Module: TaxonNamesHelper

Defined in:
app/helpers/taxon_names_helper.rb

Constant Summary collapse

VALID_MARK =

checkmark

'✓'.html_safe.freeze
INVALID_MARK = 
'❌'.html_safe.freeze
COMBINATION_MARK = 
'[c]'.freeze

Instance Method Summary collapse

Instance Method Details



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# File 'app/helpers/taxon_names_helper.rb', line 355

def ancestor_browse_taxon_name_link(taxon_name, path = :browse_nomenclature_task_path)
  text = 'Up'
  if taxon_name.ancestors.any?
    a = taxon_name.ancestors.first.metamorphosize
    text = object_tag(a)
    link_to(content_tag(:span, text, data: {icon: 'arrow-up'}, class: 'small-icon'), taxon_name_link_path(a, path), class: 'navigation-item', data: {arrow: 'ancestor'})
  else
    content_tag(:div, content_tag(:span, text, class: 'small-icon', data: {icon: 'arrow-up'}), class: 'navigation-item disable')
  end
end

#author_chart_data(author_data) ⇒ Hash

Format author data for Chartkick column chart

Parameters:

  • author_data (Hash) —
    • hash of authors with year data, keyed by person_id

Returns:

  • (Hash) —
    • formatted data for chartkick


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# File 'app/helpers/taxon_names_helper.rb', line 769

def author_chart_data(author_data)
  authors_per_year = {}

  # Count unique authors per year
  author_data.each do |person_id, author_info|
    author_info[:years].each_key do |year|
      authors_per_year[year] = (authors_per_year[year] || 0) + 1
    end
  end

  # Return single series of unique author counts
  {
    data: [
      { name: 'Unique Authors', data: authors_per_year }
    ]
  }
end

#author_coauthorship_data(taxon_names) ⇒ Hash

Calculate co-authorship relationships for Sankey diagram

Parameters:

  • taxon_names (ActiveRecord::Relation) —
    • filtered taxon names

Returns:

  • (Hash) —
    • nodes and links for Sankey diagram


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# File 'app/helpers/taxon_names_helper.rb', line 833

def author_coauthorship_data(taxon_names)
  coauthorship_counts = {}
  author_names = {}

  # Find all taxon names with multiple authors
  taxon_names.left_joins(:taxon_name_authors).find_each do |taxon_name|
    authors = taxon_name.taxon_name_authors.to_a
    next if authors.length < 2

    # Store author names
    authors.each { |author| author_names[author.id] = author.cached }

    # Count co-authorships (combinations of authors on same taxon name)
    authors.combination(2).each do |author1, author2|
      # Create consistent ordering for the pair
      source_id, target_id = [author1.id, author2.id].sort
      key = "#{source_id}-#{target_id}"
      coauthorship_counts[key] ||= { source_id: source_id, target_id: target_id, count: 0 }
      coauthorship_counts[key][:count] += 1
    end
  end

  # Only include authors that have links
  linked_author_ids = coauthorship_counts.values.flat_map { |link| [link[:source_id], link[:target_id]] }.uniq
  nodes_data = author_names.select { |id, name| linked_author_ids.include?(id) }

  # Create node array with indices for d3-sankey
  nodes = nodes_data.map.with_index { |(id, name), index| { id: index, name: name, person_id: id } }

  # Create id to index mapping
  id_to_index = {}
  nodes.each { |node| id_to_index[node[:person_id]] = node[:id] }

  # Convert links to use node indices
  links = coauthorship_counts.values.map do |link|
    {
      source: id_to_index[link[:source_id]],
      target: id_to_index[link[:target_id]],
      value: link[:count]
    }
  end

  {
    nodes: nodes,
    links: links
  }
end

#author_individual_chart_data(author_years) ⇒ Array

Format individual author data for Chartkick column chart Scopes to min/max year observed per author

Parameters:

  • author_years (Hash) —
    • hash of year data for a single author

Returns:

  • (Array) —
    • formatted data for chartkick


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# File 'app/helpers/taxon_names_helper.rb', line 791

def author_individual_chart_data(author_years)
  return { data: [], width: '0px' } if author_years.empty?

  valid_data = {}
  invalid_data = {}

  years = author_years.keys.reject { |y| y == 'Unknown' }.sort
  min_year = years.min
  max_year = years.max

  if min_year && max_year
    (min_year..max_year).each do |year|
      if author_years[year]
        valid_data[year] = author_years[year][:valid] || 0
        invalid_data[year] = author_years[year][:invalid] || 0
      else
        valid_data[year] = 0
        invalid_data[year] = 0
      end
    end
  end

  if author_years['Unknown']
    valid_data['Unknown'] = author_years['Unknown'][:valid] || 0
    invalid_data['Unknown'] = author_years['Unknown'][:invalid] || 0
  end

  year_span = (max_year.to_i - min_year.to_i)
  chart_width = [120 + year_span * 20, 800].min

  {
    data: [
      { name: 'Valid', data: valid_data },
      { name: 'Invalid', data: invalid_data }
    ],
    width: "#{chart_width}px"
  }
end

#cached_classified_as_tag(taxon_name) ⇒ Object 



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# File 'app/helpers/taxon_names_helper.rb', line 253

def cached_classified_as_tag(taxon_name)
  taxon_name.cached_classified_as ? taxon_name.cached_classified_as.strip.html_safe : ''
end

#current_author_year(taxon_name) ⇒ String

Returns:

  • (String) 


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# File 'app/helpers/taxon_names_helper.rb', line 142

def current_author_year(taxon_name)
  return nil if taxon_name.nil? || taxon_name.cached_author_year.nil?
  taxon_name.cached_author_year
end

#defined_full_original_taxon_name_tag(taxon_name) ⇒ String?

