From d80ea8d7d47171c7eda8e136a341219c99dfae09 Mon Sep 17 00:00:00 2001
From: vangberg <harry@vangberg.name>
Date: Fri, 2 Oct 2026 10:30:27 +0200
Subject: [PATCH 1/2] Track history for PublicationName

---
 app/assets/stylesheets/names.scss             |  4 +
 app/controllers/concerns/filterable.rb        |  2 +-
 .../publication_names_controller.rb           |  4 +-
 app/helpers/names_helper.rb                   | 42 +++++++--
 app/models/concerns/unlinkable.rb             | 15 ++++
 app/models/name.rb                            | 10 ++-
 app/models/name/public_history.rb             | 57 +++++++++---
 app/models/publication.rb                     |  3 +-
 app/models/publication_name.rb                |  3 +
 app/views/names/history.html.erb              | 19 +++-
 app/views/publications/_names.html.erb        |  2 +-
 ...00_add_unlinked_at_to_publication_names.rb |  8 ++
 db/schema.rb                                  |  5 +-
 test/controllers/names/history_test.rb        |  5 +-
 test/helpers/names_helper_test.rb             | 39 ++++++++-
 test/models/name/public_history_test.rb       | 87 +++++++++++++++++++
 16 files changed, 268 insertions(+), 37 deletions(-)
 create mode 100644 app/models/concerns/unlinkable.rb
 create mode 100644 db/migrate/20261002100000_add_unlinked_at_to_publication_names.rb

diff --git a/app/assets/stylesheets/names.scss b/app/assets/stylesheets/names.scss
index e0c46162..620fcf95 100644
--- a/app/assets/stylesheets/names.scss
+++ b/app/assets/stylesheets/names.scss
@@ -43,6 +43,10 @@
     border-top: 0.75rem solid var(--white);
   }
 
+  .name-history-record ~ .name-history-change th {
+    padding-left: 1.5rem;
+  }
+
   .name-history-before,
   .name-history-after {
     white-space: pre-wrap;
diff --git a/app/controllers/concerns/filterable.rb b/app/controllers/concerns/filterable.rb
index 4d3bc2ff..8c372865 100644
--- a/app/controllers/concerns/filterable.rb
+++ b/app/controllers/concerns/filterable.rb
@@ -31,7 +31,7 @@ def apply_sort(query, sort_by: nil, sort_direction: nil)
     # Handle special sorting cases (e.g., 'citations' for Name model)
     case sort_by.to_s.downcase
     when 'citations'
-      query.left_joins(:publication_names).group(:id).order("COUNT(publication_names.id) #{sort_direction.upcase}")
+      query.left_joins(:publication_names).group(:id).order("COUNT(CASE WHEN publication_names.unlinked_at IS NULL THEN publication_names.id END) #{sort_direction.upcase}")
     when 'date'
       # Use validated_at if available, otherwise fall back to created_at
       if query.model.column_names.include?('validated_at')
diff --git a/app/controllers/publication_names_controller.rb b/app/controllers/publication_names_controller.rb
index 73808d7f..19132db7 100644
--- a/app/controllers/publication_names_controller.rb
+++ b/app/controllers/publication_names_controller.rb
@@ -19,7 +19,7 @@ def destroy
       if name.assigned_in? publication
         name.update(assigned_in: nil)
       end
-      @publication_name.destroy
+      @publication_name.unlink!
     end
 
     redirect_to(
@@ -60,7 +60,7 @@ def link_name_commit
   private
     # Use callbacks to share common setup or constraints between actions.
     def set_publication_name
-      @publication_name = PublicationName.find(params[:id])
+      @publication_name = PublicationName.linked.find(params[:id])
     end
 
