edit this aspect of the name'
+        redirect_to(@name)
       end
     end
 
     def authenticate_can_edit!
       unless @name.can_edit?(current_user)
         flash[:alert] = 'User cannot edit name'
-        redirect_to(root_path)
+        redirect_to(@name)
       end
     end
 
     # Never trust parameters from the scary internet, only allow the white list
     # through
     def name_params
       @name_params ||=
-        params.require(:name)
-          .permit(
-            :name, :rank, :description, :notes, :ncbi_taxonomy, :lpsn_url,
-            :gtdb_accession, :algaebase_species, :algaebase_taxonomy,
+        @name.can_edit?(current_user) ?
+          params.require(:name).permit(
+            :name, :rank, :description, :notes,
+            :ncbi_taxonomy, :lpsn_url, :gtdb_accession,
+            :algaebase_species, :algaebase_taxonomy,
             :syllabication, :syllabication_reviewed,
             :type_material, :type_accession, :etymology_text, :register,
             :genome_strain,
             *etymology_pars
+          ) :
+          params.require(:name).permit(
+            :notes,
+            :ncbi_taxonomy, :lpsn_url, :gtdb_accession,
+            :algaebase_species, :algaebase_taxonomy
           )
     end
 

app/controllers/placements_controller.rb

@@ -171,7 +171,7 @@ def set_name
   end
 
   def authenticate_can_edit!
-    unless @name.can_edit_placements?(current_user)
+    unless @name.can_edit_validated?(current_user)
       flash[:alert] = 'User cannot edit name placements'
       redirect_to(@name)
     end

app/controllers/pseudonyms_controller.rb

@@ -70,7 +70,7 @@ def set_name
     end
 
     def authenticate_can_edit!
-      unless @name&.can_edit_placements?(current_user)
+      unless @name&.can_edit_validated?(current_user)
         flash[:alert] = 'User cannot edit pseudonyms'
         redirect_to(root_path)
       end

app/models/name.rb

@@ -158,6 +158,48 @@ def rank_suffixes
       { phylum: 'ota', class: 'ia', order: 'ales', family: 'aceae' }
     end
 
+    def rank_variant(rank, opts = {})
+      list =
+        if opts[:abbr]
+            {
+              domain: 'dom.',     kingdom: 'regn.',    phylum: 'phy.',
+              class:  'classis',  order:   'ord.',     family: 'fam.',
+              genus:  'gen.',     species: 'sp.',      subspecies: 'subsp.'
+            }
+        elsif opts[:latin]
+          if opts[:plural]
+            {
+              domain: 'dominia',  kingdom: 'regna',    phylum: 'phyla',
+              class:  'classis',  order:   'ordines',  family: 'familiae',
+              genus:  'genera',   species: 'species',  subspecies: 'subspecies'
+            }
+          else
+            {
+              domain: 'dominium', kingdom: 'regnum',   phylum: 'phylum',
+              class:  'classes',  order:   'ordo',     family: 'familia',
+              genus:  'genus',    species: 'species',  subspecies: 'subspecies'
+            }
+          end
+        else
+          if opts[:plural]
+            {
+              domain: 'domains',  kingdom: 'kingdoms', phylum: 'phyla',
+              class:  'classes',  order:   'orders',   family: 'family',
+              genus:  'genera',   species: 'species',  subspecies: 'subspecies'
+            }
+          else
+            {
+              domain: 'domain',   kingdom: 'kingdom',  phylum: 'phylum',
+              class:  'class',    order:   'order',    family: 'families',
+              genus:  'genus',    species: 'species',  subspecies: 'subspecies'
+            }
+          end
+        end
+      return list unless rank.present?
+      var = list[rank.to_s.downcase.to_sym]
+      opts[:title] ? var.titleize : var
+    end
+
     def rank_regexps
       Hash[rank_suffixes.map { |k, v| [k, /#{v}$/] }]
     end
@@ -454,6 +496,13 @@ def name_html(name = nil, assume_valid = false)
     end
   end
 