!! This is used in taxon_name attributes now! TODO: Refactor our logic for display contexts and value contexts to better reflect presence of data vs. utility of report.

Returns:

  • (String, nil) —

    if no cached_original_combination is defined return nothing



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# File 'app/helpers/taxon_names_helper.rb', line 120

def defined_full_original_taxon_name_tag(taxon_name)
  return nil if taxon_name.nil?  || taxon_name.cached_original_combination_html.blank?
  full_original_taxon_name_tag(taxon_name)
end

#descendant_browse_taxon_name_link(taxon_name, path = :browse_nomenclature_task_path) ⇒ Object 



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# File 'app/helpers/taxon_names_helper.rb', line 366

def descendant_browse_taxon_name_link(taxon_name, path = :browse_nomenclature_task_path)
  text = 'Down'
  if taxon_name.descendants.unscope(:order).any?
    a = taxon_name.descendants.first.metamorphosize
    text = taxon_name_tag(a)
    link_to(content_tag(:span, text, data: {icon: 'arrow-down'}, class: 'small-icon'), taxon_name_link_path(a, path), class: 'navigation-item', data: {arrow: 'descendant'})
  else
    content_tag(:div, content_tag(:span, text, class: 'small-icon', data: {icon: 'arrow-down'}), class: 'navigation-item disable')
  end
end

#document_names_per_year(names) ⇒ Object 



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# File 'app/helpers/taxon_names_helper.rb', line 645

def document_names_per_year(names)
  taxon_names_per_year(
    taxon_names_by_year_count(names)
  )
end

#edit_original_combination_task_link(taxon_name) ⇒ Object 



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# File 'app/helpers/taxon_names_helper.rb', line 307

def edit_original_combination_task_link(taxon_name)
  link_to('Edit original combination', edit_protonym_original_combination_task_path(taxon_name)) if GENUS_AND_SPECIES_RANK_NAMES.include?(taxon_name.rank_string)
end

#edit_taxon_name_link(taxon_name, target: nil) ⇒ Object 



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# File 'app/helpers/taxon_names_helper.rb', line 322

def edit_taxon_name_link(taxon_name, target: nil)
  i = {'Combination': :combination, 'Protonym': :taxon_name}[taxon_name.type.to_sym]
  t = taxon_name.metamorphosize
  icon = content_tag(:span, '', data: { icon: 'edit' }, class: 'small-icon')

  case target
  when :edit_task
    path = case i
           when :taxon_name
             new_taxon_name_task_path(taxon_name_id: t.id)
           when :combination
             new_combination_task_path(taxon_name_id: t.id, literal: URI.encode_www_form_component(t.cached)) # only spaces should be an issue
           end

    link_to(safe_join([icon, 'Edit (task)'], ''), path, class: 'navigation-item', 'data-task' => 'new_taxon_name')
  else
    link_to(safe_join([icon, 'Edit'], ''), send("edit_#{i}_path}", taxon_name.metamorphosize), 'class' => 'navigation-item')
  end
end

#edit_taxon_name_path_string(taxon_name) ⇒ Object

See #edit_object_path_string in navigation_helper.rb



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# File 'app/helpers/taxon_names_helper.rb', line 312

def edit_taxon_name_path_string(taxon_name)
  if taxon_name.type == 'Protonym'
    'edit_taxon_name_path'
  elsif taxon_name.type == 'Combination'
    'edit_combination_path'
  else
    nil
  end
end

#full_original_taxon_name_label(taxon_name) ⇒ String

Returns the name in original combination, with author year, without HTML.

Returns:

  • (String) —

    the name in original combination, with author year, without HTML



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# File 'app/helpers/taxon_names_helper.rb', line 127

def full_original_taxon_name_label(taxon_name)
  return nil if taxon_name.nil? || taxon_name.cached_original_combination.nil?
  [ taxon_name.cached_original_combination,
    taxon_name.original_author_year
  ].compact.join(' ')
end

#full_original_taxon_name_tag(taxon_name) ⇒ String

Returns the name in original combination, with author year, with HTML.

Returns:

  • (String) —

    the name in original combination, with author year, with HTML



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# File 'app/helpers/taxon_names_helper.rb', line 108

def full_original_taxon_name_tag(taxon_name)
  return nil if taxon_name.nil?
  [ original_taxon_name_tag(taxon_name),
    history_author_year_tag(taxon_name)
  ].compact.join(' ').html_safe
end

#full_taxon_name_tag(taxon_name) ⇒ String

Returns the current name/combination with author year, with HTML.