     def set_publication
diff --git a/app/helpers/names_helper.rb b/app/helpers/names_helper.rb
index fba9f636..b7aaaa24 100644
--- a/app/helpers/names_helper.rb
+++ b/app/helpers/names_helper.rb
@@ -1,15 +1,13 @@
 module NamesHelper
-  def history_values(changes, attribute:)
+  def history_values(changes, attribute:, record_type: 'Name')
     values =
-      case attribute
-      when 'etymology'
-        history_diff_parts(*changes.map { |attributes| Name.new(attributes).full_etymology })
-      when 'proposed_in_id'
-        changes.map { |id| history_publication_reference(id) }
-      when 'status'
-        changes.map { |code| Name.status_hash.dig(code, :name) || code }
+      case record_type
+      when 'PublicationName'
+        history_publication_name_values(changes)
+      when 'Name'
+        history_name_values(changes, attribute)
       else
-        changes.any? { |value| value.is_a?(String) } ? history_diff_parts(*changes) : changes
+        raise ArgumentError, "Unsupported public history record type: #{record_type}"
       end
 
     values.map { |value| safe_join(Array(value)).presence || '—' }
@@ -109,4 +107,30 @@ def name_lineage(name, links: true, last: true, register: nil, visited: [])
 
   private
 
+  def history_name_values(changes, attribute)
+    case attribute
+    when 'etymology'
+      history_diff_parts(*changes.map { |attributes| Name.new(attributes).full_etymology })
+    when 'proposed_in_id'
+      changes.map { |id| history_publication_reference(id) }
+    when 'status'
+      changes.map { |code| Name.status_hash.dig(code, :name) || code }
+    else
+      history_text_values(changes)
+    end
+  end
+
+  def history_publication_name_values(changes)
+    history_text_values(changes).map do |value|
+      case value
+      when true then 'Yes'
+      when false then 'No'
+      else value
+      end
+    end
+  end
+
+  def history_text_values(changes)
+    changes.any? { |value| value.is_a?(String) } ? history_diff_parts(*changes) : changes
+  end
 end
diff --git a/app/models/concerns/unlinkable.rb b/app/models/concerns/unlinkable.rb
new file mode 100644
index 00000000..58e98566
--- /dev/null
+++ b/app/models/concerns/unlinkable.rb
@@ -0,0 +1,15 @@
+module Unlinkable
+  extend ActiveSupport::Concern
+
+  included do
+    scope :linked, -> { where(unlinked_at: nil) }
+  end
+
+  def unlink!
+    update!(unlinked_at: Time.current)
+  end
+
+  def unlinked?
+    unlinked_at.present?
+  end
+end
diff --git a/app/models/name.rb b/app/models/name.rb
index c6a240ff..103f5bba 100644
--- a/app/models/name.rb
+++ b/app/models/name.rb
@@ -1,7 +1,9 @@
 class Name < ApplicationRecord
   has_many(:pseudonyms, dependent: :destroy)
+  # A deleted name no longer needs its publication links, including unlinked ones.
   has_many(:publication_names, dependent: :destroy)
-  has_many(:publications, through: :publication_names)
+  has_many(:publications, -> { merge(PublicationName.linked) },
+           through: :publication_names)
   has_many(
     :name_correspondences, -> { order(:created_at) }, dependent: :destroy
   )
@@ -663,7 +665,7 @@ def hard_to_pronounce?
   end
 
   def publication_names_ordered
-    publication_names.left_joins(:publication).order(journal_date: :desc)
+    publication_names.linked.left_joins(:publication).order(journal_date: :desc)
   end
 
   def citations
@@ -827,7 +829,7 @@ def corrigendum_source
   end
 
   def emended_in
-    publication_names.where(emends: true).map(&:publication)
+    publication_names.linked.where(emends: true).map(&:publication)
   end
 
   def emended_in?(publication)
@@ -835,7 +837,7 @@ def emended_in?(publication)
   end
 
   def not_validly_proposed_in
-    publication_names.where(not_valid_proposal: true).map(&:publication)
+    publication_names.linked.where(not_valid_proposal: true).map(&:publication)
   end
 
   def not_validly_proposed_in?(publication)
diff --git a/app/models/name/public_history.rb b/app/models/name/public_history.rb
index 00bb1040..1c8b7e0e 100644
--- a/app/models/name/public_history.rb
+++ b/app/models/name/public_history.rb
@@ -10,21 +10,39 @@ def initialize(name)
     @name = name
   end
 
