diff --git a/Gemfile b/Gemfile
index 6cc3e289..8b4a2ef4 100644
--- a/Gemfile
+++ b/Gemfile
@@ -14,6 +14,7 @@ gem 'bootstrap', '~> 4.6.2'
gem 'coffee-rails', '~> 5.0'
gem 'csv'
gem 'd3-rails'
+gem 'diff-lcs', '~> 2.0'
gem 'dartsass-sprockets' # Sass engine (required by bootstrap
gem 'devise'
gem 'dkim', '~> 1.1'
diff --git a/Gemfile.lock b/Gemfile.lock
index 9e1cbdb6..27949cdc 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -114,6 +114,7 @@ GEM
railties (>= 4.1.0)
responders
warden (~> 1.2.3)
+ diff-lcs (2.0.0)
dkim (1.1.0)
erb (6.0.4)
erubi (1.13.1)
@@ -487,6 +488,7 @@ DEPENDENCIES
d3-rails
dartsass-sprockets
devise
+ diff-lcs (~> 2.0)
dkim (~> 1.1)
font_awesome5_rails (~> 1.5)
httparty (~> 0.23)
diff --git a/app/assets/stylesheets/names.scss b/app/assets/stylesheets/names.scss
index 6064a6a6..e0c46162 100644
--- a/app/assets/stylesheets/names.scss
+++ b/app/assets/stylesheets/names.scss
@@ -16,3 +16,36 @@
}
}
+.name-history-table {
+ table-layout: fixed;
+ min-width: 42rem;
+
+ thead th:first-child {
+ width: 12rem;
+ }
+
+ thead th:nth-child(2) {
+ width: 10rem;
+ }
+
+ .name-history-date {
+ color: #6c757d;
+ font-size: 0.875rem;
+ font-weight: normal;
+ white-space: nowrap;
+ }
+
+ .name-history-version:nth-of-type(even) {
+ background-color: #f7f8fa;
+ }
+
+ .name-history-version + .name-history-version {
+ border-top: 0.75rem solid var(--white);
+ }
+
+ .name-history-before,
+ .name-history-after {
+ white-space: pre-wrap;
+ overflow-wrap: anywhere;
+ }
+}
diff --git a/app/controllers/names_controller.rb b/app/controllers/names_controller.rb
index a7c26ee3..c9870b03 100644
--- a/app/controllers/names_controller.rb
+++ b/app/controllers/names_controller.rb
@@ -12,7 +12,7 @@ class NamesController < ApplicationController
before_action(
:set_name,
only: %i[
- edit update destroy network wiki
+ edit update destroy network wiki history
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
@@ -215,6 +215,13 @@ def show
end
end
+ # GET /names/1/history
+ def history
+ @history = Name::PublicHistory.new(@name)
+ @versions = @history.versions(page: params[:page])
+ @crumbs = [['Names', names_path], [@name.abbr_name, @name], 'History']
+ end
+
# GET /names/linkout.xml
# GET /names/1/linkout.xml
def linkout
diff --git a/app/helpers/names_helper.rb b/app/helpers/names_helper.rb
index 0fd59158..fba9f636 100644
--- a/app/helpers/names_helper.rb
+++ b/app/helpers/names_helper.rb
@@ -1,4 +1,46 @@
module NamesHelper
+ def history_values(changes, attribute:)
+ 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 }
+ else
+ changes.any? { |value| value.is_a?(String) } ? history_diff_parts(*changes) : changes
+ end
+
+ values.map { |value| safe_join(Array(value)).presence || '—' }
+ end
+
+ def history_publication_reference(publication_id)
+ publication = Publication.find_by(id: publication_id) if publication_id
+ if publication
+ link_to(publication.short_citation, publication)
+ elsif publication_id
+ "Publication ##{publication_id} (deleted)"
+ end
+ end
+
+ def history_diff_parts(before, after)
+ chunks = TextDiff.chunks(before, after)
+
+ before_parts = chunks.filter_map do |unchanged, text, _|
+ next if text.empty?
+
+ unchanged ? text : content_tag(:del, text, class: 'text-danger')
+ end
+ after_parts = chunks.filter_map do |unchanged, _, text|
+ next if text.empty?
+
+ unchanged ? text : content_tag(:ins, text, class: 'text-success')
+ end
+
+ [before_parts, after_parts]
+ end
+
def link_to_name_type(name)
if name.type_is_name?
if name.type_name
@@ -64,4 +106,7 @@ def name_lineage(name, links: true, last: true, register: nil, visited: [])
out.inject(:+)
end
+
+ private
+
end
diff --git a/app/models/concerns/versioned.rb b/app/models/concerns/versioned.rb
new file mode 100644
index 00000000..d0a8ed37
--- /dev/null
+++ b/app/models/concerns/versioned.rb
@@ -0,0 +1,62 @@
+module Versioned
+ extend ActiveSupport::Concern
+
+ included do
+ has_many :versions, as: :record
+ class_attribute :versioned_attribute_sets, default: []
+
+ after_create :record_create_version
+ after_update :record_update_version
+ after_destroy :record_delete_version
+ end
+
+ class_methods do
+ # Changing any member records before/after values for every member.