Returns:

  • (String) —

    the current name/combination with author year, with HTML



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# File 'app/helpers/taxon_names_helper.rb', line 101

def full_taxon_name_tag(taxon_name)
  return nil if taxon_name.nil?
  [taxon_name_tag(taxon_name), taxon_name.cached_author_year].compact.join(' ').html_safe
end

#label_for_taxon_name(taxon_name) ⇒ String

!! Unified deprecated taxon_name_name_string() here

Returns:

  • (String) —

    the current name/combination with author year, without HTML



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# File 'app/helpers/taxon_names_helper.rb', line 40

def label_for_taxon_name(taxon_name)
  return nil if taxon_name.nil?
  [taxon_name.cached, taxon_name.cached_author_year].compact.join(' ')
end

#next_sibling_browse_taxon_name_link(taxon_name, path = :browse_nomenclature_task_path) ⇒ Object 



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# File 'app/helpers/taxon_names_helper.rb', line 377

def next_sibling_browse_taxon_name_link(taxon_name, path = :browse_nomenclature_task_path)
  text = 'Next'
  link_object = taxon_name.next_sibling
  if link_object.nil?
    content_tag(:div, content_tag(:span, text), class:  'navigation-item disable')
  else
    link_to(text, taxon_name_link_path(link_object, path), title: taxon_name_tag(link_object), class: 'navigation-item', data: { button: 'next' })
  end
end

#original_author_year(taxon_name) ⇒ String

Returns removes parens.

Returns:

  • (String) —

    removes parens



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# File 'app/helpers/taxon_names_helper.rb', line 136

def original_author_year(taxon_name)
  return nil if taxon_name.nil? || taxon_name.cached_author_year.nil?
  taxon_name.original_author_year || ''
end

#original_taxon_name_link(taxon_name) ⇒ Object 



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# File 'app/helpers/taxon_names_helper.rb', line 284

def original_taxon_name_link(taxon_name)
  return nil if taxon_name.nil?
  [ link_to(original_taxon_name_tag(taxon_name).html_safe, browse_nomenclature_task_path(taxon_name_id: taxon_name.id)).html_safe, taxon_name.original_author_year].compact.join(' ').html_safe
end

#original_taxon_name_tag(taxon_name) ⇒ String

Returns the taxon name in original combination, without author year, with HTML.

Returns:

  • (String) —

    the taxon name in original combination, without author year, with HTML



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# File 'app/helpers/taxon_names_helper.rb', line 90

def original_taxon_name_tag(taxon_name)
  return nil if taxon_name.nil?
  if taxon_name.cached_original_combination_html.nil?
    taxon_name_tag(taxon_name)
  else
    taxon_name.cached_original_combination_html.html_safe
  end
end

#parent_taxon_name_for_select(taxon_name) ⇒ Object

@taxon_name.parent.andand.display_name(:type => :for_select_list)



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# File 'app/helpers/taxon_names_helper.rb', line 294

def parent_taxon_name_for_select(taxon_name)
  taxon_name.parent ? taxon_name_for_select(taxon_name.parent) : nil
end

#previous_sibling_browse_taxon_name_link(taxon_name, path = :browse_nomenclature_task_path) ⇒ Object 



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# File 'app/helpers/taxon_names_helper.rb', line 387

def previous_sibling_browse_taxon_name_link(taxon_name, path = :browse_nomenclature_task_path)
  text = 'Previous'
  link_object = taxon_name.previous_sibling

  if link_object.nil?
    content_tag(:div, content_tag(:span, text), class: 'navigation-item disable')
  else
    link_to(text, taxon_name_link_path(link_object, path), class: 'navigation-item', data: { button: 'back' })
  end
end

#rank_tag(taxon_name) ⇒ Object 



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# File 'app/helpers/taxon_names_helper.rb', line 342

def rank_tag(taxon_name)
  case taxon_name.type
  when 'Protonym'
    if taxon_name.rank_class
      taxon_name.rank.downcase
    else
      content_tag(:em, 'ERROR')
    end
  when 'Combination'
    content_tag(:em, 'Combination')
  end
end

#simple_hierarchy_tag(names, selected_names = nil) ⇒ String

!! Does not try to sort names, works best in combination with ancestrify: true in ::Queries::TaxonNames::Filter TODO: there is some missalignment on the name matching, you'll see some names that likely matched not linked.

Returns:

  • (String) —

    with HTML



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# File 'app/helpers/taxon_names_helper.rb', line 656

def simple_hierarchy_tag(names, selected_names = nil)
  match = []

  if selected_names
    match = selected_names.select("CASE WHEN taxon_names.type = 'Protonym' THEN taxon_names.id ELSE taxon_names.cached_valid_taxon_name_id END as id").pluck(:id)
  end