-  # Filter before paginating so each page contains public updates only.
+  # Load both histories and filter displayable changes in Ruby before pagination.
   def versions(page:)
-    @name.versions
-         .where(operation: 'update')
-         .where(
-           'EXISTS (SELECT 1 FROM jsonb_object_keys(versions.changeset) AS key WHERE key IN (?))',
-           KEYS
-         )
-         .order(created_at: :desc, id: :desc)
-         .paginate(page: page, per_page: 25)
+    name_versions.or(publication_versions)
+                 .order(created_at: :desc, id: :desc)
+                 .select { |version| changes_for(version).any? }
+                 .paginate(page: page, per_page: 25)
+  end
+
+  def changes_for(version)
+    case version.record_type
+    when 'Name'
+      name_changes_for(version)
+    when 'PublicationName'
+      publication_changes_for(version)
+    else
+      raise ArgumentError, "Unsupported public history record type: #{version.record_type}"
+    end
+  end
+
+  def publication_id_for(version)
+    @publication_ids ||= @name.publication_names.pluck(:id, :publication_id).to_h
+    @publication_ids.fetch(version.record_id)
+  end
+
+  private
+
+  def name_versions
+    @name.versions.where(operation: 'update')
   end
 
   # Ordinary fields keep their [before, after] pairs. Etymology fields become
   # one pair of attribute snapshots for the view to render together.
-  def changes_for(version)
+  def name_changes_for(version)
     changes = version.changeset.slice(*KEYS)
     etymology = changes.extract!(*Name::ETYMOLOGY_COLUMNS)
     if etymology.any?
@@ -35,7 +53,24 @@ def changes_for(version)
     changes
   end
 
-  private
+  def publication_versions
+    Version.where(
+      record_type: 'PublicationName', record_id: @name.publication_names.select(:id)
+    )
+  end
+
+  def publication_changes_for(version)
+    return { 'linked' => [false, true] } if version.operation == 'create'
+    return {} unless version.operation == 'update'
+
+    changes = version.changeset.dup
+    if unlinked_at = changes.delete('unlinked_at')
+      # A nil unlinked_at means the publication is linked.
+      linked = unlinked_at.map(&:nil?)
+      changes = { 'linked' => linked }.merge(changes) unless linked.first == linked.last
+    end
+    changes
+  end
 
   # Include the name because full_etymology derives the :xx particle from its
   # last word. Older versions without a name pair use the current name.
diff --git a/app/models/publication.rb b/app/models/publication.rb
index 5ab374dc..1295cde4 100644
--- a/app/models/publication.rb
+++ b/app/models/publication.rb
@@ -21,7 +21,8 @@ class Publication < ApplicationRecord
   has_many(:publication_names, dependent: :destroy)
   has_many(:authors, through: :publication_authors)
   has_many(:subjects, through: :publication_subjects)
-  has_many(:names, through: :publication_names)
+  has_many(:names, -> { merge(PublicationName.linked) },
+           through: :publication_names)
   has_many(:registers)
   has_many(
     :proposed_names, class_name: 'Name',
diff --git a/app/models/publication_name.rb b/app/models/publication_name.rb
index 4d49c06d..7818ccba 100644
--- a/app/models/publication_name.rb
+++ b/app/models/publication_name.rb
@@ -1,4 +1,7 @@
 class PublicationName < ApplicationRecord
+  include Unlinkable
+  include Versioned
+
   belongs_to(:publication)
   belongs_to(:name)
 