+ def versioned_together(*attributes)
+ self.versioned_attribute_sets = versioned_attribute_sets + [attributes.map(&:to_s)]
+ end
+ end
+
+ private
+
+ def record_create_version
+ versions.create!(operation: 'create', changeset: {})
+ end
+
+ def record_update_version
+ changeset = versioned_changes
+ versions.create!(operation: 'update', changeset: changeset) if changeset.any?
+ end
+
+ def record_delete_version
+ # The owner is already destroyed, so create directly rather than through
+ # its association. Deletion records only the event and retains history.
+ Version.create!(record: self, operation: 'delete', changeset: {})
+ end
+
+ # An update changeset maps each changed attribute to [before, after], e.g.
+ # { 'syllabication' => [nil, 'co.li'] } for E. coli.
+ # Create and delete versions have an empty changeset; timestamps are omitted.
+ def versioned_changes
+ changeset = saved_changes.except('created_at', 'updated_at')
+
+ changed_columns = changeset.keys
+ self.class.versioned_attribute_sets.each do |columns|
+ changeset.merge!(versioned_together_changes(columns, changed_columns))
+ end
+ changeset
+ end
+
+ # If any listed column changed, include each member with a value as an
+ # ordinary [before, after] pair, including unchanged columns such as language:
+ # { 'etymology_xx_lang' => ['N.L.', 'N.L.'],
+ # 'etymology_xx_description' => ['of the colon', 'from the colon'] }.
+ def versioned_together_changes(columns, changed_columns)
+ return {} if (changed_columns & columns).empty?
+
+ columns.filter_map do |column|
+ values = [attribute_before_last_save(column), self[column]]
+ [column, values] unless values == [nil, nil]
+ end.to_h
+ end
+end
diff --git a/app/models/name.rb b/app/models/name.rb
index 9fef19ca..c6a240ff 100644
--- a/app/models/name.rb
+++ b/app/models/name.rb
@@ -147,6 +147,10 @@ class Name < ApplicationRecord
include Name::Wiki
include Name::FuzzySearch
include TypeMaterial
+ include Versioned
+
+ ETYMOLOGY_COLUMNS = column_names.grep(/\Aetymology_/).freeze
+ versioned_together(:name, *ETYMOLOGY_COLUMNS)
attr_accessor :only_display
attr_accessor :nomenclatural_type_entry
diff --git a/app/models/name/public_history.rb b/app/models/name/public_history.rb
new file mode 100644
index 00000000..00bb1040
--- /dev/null
+++ b/app/models/name/public_history.rb
@@ -0,0 +1,52 @@
+class Name::PublicHistory
+ # Only these recorded attributes appear in the public history.
+ KEYS = %w[
+ name rank syllabication status priority_date authority
+ nomenclatural_status taxonomic_status proposal_kind corrigendum_from
+ type_material type_accession proposed_in_id
+ ].concat(Name::ETYMOLOGY_COLUMNS).freeze
+
+ def initialize(name)
+ @name = name
+ end
+
+ # Filter before paginating so each page contains public updates only.
+ 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)
+ 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)
+ changes = version.changeset.slice(*KEYS)
+ etymology = changes.extract!(*Name::ETYMOLOGY_COLUMNS)
+ if etymology.any?
+ changes['etymology'] = etymology_snapshots(etymology, changes['name'])
+ end
+ # versioned_together records unchanged companion values too.
+ changes.reject! { |_, values| values.first == values.last }
+ changes
+ end
+
+ private
+
+ # Include the name because full_etymology derives the :xx particle from its
+ # last word. Older versions without a name pair use the current name.