  # taxon_names.cached as alias, \

  objects = names.left_joins(:valid_taxon_name)
    .select("CASE WHEN taxon_names.type = 'Protonym' THEN taxon_names.id ELSE taxon_names.cached_valid_taxon_name_id END as id, \
             CASE WHEN taxon_names.type = 'Protonym' THEN taxon_names.parent_id ELSE valid_taxon_names_taxon_names.parent_id END as parent_id, \
             COALESCE(taxon_names.name, valid_taxon_names_taxon_names.name, valid_taxon_names_taxon_names.name, valid_taxon_Names_taxon_names.cached) as label")
    .order('parent_id, label')
    .distinct

  d = Utilities::Hierarchy.new(objects:, match:).to_a

  rows = []

  d.each do |r|
    s = '&nbsp;' * r[3] * 10 # space
    a = (r[2]  ? " [#{r[2]}]" : '') # alias
    if r[4] # matched
      rows.push s + link_to( tag.b(r[1] + a), browse_nomenclature_task_path(taxon_name_id: r[0]))
    else # unmatched
      rows.push s + r[1] + a
    end
  end

  rows.join('<br>').html_safe
end

#summarize_authors_by_year(taxon_names) ⇒ Hash

Summarize People instances through taxon_name_author roles per year

Parameters:

  • taxon_names (ActiveRecord::Relation) —
    • filtered taxon names

Returns:

  • (Hash) —
    • hash of authors with year data, keyed by person_id


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# File 'app/helpers/taxon_names_helper.rb', line 740

def summarize_authors_by_year(taxon_names)
  author_summary = {}

  taxon_names.left_joins(:taxon_name_authors).find_each do |taxon_name|
    year = taxon_name.cached_nomenclature_date&.year || 'Unknown'
    is_valid = taxon_name.cached_is_valid

    taxon_name.taxon_name_authors.each do |person|
      next unless person

      author_key = person.id
      author_summary[author_key] ||= { name: person.cached, years: {} }
      author_summary[author_key][:years][year] ||= { valid: 0, invalid: 0, total: 0 }

      if is_valid
        author_summary[author_key][:years][year][:valid] += 1
      else
        author_summary[author_key][:years][year][:invalid] += 1
      end
      author_summary[author_key][:years][year][:total] += 1
    end
  end

  author_summary
end

#taxon_name_autocomplete_selected_tag(taxon_name) ⇒ String

DEPRECATE!

Returns:

  • (String) —

    no HTML inside 



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# File 'app/helpers/taxon_names_helper.rb', line 61

def taxon_name_autocomplete_selected_tag(taxon_name)
  label_for_taxon_name(taxon_name)
end

#taxon_name_autocomplete_tag(taxon_name, term) ⇒ Object 



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# File 'app/helpers/taxon_names_helper.rb', line 45

def taxon_name_autocomplete_tag(taxon_name, term)
  return nil if taxon_name.nil?
  klass = taxon_name.rank_class ? taxon_name.rank_class.nomenclatural_code : nil
  a = [
    content_tag(:span, mark_tag(taxon_name.cached_html_name_and_author_year, term),  class: :klass),
    taxon_name_rank_tag(taxon_name),
    taxon_name_parent_tag(taxon_name),
    taxon_name_original_combination_tag(taxon_name, term:),
    taxon_name_type_short_tag(taxon_name)
    # " [#{taxon_name.sml_t}]"
  ].compact.join('&nbsp;').html_safe
end

#taxon_name_autoselect_info(taxon_name) ⇒ Object

Disambiguation info Array for the autoselect dropdown (right-justified). Only called for real TaxonName AR records (external levels render their own info).



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# File 'app/helpers/taxon_names_helper.rb', line 19

def taxon_name_autoselect_info(taxon_name)
  return [] if taxon_name.nil?
  [
    taxon_name_rank_tag(taxon_name),
    taxon_name_parent_tag(taxon_name),
    taxon_name_original_combination_tag(taxon_name),
    taxon_name_type_short_tag(taxon_name)
  ]
end

#taxon_name_autoselect_tag(taxon_name, term = nil) ⇒ Object

HTML label for the autoselect dropdown (left-justified). Uses cached_html for real records; falls back to cached for CoL pseudo-records.



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# File 'app/helpers/taxon_names_helper.rb', line 9

def taxon_name_autoselect_tag(taxon_name, term = nil)
  return nil if taxon_name.nil?
  tag.span(
   mark_tag(
    taxon_name.cached_html_name_and_author_year.html_safe, term
   ), class: :klass)
end

#taxon_name_browse_link(taxon_name) ⇒ Object 



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# File 'app/helpers/taxon_names_helper.rb', line 267

def taxon_name_browse_link(taxon_name)
  return nil if taxon_name.nil?
  [ link_to(taxon_name_tag(taxon_name), browse_nomenclature_task_path(taxon_name_id: taxon_name.id)).html_safe, taxon_name.cached_author_year].compact.join(' ').html_safe
end

#taxon_name_decorator_status(taxon_name) ⇒ Object 



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# File 'app/helpers/taxon_names_helper.rb', line 231

def taxon_name_decorator_status(taxon_name)
  return nil if taxon_name.nil?
  taxon_name.taxon_name_classifications
    .where(taxon_name_classifications: {type: TAXON_NAME_CLASSIFICATIONS_FOR_DECORATION})
    .select('taxon_name_classifications.type')
    .map{|a| a.type.demodulize.underscore.gsub(/(\d+)/,  ' \1').gsub('_', ' ').capitalize}
end