diff --git a/app/views/names/history.html.erb b/app/views/names/history.html.erb
index 23020cb6..94d804e2 100644
--- a/app/views/names/history.html.erb
+++ b/app/views/names/history.html.erb
@@ -18,18 +18,31 @@
       </thead>
       <% @versions.each do |version| %>
         <% changes = @history.changes_for(version) %>
+        <% publication_change = version.record_type == 'PublicationName' %>
         <tbody class="name-history-version" data-version-id="<%= version.id %>">
+          <% if publication_change %>
+            <tr class="name-history-record">
+              <th class="name-history-date" scope="rowgroup" rowspan="<%= changes.size + 1 %>">
+                <time datetime="<%= version.created_at.iso8601 %>">
+                  <%= version.created_at.strftime('%F %H:%M %Z') %>
+                </time>
+              </th>
+              <th colspan="3">
+                Publication: <%= history_publication_reference(@history.publication_id_for(version)) %>
+              </th>
+            </tr>
+          <% end %>
           <% changes.each_with_index do |(attribute, values), index| %>
-            <% before, after = history_values(values, attribute: attribute) %>
+            <% before, after = history_values(values, attribute: attribute, record_type: version.record_type) %>
             <tr class="name-history-change">
-              <% if index.zero? %>
+              <% if index.zero? && !publication_change %>
                 <th class="name-history-date" scope="rowgroup" rowspan="<%= changes.size %>">
                   <time datetime="<%= version.created_at.iso8601 %>">
                     <%= version.created_at.strftime('%F %H:%M %Z') %>
                   </time>
                 </th>
               <% end %>
-              <th scope="row"><%= Name.human_attribute_name(attribute) %></th>
+              <th scope="row"><%= (publication_change ? PublicationName : Name).human_attribute_name(attribute) %></th>
               <td class="name-history-before"><%= before %></td>
               <td class="name-history-after"><%= after %></td>
             </tr>
diff --git a/app/views/publications/_names.html.erb b/app/views/publications/_names.html.erb
index ea6e29be..6ce92fad 100644
--- a/app/views/publications/_names.html.erb
+++ b/app/views/publications/_names.html.erb
@@ -1,4 +1,4 @@
-<% publication.publication_names.each do |publication_name| %>
+<% publication.publication_names.linked.each do |publication_name| %>
   <% name = publication_name.name %>
   <%= link_to(
         name.abbr_name, name, class: 'badge badge-pill badge-primary') %>
diff --git a/db/migrate/20261002100000_add_unlinked_at_to_publication_names.rb b/db/migrate/20261002100000_add_unlinked_at_to_publication_names.rb
new file mode 100644
index 00000000..a47a6af9
--- /dev/null
+++ b/db/migrate/20261002100000_add_unlinked_at_to_publication_names.rb
@@ -0,0 +1,8 @@
+class AddUnlinkedAtToPublicationNames < ActiveRecord::Migration[6.1]
+  def change
+    add_column :publication_names, :unlinked_at, :datetime
+    remove_index :publication_names, column: %i[publication_id name_id], unique: true
+    add_index :publication_names, %i[publication_id name_id],
+              unique: true, where: 'unlinked_at IS NULL'
+  end
+end
diff --git a/db/schema.rb b/db/schema.rb
index e166d71f..3dd352c0 100644
--- a/db/schema.rb
+++ b/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_09_17_100000) do
+ActiveRecord::Schema.define(version: 2026_10_02_100000) do
 
   # These are extensions that must be enabled in order to support this database
   enable_extension "fuzzystrmatch"
@@ -367,8 +367,9 @@
     t.datetime "updated_at", null: false
     t.boolean "emends", default: false
     t.boolean "not_valid_proposal", default: false
+    t.datetime "unlinked_at"
     t.index ["name_id"], name: "index_publication_names_on_name_id"
-    t.index ["publication_id", "name_id"], name: "index_publication_names_on_publication_id_and_name_id", unique: true
+    t.index ["publication_id", "name_id"], name: "index_publication_names_on_publication_id_and_name_id", unique: true, where: "(unlinked_at IS NULL)"
     t.index ["publication_id"], name: "index_publication_names_on_publication_id"
   end
 
diff --git a/test/controllers/names/history_test.rb b/test/controllers/names/history_test.rb
index a8949e5b..c9179177 100644
--- a/test/controllers/names/history_test.rb
+++ b/test/controllers/names/history_test.rb
@@ -4,12 +4,12 @@ class NamesHistoryTest < ActionDispatch::IntegrationTest
   test 'renders public history' do
     name = names(:escherichia_coli)
     name.update!(authority: 'Smith', etymology_xx_description: 'of the colon')
+    PublicationName.create!(name: name, publication: publications(:one))
 
     get history_name_path(name)
 
     assert_response :success
-    assert_select '.name-history-version', count: 1
-    assert_select '.name-history-change', count: 2
+    assert_select '.name-history-version', count: 2
   end
 
   test 'does not reveal private name history' do
@@ -17,6 +17,7 @@ class NamesHistoryTest < ActionDispatch::IntegrationTest
       name: 'E. coli', rank: 'species', status: 5, created_by: users(:contributor)
     )
     name.update!(syllabication: 'co.li')
+    PublicationName.create!(name: name, publication: publications(:one)).unlink!
 