+ def etymology_snapshots(etymology, names)
+ before_name, after_name = names || [@name.name, @name.name]
+ before_attributes = etymology.transform_values(&:first)
+ after_attributes = etymology.transform_values(&:last)
+
+ [
+ before_attributes.merge('name' => before_name),
+ after_attributes.merge('name' => after_name)
+ ]
+ end
+end
diff --git a/app/models/version.rb b/app/models/version.rb
new file mode 100644
index 00000000..588d1a2a
--- /dev/null
+++ b/app/models/version.rb
@@ -0,0 +1,3 @@
+class Version < ApplicationRecord
+ belongs_to :record, polymorphic: true, optional: true
+end
diff --git a/app/views/names/_title.html.erb b/app/views/names/_title.html.erb
index 636bf2e2..b85062bb 100644
--- a/app/views/names/_title.html.erb
+++ b/app/views/names/_title.html.erb
@@ -18,6 +18,7 @@
%>
<%=
download_buttons([
+ [history_name_path(@name), 'history', 'History'],
[name_url(@name, format: :json), 'file-code', 'JSON'],
[name_url(@name, format: :pdf), 'file-pdf', 'PDF'],
observe
@@ -78,4 +79,3 @@
<% end %>
-
diff --git a/app/views/names/history.html.erb b/app/views/names/history.html.erb
new file mode 100644
index 00000000..23020cb6
--- /dev/null
+++ b/app/views/names/history.html.erb
@@ -0,0 +1,43 @@
+<% provide(:title, "History of #{@name.abbr_name_raw}") %>
+
+History of <%= @name.name_html %>
+<%= link_to('Back to name', @name) %>
+
+<% if @versions.empty? %>
+ No history has been recorded for this name.
+<% else %>
+
+
+
+
+ | Date |
+ Attribute |
+ Before |
+ After |
+
+
+ <% @versions.each do |version| %>
+ <% changes = @history.changes_for(version) %>
+
+ <% changes.each_with_index do |(attribute, values), index| %>
+ <% before, after = history_values(values, attribute: attribute) %>
+
+ <% if index.zero? %>
+ |
+
+ |
+ <% end %>
+ <%= Name.human_attribute_name(attribute) %> |
+ <%= before %> |
+ <%= after %> |
+
+ <% end %>
+
+ <% end %>
+
+
of the colon', before
+ assert_equal 'coli, from the colon', after
+ end
+
+ test 'keeps distant edits separate and escapes their content' do
+ changes = [
+ { name: 'E. coli', etymology_xx_description: '< E. coli >' },
+ { name: 'E. coli', etymology_xx_description: '& E. coli !' }
+ ]
+ before, after = history_values(changes, attribute: 'etymology')
+
+ assert_equal 'coli, < E. coli >', before
+ assert_equal 'coli, & E. coli !', after
+ end
+
+ test 'renders proposed publication changes as citations' do
+ publication = publications(:one)
+ citation = link_to(publication.short_citation, publication)
+ assert_equal [citation, '—'],
+ history_values([publication.id, nil], attribute: 'proposed_in_id')
+ assert_equal ['—', citation],
+ history_values([nil, publication.id], attribute: 'proposed_in_id')
+ end
+ test 'renders a retained publication id when the publication no longer exists' do
+ publication = publications(:no_doi)
+ publication.destroy!
+
+ assert_equal ['—', "Publication ##{publication.id} (deleted)"],
+ history_values([nil, publication.id], attribute: 'proposed_in_id')
+ end
+end
diff --git a/test/lib/text_diff_test.rb b/test/lib/text_diff_test.rb
new file mode 100644
index 00000000..c31c04dc
--- /dev/null
+++ b/test/lib/text_diff_test.rb
@@ -0,0 +1,39 @@
+require 'minitest/autorun'
+require_relative '../../lib/text_diff'
+
+class TextDiffTest < Minitest::Test
+ def test_groups_nearby_edits_and_preserves_surrounding_text
+ assert_equal [
+ [true, 'E. coli: ', 'E. coli: '],
+ [false, 'of', 'from'],
+ [true, ' the colon', ' the colon']
+ ], TextDiff.chunks('E. coli: of the colon', 'E. coli: from the colon')
+ end
+
+ def test_keeps_distant_edits_separate
+ assert_equal [
+ [false, '<', '&'],
+ [true, ' E. coli ', ' E. coli '],
+ [false, '>', '!']
+ ], TextDiff.chunks('< E. coli >', '& E. coli !')