#taxon_name_for_select(taxon_name) ⇒ Object 



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# File 'app/helpers/taxon_names_helper.rb', line 289

def taxon_name_for_select(taxon_name)
  taxon_name.name if taxon_name
end

#taxon_name_gender_sentence_tag(taxon_name) ⇒ Object 



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# File 'app/helpers/taxon_names_helper.rb', line 248

def taxon_name_gender_sentence_tag(taxon_name)
  return nil if taxon_name.nil?
  "The name is #{taxon_name.cached_gender}." if taxon_name.cached_gender
end

#taxon_name_inferred_combination_tag(taxon_name) ⇒ Object 



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# File 'app/helpers/taxon_names_helper.rb', line 239

def taxon_name_inferred_combination_tag(taxon_name)
  return nil if taxon_name.nil? || taxon_name.is_combination? || taxon_name.is_valid?
  if taxon_name.is_protonym?
    return nil if taxon_name.cached_primary_homonym == taxon_name.cached_secondary_homonym
  end

  tag.span(tag.em('inferred combination'), class: :subtle)
end

#taxon_name_inventory_stats(taxon_name) ⇒ Object 



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# File 'app/helpers/taxon_names_helper.rb', line 411

def taxon_name_inventory_stats(taxon_name)
  # Code mostly by chatgpt 5 (with comment/naming revsisions)
  d = []

  # Query 1. Get all ranks for ordering
  ranks = ::Queries::TaxonName::Filter
    .new(synonymify: true, descendants: false, taxon_name_id: taxon_name.id)
    .all
    .where(type: 'Protonym')
    .distinct
    .pluck(:rank_class)
    .compact
    .sort_by { |r| RANKS.index(r) || RANKS.length }

  return [] if ranks.empty?

  # Query 2. VALID
  valid = ::Queries::TaxonName::Filter.new(
    validity: true,
    descendants: false,
    taxon_name_id: taxon_name.id,
    taxon_name_type: 'Protonym'
  ).all

  valid_by_rank = valid
    .group('rank_class')
    .count

  # Query 3. VALID FOSSILS
  valid_fossil_names_by_rank = valid
    .joins(:taxon_name_classifications)
    .where(taxon_name_classifications: { type: TAXON_NAME_CLASSIFICATIONS_FOR_FOSSILS })
    .group('rank_class')
    .count

 # Query 4. INVALID
 invalid_scope = ::Queries::TaxonName::Filter.new(
    descendants: false,
    synonymify: true,
    taxon_name_id: taxon_name.id,
    taxon_name_type: 'Protonym'
  ).all.that_is_invalid

  # Count invalid names at the rank of their valid name.
  invalid_by_rank = TaxonName
    .from("(#{invalid_scope.to_sql}) invalid")
    .joins('JOIN taxon_names valid ON valid.id = invalid.cached_valid_taxon_name_id')
    .group('valid.rank_class')
    .count

  # Query 5: Coordinatified OTU counts
  # In brief: Let S be the subtree of taxon_name.
  # 1) To each name in S, assign the rank of its valid name (may be itself).
  # 2) Coordinatify all otus corresponding to S (expand in both directions
  #    from S via valid-name-of/invalid-name-of name in S).
  # 3) Join 2) to 1) via the expansion described in 2).
  # 4) Group that join by the valid rank assigned to elements of S in 1).
  # 5) Count by that valid rank.
  base_scope = ::Queries::TaxonName::Filter.new(
    descendants: false,
    taxon_name_id: taxon_name.id,
    taxon_name_type: 'Protonym'
  ).all

  # Count invalid names with their valid name's rank.
  valid_rank = TaxonName
    .from(base_scope, :tn)
    .joins('LEFT JOIN taxon_names valid ON valid.id = tn.cached_valid_taxon_name_id')
    .select(
      'tn.id,
      COALESCE(valid.rank_class, tn.rank_class) AS valid_rank,
      tn.cached_is_valid'.squish
    )

  otus_scope = ::Otu.where(taxon_name_id: valid_rank.except(:select).select('tn.id'))

  # This is a little janky, but it's what allows us to avoid an extra query
  # (and it gives project_id context).
  otus_coordinatified = ::Queries::Otu::Filter.new({}).coordinatify_result(otus_scope)

  rows = TaxonName
    .with(valid_rank:)
    .from(otus_coordinatified, :o)
    .joins('JOIN taxon_names tn ON tn.id = o.taxon_name_id')
    .joins('JOIN valid_rank vr ON tn.id = vr.id OR tn.cached_valid_taxon_name_id = vr.id')
    .group('vr.valid_rank')
    .pluck('vr.valid_rank', Arel.sql('COUNT(DISTINCT o.id)'))

  otu_by_rank = rows.each_with_object({}) { |(rank, cnt), h| h[rank] = cnt.to_i }

  # Stitch results per rank
  ranks.each do |rank_class|
    n = rank_class.safe_constantize.rank_name.to_sym
    valid = valid_by_rank[rank_class] || 0
    valid_fossil = valid_fossil_names_by_rank[rank_class] || 0
    invalid = invalid_by_rank[rank_class] || 0
    taxa = otu_by_rank[rank_class] || 0

    d << {
      rank: n,
      taxa: taxa,
      names: {
        valid: valid,
        valid_fossil: valid_fossil,
        valid_extant: valid - valid_fossil,
        invalid: invalid
      }
    }
  end

  d
end

#taxon_name_latinization_tag(taxon_name) ⇒ Object 



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# File 'app/helpers/taxon_names_helper.rb', line 257

def taxon_name_latinization_tag(taxon_name)
  list = taxon_name.taxon_name_classifications.with_type_array(LATINIZED_TAXON_NAME_CLASSIFICATION_NAMES).map(&:classification_label)
  content_tag(:span,  "The word \"#{taxon_name.name}\" has the following Latin-based classifications: #{list.to_sentence}.", class: 'history__latinized_classifications') if list.any?
end