     get history_name_path(name)
 
diff --git a/test/helpers/names_helper_test.rb b/test/helpers/names_helper_test.rb
index 699ab95a..bf2b9aa0 100644
--- a/test/helpers/names_helper_test.rb
+++ b/test/helpers/names_helper_test.rb
@@ -23,7 +23,7 @@ class NamesHelperTest < ActionView::TestCase
     assert_equal 'coli, <ins class="text-success">&amp;</ins> E. coli <ins class="text-success">!</ins>', after
   end
 
-  test 'renders proposed publication changes as citations' do
+  test 'renders publication changes as citations' do
     publication = publications(:one)
     citation = link_to(publication.short_citation, publication)
     assert_equal [citation, '—'],
@@ -31,6 +31,35 @@ class NamesHelperTest < ActionView::TestCase
     assert_equal ['—', citation],
                  history_values([nil, publication.id], attribute: 'proposed_in_id')
   end
+
+  test 'diffs text additions and removals in either record context' do
+    %w[Name PublicationName].each do |record_type|
+      assert_equal ['—', '<ins class="text-success">Smith &amp; Jones</ins>'],
+                   history_values([nil, 'Smith & Jones'], attribute: 'authority', record_type: record_type)
+      assert_equal ['<del class="text-danger">Smith &amp; Jones</del>', '—'],
+                   history_values(['Smith & Jones', nil], attribute: 'authority', record_type: record_type)
+    end
+  end
+
+  test 'formats name status labels without diffing them' do
+    assert_equal ['Draft', 'Submitted'], history_values([5, 10], attribute: 'status')
+    assert_equal ['—', '99'], history_values([nil, 99], attribute: 'status')
+    assert_equal ['5', '10'], history_values(
+      [5, 10], attribute: 'status', record_type: 'PublicationName'
+    )
+  end
+
+  test 'renders publication relationship values in their own record context' do
+    %w[linked emends not_valid_proposal].each do |attribute|
+      assert_equal ['No', 'Yes'], history_values(
+        [false, true], attribute: attribute, record_type: 'PublicationName'
+      )
+      assert_equal ['Yes', 'No'], history_values(
+        [true, false], attribute: attribute, record_type: 'PublicationName'
+      )
+    end
+  end
+
   test 'renders a retained publication id when the publication no longer exists' do
     publication = publications(:no_doi)
     publication.destroy!
@@ -38,4 +67,12 @@ class NamesHelperTest < ActionView::TestCase
     assert_equal ['—', "Publication ##{publication.id} (deleted)"],
                  history_values([nil, publication.id], attribute: 'proposed_in_id')
   end
+
+  test 'preserves nonboolean publication relationship values' do
+    ids = [publications(:one).id, publications(:no_doi).id]
+
+    assert_equal ids.map(&:to_s), history_values(
+      ids, attribute: 'publication_id', record_type: 'PublicationName'
+    )
+  end
 end
diff --git a/test/models/name/public_history_test.rb b/test/models/name/public_history_test.rb
index 544948f4..c36211f1 100644
--- a/test/models/name/public_history_test.rb
+++ b/test/models/name/public_history_test.rb
@@ -28,4 +28,91 @@ class Name::PublicHistoryTest < ActiveSupport::TestCase
     }, @history.changes_for(version))
   end
 