+ end
+
+ def test_represents_additions_and_removals_with_an_empty_side
+ assert_equal [[true, 'E. coli', 'E. coli'], [false, '', ' strain']],
+ TextDiff.chunks('E. coli', 'E. coli strain')
+ assert_equal [[true, 'E. coli', 'E. coli'], [false, ' strain', '']],
+ TextDiff.chunks('E. coli strain', 'E. coli')
+ end
+
+ def test_handles_empty_and_unchanged_text
+ assert_equal [], TextDiff.chunks(nil, '')
+ assert_equal [[true, 'E. coli', 'E. coli']], TextDiff.chunks('E. coli', 'E. coli')
+ end
+
+ def test_preserves_unicode_graphemes
+ assert_equal [[true, 'M', 'M'], [false, 'ü', 'ö'], [true, 'ller', 'ller']],
+ TextDiff.chunks('Müller', 'Möller')
+ assert_equal [[true, 'E. coli: ', 'E. coli: '], [false, "e\u0301", 'ö']],
+ TextDiff.chunks("E. coli: e\u0301", 'E. coli: ö')
+ end
+end
diff --git a/test/models/name/public_history_test.rb b/test/models/name/public_history_test.rb
new file mode 100644
index 00000000..544948f4
--- /dev/null
+++ b/test/models/name/public_history_test.rb
@@ -0,0 +1,31 @@
+require 'test_helper'
+
+class Name::PublicHistoryTest < ActiveSupport::TestCase
+ setup do
+ @name = names(:escherichia_coli)
+ @history = Name::PublicHistory.new(@name)
+ end
+
+ test 'keeps public changes and groups etymology snapshots without unchanged companions' do
+ version = Version.new(record_type: 'Name', changeset: {
+ 'name' => ['E. coli', 'E. coli'],
+ 'authority' => [nil, 'Smith'],
+ 'proposed_in_id' => [nil, publications(:one).id],
+ 'gtdb_accession' => [nil, 'GB_GCA_000005845.2'],
+ 'etymology_xx_lang' => ['N.L.', 'N.L.'],
+ 'etymology_xx_description' => ['of the colon', 'from the colon']
+ })
+
+ assert_equal({
+ 'authority' => [nil, 'Smith'],
+ 'proposed_in_id' => [nil, publications(:one).id],
+ 'etymology' => [
+ { 'name' => 'E. coli', 'etymology_xx_lang' => 'N.L.',
+ 'etymology_xx_description' => 'of the colon' },
+ { 'name' => 'E. coli', 'etymology_xx_lang' => 'N.L.',
+ 'etymology_xx_description' => 'from the colon' }
+ ]
+ }, @history.changes_for(version))
+ end
+
+end
diff --git a/test/models/name/versioned_test.rb b/test/models/name/versioned_test.rb
new file mode 100644
index 00000000..f1c18178
--- /dev/null
+++ b/test/models/name/versioned_test.rb
@@ -0,0 +1,92 @@
+require 'test_helper'
+
+class Name::VersionedTest < ActiveSupport::TestCase
+ setup do
+ @name = Name.new(name: 'E. coli', rank: 'species')
+ end
+
+ test 'creating a name records an empty changeset' do
+ assert_difference -> { @name.versions.count } do
+ @name.save!
+ end
+
+ version = @name.versions.last
+ assert_equal 'create', version.operation
+ assert_empty version.changeset
+ end
+
+ test 'updating a name records only changed attributes' do
+ @name.save!
+
+ assert_difference -> { @name.versions.count } do
+ @name.update!(syllabication: 'co.li')
+ end
+
+ version = @name.versions.last
+ assert_equal 'update', version.operation
+ assert_equal [nil, 'co.li'], version.changeset['syllabication']
+ assert_equal %w[syllabication], version.changeset.keys
+ end
+
+ test 'updating only timestamps does not add a version' do
+ @name.save!
+
+ assert_no_difference -> { @name.versions.count } do
+ @name.update!(created_at: 1.day.ago, updated_at: 1.hour.ago)
+ end
+ end
+
+ test 'changing an etymology description snapshots valued etymology attributes' do
+ @name.assign_attributes(
+ etymology_xx_lang: 'N.L.', etymology_xx_description: 'of the colon'
+ )
+ @name.save!
+
+ @name.update!(etymology_xx_description: 'from the colon')
+
+ changeset = @name.versions.last.changeset
+ assert_equal %w[etymology_xx_description etymology_xx_lang name], changeset.keys.sort
+ assert_equal ['of the colon', 'from the colon'], changeset['etymology_xx_description']
+ assert_equal ['N.L.', 'N.L.'], changeset['etymology_xx_lang']
+ assert_equal ['E. coli', 'E. coli'], changeset['name']
+ end
+
+ test 'saving an unchanged name does not add a version' do
+ @name.save!
+
+ assert_no_difference -> { @name.versions.count } do
+ @name.save!
+ end
+ end
+
+ test 'deleting a name records an empty changeset' do
+ @name.save!
+ versions = Version.where(record: @name)
+
+ assert_difference -> { versions.count } do
+ @name.destroy!
+ end
+
+ version = versions.last
+ assert_equal 'delete', version.operation
+ assert_empty version.changeset
+ end
+
+ test 'deleting a name retains its history' do
+ @name.save!
+ version = @name.versions.last
+
+ @name.destroy!
+
+ assert Version.exists?(version.id)
+ end
+
+ test 'versions roll back with the name' do
+ assert_no_difference -> { Version.count } do
+ Name.transaction do
+ @name.save!
+ raise ActiveRecord::Rollback
+ end
+ end
+ end
+end