#taxon_name_link(taxon_name) ⇒ Object 



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# File 'app/helpers/taxon_names_helper.rb', line 262

def taxon_name_link(taxon_name)
  return nil if taxon_name.nil?
  link_to(taxon_name_tag(taxon_name), taxon_name.metamorphosize).html_safe
end

#taxon_name_link_path(taxon_name, path) ⇒ Object (protected) 



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# File 'app/helpers/taxon_names_helper.rb', line 883

def taxon_name_link_path(taxon_name, path)
  if path == :taxon_name_path
    send(path, taxon_name)
  else
    send(path, taxon_name_id: taxon_name.id)
  end
end

#taxon_name_now_tag(taxon_name, css_class = [:feedback, 'feedback-warning', 'feedback-thin']) ⇒ Object

Styling indicating the current valid name



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# File 'app/helpers/taxon_names_helper.rb', line 83

def taxon_name_now_tag(taxon_name, css_class = [:feedback, 'feedback-warning', 'feedback-thin'] )
  return nil if taxon_name.nil? || !taxon_name.is_valid?
  content_tag(:span, ('now ' + taxon_name.cached_html).html_safe, class: css_class)
end

#taxon_name_original_combination_tag(taxon_name, css_class = [:feedback, 'feedback-notice', 'feedback-thin'], term: nil) ⇒ Object

Parameters:

  • term (String, nil) (defaults to: nil) —

    the autocomplete search term, if any; matches are wrapped in <mark>



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# File 'app/helpers/taxon_names_helper.rb', line 77

def taxon_name_original_combination_tag(taxon_name, css_class = [:feedback, 'feedback-notice', 'feedback-thin'], term: nil)
  return nil if taxon_name.nil? || taxon_name.cached_original_combination.blank?
  content_tag(:span, mark_tag(h(taxon_name.cached_original_combination), term), class: css_class)
end

#taxon_name_otus_links(taxon_name) ⇒ Object 



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# File 'app/helpers/taxon_names_helper.rb', line 398

def taxon_name_otus_links(taxon_name)
  if taxon_name.otus.load.any?
    ('The following Otus are linked to this name: ' +
     content_tag(:ul, class: 'no_bullets') do
       taxon_name.otus.each do |o|
         concat(content_tag(:li, otu_link(o) ))
       end
     end.html_safe).html_safe
  else
    content_tag(:em, 'There are no Otus linked to this name.')
  end
end

#taxon_name_parent_navigator_item_link(taxon_name, target = :taxon_name_path) ⇒ Object 



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# File 'app/helpers/taxon_names_helper.rb', line 272

def taxon_name_parent_navigator_item_link(taxon_name, target = :taxon_name_path)
  return nil if taxon_name.nil? || target.nil?
  if target
    case target.to_sym
    when :taxon_name_path
      link_to(taxon_name_tag(taxon_name), taxon_name.metamorphosize)
    else
      link_to(taxon_name_tag(taxon_name), send(target, {taxon_name_id: taxon_name.id}))
    end
  end
end

#taxon_name_parent_tag(taxon_name, css_class = [:feedback, 'feedback-secondary', 'feedback-thin']) ⇒ Object 



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# File 'app/helpers/taxon_names_helper.rb', line 70

def taxon_name_parent_tag(taxon_name, css_class = [:feedback, 'feedback-secondary', 'feedback-thin'] )
  return nil if taxon_name.nil? || taxon_name.parent_id.nil?
  content_tag(:span, taxon_name_tag(taxon_name.parent).html_safe, class: css_class)
end

#taxon_name_rank_select_tag(taxon_name: TaxonName.new, code: nil) ⇒ Object

TODO: Scope to code



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# File 'app/helpers/taxon_names_helper.rb', line 299

def taxon_name_rank_select_tag(taxon_name: TaxonName.new, code:  nil)
  select(:taxon_name, :rank_class, options_for_select(RANKS_SELECT_OPTIONS, selected: taxon_name.rank_string) )
end

#taxon_name_rank_tag(taxon_name, css_class = [:feedback, 'feedback-info', 'feedback-thin']) ⇒ Object 



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# File 'app/helpers/taxon_names_helper.rb', line 65

def taxon_name_rank_tag(taxon_name, css_class = [:feedback, 'feedback-info', 'feedback-thin'] )
  return nil if taxon_name.nil?
  content_tag(:span, taxon_name.rank || 'Combination', class: css_class)
end