+  test 'combines publication links unlinks and relinks with name updates newest first' do
+    publication = publications(:one)
+    start = Time.zone.local(2026, 10, 1, 12)
+    link = nil
+    travel_to(start) do
+      link = PublicationName.create!(name: @name, publication: publication)
+    end
+    travel_to(start + 1.minute) { @name.update!(authority: 'Smith') }
+    travel_to(start + 2.minutes) { link.unlink! }
+    travel_to(start + 3.minutes) { link.update!(unlinked_at: nil) }
+
+    versions = @history.versions(page: 1)
+
+    assert_equal [
+      { 'linked' => [false, true] },
+      { 'linked' => [true, false] },
+      { 'authority' => [nil, 'Smith'] },
+      { 'linked' => [false, true] }
+    ], versions.map { |version| @history.changes_for(version) }
+    assert_equal [3, 2, 1, 0].map { |minutes| start + minutes.minutes },
+                 versions.map(&:created_at)
+  end
+
+  test 'filters nonpublic changes before paginating the combined history' do
+    link = PublicationName.create!(name: @name, publication: publications(:one))
+    linked_version = link.versions.last
+    link.unlink!
+    unlinked_version = link.versions.last
+    24.times { |index| @name.update!(authority: "Smith #{index}") }
+    @name.update!(gtdb_accession: 'GB_GCA_000005845.2')
+    link.update!(emends: true)
+
+    first_page = @history.versions(page: 1)
+    second_page = @history.versions(page: 2)
+
+    assert_equal 25, first_page.size
+    assert_equal({ 'emends' => [false, true] },
+                 @history.changes_for(first_page.first))
+    assert_equal [unlinked_version, linked_version], second_page
+  end
+
+  test 'identifies the publication for each relationship history including unlinks' do
+    first_link = PublicationName.create!(name: @name, publication: publications(:one))
+    second_link = PublicationName.create!(name: @name, publication: publications(:no_doi))
+    first_link.unlink!
+
+    first_link.versions.each do |version|
+      assert_equal publications(:one).id, @history.publication_id_for(version)
+    end
+    assert_equal publications(:no_doi).id, @history.publication_id_for(second_link.versions.last)
+  end
+
+  test 'shows publication role additions and removals alongside unlink changes' do
+    link = PublicationName.create!(name: @name, publication: publications(:one))
+    link.update!(emends: true, not_valid_proposal: true)
+
+    assert_equal({
+      'emends' => [false, true],
+      'not_valid_proposal' => [false, true]
+    }, @history.changes_for(link.versions.last))
+
+    link.update!(emends: false, not_valid_proposal: false, unlinked_at: Time.current)
+
+    assert_equal({
+      'linked' => [true, false],
+      'emends' => [true, false],
+      'not_valid_proposal' => [true, false]
+    }, @history.changes_for(link.versions.last))
+  end
+
+  test 'omits timestamp-only unlink changes while retaining role changes' do
+    version = Version.new(record_type: 'PublicationName', operation: 'update', changeset: {
+      'unlinked_at' => ['2026-10-01T12:00:00Z', '2026-10-01T12:01:00Z'],
+      'emends' => [false, true]
+    })
+
+    assert_equal({ 'emends' => [false, true] }, @history.changes_for(version))
+  end
+
+  test 'includes publication relationship changes without an attribute allowlist' do
+    values = [publications(:one).id, publications(:no_doi).id]
+    version = Version.new(record_type: 'PublicationName', operation: 'update', changeset: {
+      'publication_id' => values
+    })
+
+    assert_equal({ 'publication_id' => values }, @history.changes_for(version))
+  end
 end

From c43a874073e8101cd05c6322b189f5e822f3985b Mon Sep 17 00:00:00 2001
From: vangberg <harry@vangberg.name>
Date: Thu, 8 Oct 2026 09:20:38 +0200
Subject: [PATCH 2/2] Simplify publication history changes with guard clauses

---
 app/models/name/public_history.rb | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/app/models/name/public_history.rb b/app/models/name/public_history.rb
index 1c8b7e0e..67806069 100644
--- a/app/models/name/public_history.rb
+++ b/app/models/name/public_history.rb
@@ -64,12 +64,14 @@ def publication_changes_for(version)
     return {} unless version.operation == 'update'
 
     changes = version.changeset.dup
-    if unlinked_at = changes.delete('unlinked_at')
-      # A nil unlinked_at means the publication is linked.
-      linked = unlinked_at.map(&:nil?)
-      changes = { 'linked' => linked }.merge(changes) unless linked.first == linked.last
-    end
-    changes
+    unlinked_at = changes.delete('unlinked_at')
+    return changes unless unlinked_at
+
+    # A nil unlinked_at means the publication is linked.
+    linked = unlinked_at.map(&:nil?)
+    return changes if linked.first == linked.last
+
+    { 'linked' => linked }.merge(changes)
   end
 
   # Include the name because full_etymology derives the :xx particle from its