+  def name_wiki(opts = {})
+    y = base_name
+    y = "[[#{y}]]" if opts[:link]
+    y = "''Candidatus'' #{y}" if !opts[:no_candidatus] && candidatus?
+    validated? ? "''#{y}''" : "\"#{y}\""
+  end
+
   def abbr_corr_name
     abbr_name(corrigendum_from)
   end
@@ -469,7 +518,7 @@ def formal_html
     if not_validly_proposed_in.any?
       y += ' (ex'
       y += not_validly_proposed_in
-             .map { |i| " #{sanitize(i.short_citation)}" }.join(';')
+             .map { |i| " #{sanitize(i.short_citation)}" }.join('; ')
       y += ')'
     end
     if authority || proposed_in
@@ -489,6 +538,26 @@ def formal_txt
     sanitize(formal_html.gsub(/&#822[01];/, "'"))
   end
 
+  def formal_wiki
+    y = name_wiki
+    y += ' corrig.' if corrigendum_from?
+    if not_validly_proposed_in.any?
+      y += ' (ex'
+      y += not_validly_proposed_in
+             .map { |i| " #{sanitize(i.short_citation(:wikispecies))}" }
+             .join('; ')
+      y += ')'
+    end
+    if authority || proposed_in
+      y += " #{sanitize(authority || proposed_in.short_citation(:wikispecies))}"
+    end
+    if emended_in.any?
+      cit = emended_in.map { |p| p.short_citation(:wikispecies) }.join('; ')
+      y += " emend. #{cit}"
+    end
+    sanitize(y)
+  end
+
   def display(html = true)
     html ? name_html : name
   end
@@ -586,6 +655,15 @@ def algaebase_url
     nil
   end
 
+  def edit_wikispecies_page_link
+    'https://species.wikimedia.org/w/index.php?title=%s&action=edit' % base_name
+  end
+
+  def edit_wikispecies_template_link
+    'https://species.wikimedia.org/w/index.php?title=Template:%s&action=edit'
+      % base_name
+  end
+
   def ncbi_taxonomy_url
     return unless ncbi_taxonomy?
 
@@ -663,7 +741,7 @@ def can_edit?(user)
     false
   end 
 
-  def can_edit_placements?(user)
+  def can_edit_validated?(user)
     can_edit?(user) || user.try(:curator?)
   end
 
@@ -967,6 +1045,14 @@ def lineage_find(rank)
     lineage.find { |par| par.rank == rank.to_s }
   end
 
+  def rank_above
+    self.class.ranks[self.class.ranks.index(inferred_rank) - 1]
+  end
+
+  def rank_below
+    self.class.ranks[self.class.ranks.index(inferred_rank) + 1]
+  end
+
   def propose_lineage_name(rank)
     return name if rank.to_s == inferred_rank
     return if above_rank?(rank)

app/models/publication.rb

@@ -174,19 +174,22 @@ def query_crossref(query)
 
   end
 
-  def authors_et_al
+  def authors_et_al(format = :text)
     family = authors.pluck(:family) # To reduce SQL requests
-    if family.empty?
-      'Anonymous'
-    elsif family.count < 3
-      family.join(', ')
-    else
-      family.first + ' et al.'
-    end
+    family.map! { |a| "{{a|#{a}}}" } if format == :wikispecies
+    y =
+      if family.empty?
+        'Anonymous'
+      elsif family.count < 3
+        family.join(', ')
+      else
+        family.first + ' et al.'
+      end
+    format == :html ? ERB::Util.h(y) : y
   end
 
   def authors_et_al_html
-    ERB::Util.h(authors_et_al)
+    authors_et_al(:html)
   end
 
   def clean_abstract
@@ -195,8 +198,8 @@ def clean_abstract
     end
   end
 
-  def short_citation
-    "#{authors_et_al}, #{journal_date.year}"
+  def short_citation(format = :text)
+    "#{authors_et_al(format)}, #{journal_date.year}"
   end
 
   def citation