#taxon_name_short_status(taxon_name) ⇒ Object 



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# File 'app/helpers/taxon_names_helper.rb', line 156

def taxon_name_short_status(taxon_name)
  if taxon_name.is_combination?
    n = taxon_name.finest_protonym
    s = ['This name is a subsequent combination of']
    if n.is_valid?
      s += [
        link_to(original_taxon_name_tag(n), browse_nomenclature_task_path(taxon_name_id: n.id)),
        history_author_year_tag(n),
      ]
    else
      v = n.valid_taxon_name
      s += [
        original_taxon_name_tag(n),
        history_author_year_tag(n),
        'whose valid/accepted name is',
        link_to(taxon_name_tag(v), browse_nomenclature_task_path(taxon_name_id: v.id) ),
        v.cached_author_year
      ]
    end

    (s.join(' ') + '.').html_safe
  else
    if taxon_name.is_valid? # taxon_name.unavailable_or_invalid?
      content_tag(:span, safe_join([
        content_tag(:span, '',data: {icon: :ok, status: :valid }),
        content_tag(:span, 'This name is valid/accepted.', data: { status: :valid })
      ], ''), class: :brief_status, data: { status: :valid })
    else
      if taxon_name.is_ambiguously_invalid?
        tag.span('This name is not valid/accepted.'.html_safe, class: :brief_status, data: {icon: :attention, status: :invalid})
      else
        tag.span("This name is not valid/accepted.<br>The valid name is #{taxon_name_browse_link(taxon_name.valid_taxon_name)}.".html_safe, class: :brief_status, data: {icon: :attention, status: :invalid})
      end
    end
  end
end

#taxon_name_short_status_label(taxon_name) ⇒ Object 



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# File 'app/helpers/taxon_names_helper.rb', line 197

def taxon_name_short_status_label(taxon_name)
  if taxon_name.is_combination?
    n = taxon_name.finest_protonym
    s = ['This name is subsequent combination of']
    if n.is_valid?
      s += [
        original_taxon_name_tag(n),
        history_author_year_tag(n),
      ]
    else
      v = n.valid_taxon_name
      s += [
        original_taxon_name_tag(n),
        history_author_year_tag(n),
        'whose valid/accepted name is',
        taxon_name_tag(v),
        v.cached_author_year
      ]
    end

    (s.join(' ') + '.')
  else
    if taxon_name.is_valid? # taxon_name.unavailable_or_invalid?
      'This name is valid/accepted.'
    else
      if taxon_name.is_ambiguously_invalid?
        'This name is not valid/accepted.'
      else
        "This name is not valid/accepted. The valid name is #{taxon_name.valid_taxon_name.cached}."
      end
    end
  end
end

#taxon_name_status_label(taxon_name) ⇒ Object 



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# File 'app/helpers/taxon_names_helper.rb', line 193

def taxon_name_status_label(taxon_name)
  taxon_name.combined_statuses.collect{|s| s}.join('; ')
end

#taxon_name_tag(taxon_name) ⇒ String

Returns the taxon name without author year, with HTML.

Returns:

  • (String) —

    the taxon name without author year, with HTML



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# File 'app/helpers/taxon_names_helper.rb', line 31

def taxon_name_tag(taxon_name)
  return nil if taxon_name.nil?
  return taxon_name.name if taxon_name.new_record? # likely not needed
  taxon_name.cached_html.try(:html_safe) || taxon_name.name
end

#taxon_name_type_short_tag(taxon_name) ⇒ Object 



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# File 'app/helpers/taxon_names_helper.rb', line 147

def taxon_name_type_short_tag(taxon_name)
  return nil if taxon_name.nil?
  if taxon_name.is_valid?
    VALID_MARK
  else
    taxon_name.is_combination? ? COMBINATION_MARK : INVALID_MARK # c or X
  end
end

#taxon_name_year_data_table(data, *attributes) ⇒ Object 



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# File 'app/helpers/taxon_names_helper.rb', line 557

def taxon_name_year_data_table(data, *attributes)
  a = data[:data].first
  b = data[:data].second

  content_tag(:table,
              safe_join([
                tag.thead(
                  tag.tr(
                    safe_join [tag.th('Year'), tag.th(a[:name]), tag.th(b[:name])]
                  )
                ),
                safe_join((data[:metadata][:min_year]..data[:metadata][:max_year]).collect{|y|
                  tag.tr(
                    safe_join([
                      tag.td(y),
                      tag.td(a[:data][y]),
                      tag.td(b[:data][y])
                    ])
                  )
                })
              ]), *attributes
             )
end

#taxon_names_by_year_count(names) ⇒ Object 



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# File 'app/helpers/taxon_names_helper.rb', line 640

def taxon_names_by_year_count(names)
  t = names.select('EXTRACT(YEAR FROM taxon_names.cached_nomenclature_date) AS year, COUNT(*) AS count').group('year').inject({}){|hsh, r| hsh[r.year.to_i] = r.count; hsh}
  t
end

#taxon_names_count_by_validity_and_year(scope = nil) ⇒ Object

Perhaps a /lib/catalog method

Returns:

  • Hash



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# File 'app/helpers/taxon_names_helper.rb', line 526

def taxon_names_count_by_validity_and_year(scope = nil)
  return {} if scope.nil?
  invalid = taxon_names_by_year_count(scope.that_is_invalid)
  valid = taxon_names_by_year_count(scope.that_is_valid)

  min = [invalid.keys.sort.first, invalid.keys.sort.first].compact.sort.first || 0
  max = [valid.keys.sort.last, valid.keys.sort.last].compact.sort.first || 0

  min = 1759 if min < 1759
  max = Time.current.year if max > Time.current.year

  invalid_data = {}
  valid_data = {}

  (min..max).each do |y|
    invalid_data[y] = invalid[y].present? ? invalid[y].to_i : 0
    valid_data[y] = valid[y].present? ? valid[y].to_i : 0
  end

  return {
    metadata: {
      max_year: max,
      min_year: min,
    },
    data: [
      { name: 'Valid', data: valid_data},
      { name: 'Invalid', data: invalid_data}
    ]
  }
end

#taxon_names_cumulative_count_by_validity_and_year(scope = nil) ⇒ Object

Perhaps a /lib/catalog method

Returns:

  • Hash



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# File 'app/helpers/taxon_names_helper.rb', line 583

def taxon_names_cumulative_count_by_validity_and_year(scope = nil)
  return {} if scope.nil?
  invalid = taxon_names_by_year_count(scope.that_is_invalid)
  valid = taxon_names_by_year_count(scope.that_is_valid)

  min = [invalid.keys.sort.first, invalid.keys.sort.first].compact.sort.first || 0
  max = [valid.keys.sort.last, valid.keys.sort.last].compact.sort.first || 0

  min = 1759 if min < 1759
  max = Time.current.year if max > Time.current.year

  invalid_data = {}
  valid_data = {}

  invalid_total = 0
  valid_total = 0

  (min..max).each do |y|

    i = ( invalid[y].present? ? invalid[y].to_i : 0 )
    v = ( valid[y].present? ? valid[y].to_i : 0  )

    invalid_total += i
    valid_total += v

    invalid_data[y] = invalid_total
    valid_data[y] =  valid_total
  end

  return {
    metadata: {
      max_year: max,
      min_year: min,
    },
    data: [
      { name: 'Valid', data: valid_data},
      { name: 'Invalid', data: invalid_data}
    ]
  }
end

#taxon_names_per_year(totals) ⇒ Object 



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# File 'app/helpers/taxon_names_helper.rb', line 624

def taxon_names_per_year(totals)
  min = totals.keys.sort.first || 0
  max = totals.keys.sort.last || 0

  min = 1759 if min < 1759
  max = Time.current.year if max > Time.current.year

  data = {}

  (min..max).each do |y|
    data[y] = totals[y].present? ? totals[y].to_i : 0
  end

  data
end

#taxon_names_search_form ⇒ Object 



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# File 'app/helpers/taxon_names_helper.rb', line 303

def taxon_names_search_form
  render '/taxon_names/quick_search_form'
end

#taxonomic_tree(taxon_name, include_ancestors = true, include_count = true) ⇒ Object 



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# File 'app/helpers/taxon_names_helper.rb', line 723

def taxonomic_tree(taxon_name, include_ancestors = true, include_count = true)
  node = {
    taxon_name: taxonomic_tree_node(taxon_name, include_count),
    descendants: taxonomic_tree_descendants(taxon_name, include_count)
  }

  if (include_ancestors)
    node[:ancestors] = taxonomic_tree_ancestors(taxon_name, include_count)
  end

  node
end

#taxonomic_tree_ancestors(taxon_name, include_count) ⇒ Object 



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# File 'app/helpers/taxon_names_helper.rb', line 709

def taxonomic_tree_ancestors(taxon_name, include_count)
  taxon_name.ancestor_protonyms.map { |ancestor| taxonomic_tree_node(ancestor, include_count) }
end

#taxonomic_tree_descendants(taxon_name, include_count) ⇒ Object 



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# File 'app/helpers/taxon_names_helper.rb', line 713

def taxonomic_tree_descendants(taxon_name, include_count)
  taxon_name
    .children
    .where(type: 'Protonym')
    .sort_by { |a|
      [RANKS.index(a.rank_string) || RANKS.length, a.cached || '', a.cached_author_year || '']
    }
    .map { |child| taxonomic_tree_node(child, include_count) }
end

#taxonomic_tree_node(taxon_name, include_count) ⇒ Object 



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# File 'app/helpers/taxon_names_helper.rb', line 689

def taxonomic_tree_node(taxon_name, include_count)
  node = {
    id: taxon_name.id,
    parent_id: taxon_name.parent_id,
    label: taxon_name.cached_html_name_and_author_year,
    is_valid: taxon_name.cached_is_valid,
    cached_valid_taxon_name_id: taxon_name.cached_valid_taxon_name_id,
    rank_string: taxon_name.rank_string,
    synonyms: taxon_name_synonyms_list(taxon_name).map { |syn| taxon_name_synonym_li(syn) },
    leaf_node: taxon_name.descendants.unscope(:order).empty?
  }

  if include_count
    node[:valid_descendants] = taxon_name.descendants.unscope(:order).that_is_valid.count
    node[:invalid_descendants] = taxon_name.descendants.unscope(:order).that_is_invalid.count
  end

  node
end