Module: TaxonNames::PaperCatalogHelper

Defined in:
app/helpers/taxon_names/paper_catalog_helper.rb

Overview

Helpers for rendering a paper catalog.

Constant Summary collapse

OPTIONS = 
{
  nest_rank_headers: true, # in
  hanging_indents: false,  # does nothing
  only_origin_sources: true,
}.freeze

Instance Method Summary collapse

Instance Method Details

#paper_catalog_entry_item_tag(catalog_entry_item) ⇒ Object

may need reference_object



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# File 'app/helpers/taxon_names/paper_catalog_helper.rb', line 150

def paper_catalog_entry_item_tag(catalog_entry_item) # may need reference_object
  nomenclature_line_tag(catalog_entry_item, catalog_entry_item.base_object) # second param might be wrong!
end

#paper_catalog_li_tag(nomenclature_catalog_item, reference_taxon_name, target = :browse_nomenclature_task_path) ⇒ Object

TODO: Add depth, Markdown



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# File 'app/helpers/taxon_names/paper_catalog_helper.rb', line 155

def paper_catalog_li_tag(nomenclature_catalog_item, reference_taxon_name, target = :browse_nomenclature_task_path)
  paper_line_tag(nomenclature_catalog_item, reference_taxon_name, target)
end

#paper_distribution_row(entry_item) ⇒ Object 



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# File 'app/helpers/taxon_names/paper_catalog_helper.rb', line 300

def paper_distribution_row(entry_item)
  o = case entry_item.object.class.name
  when 'TypeMaterial'
    entry_item.object.collection_object
  else
    entry_item.object
  end

  if o.dwc_occurrence
    [ '| ',
      o.dwc_occurrence.attributes.slice(
        'kingdom',
        'family',
        'genus',
        'specificEpithet',
        'infraspecificEpithet',
        'scientificName',
        'scientificNameAuthorship',
        'taxonRank',
        'country',
        'stateProvince',
        'county',
        'occurrenceStatus',
      ).values.join('| '),
      '| ',
      o.sources.collect{|s| source_author_year_label(s)}.join('; ')
    ].join(' ')
  else
   "| Record not indexed: #{label_for(o)}" + (['|'] * 12).join
  end
end

#paper_header_prefix(taxon_name, options) ⇒ Object 



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# File 'app/helpers/taxon_names/paper_catalog_helper.rb', line 71

def paper_header_prefix(taxon_name, options)
  r = nil
  if options[:nest_rank_headers]
    if taxon_name.is_species_rank?
      r= :species
    elsif taxon_name.is_genus_rank?
      r = :genus
    elsif taxon_name.is_family_rank?
      r = :family
    end
  end

  case r
  when :species
    '===== '
  when :genus
    '==== '
  else # family, or nest rank is false
    '=== '
  end
end

#paper_history_author_year(taxon_name, citation) ⇒ String

Returns the name, or citation author year, prioritized by original/new with punctuation.

Returns:

  • (String) —

    the name, or citation author year, prioritized by original/new with punctuation



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# File 'app/helpers/taxon_names/paper_catalog_helper.rb', line 205

def paper_history_author_year(taxon_name, citation)
  return 'Source is verbatim, requires parsing' if citation&.source&.type == 'Source::Verbatim'

  a = paper_history_author_year_tag(taxon_name)
  return str = ' ' + a unless a.nil?

  #   return nil if str.blank?
  #
  #   if citation
  #     a = history_author_year_tag(taxon_name)
  #     b = source_author_year_tag(citation.source)
  #   end
  #
  #   s
  #   if citation.blank? || a != b
  #     content_tag(:span, ' ' + str, class: [:history_author_year])
  #   else
  #     content_tag(:em, ' ') + link_to(content_tag(:span, str, title: citation.source.cached, class: 'history__pages'), send(:nomenclature_by_source_task_path, source_id: citation.source.id) )
  #   end
  #    str.blank? ? nil :
  #      content_tag(:span, ' ' + str, class: [:history_author_year])
end

#paper_history_author_year_tag(taxon_name) ⇒ Object

# @return [String, nil]

#   variably return the author year for taxon name in question
#   !! NO span, is used in comparison !!



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# File 'app/helpers/taxon_names/paper_catalog_helper.rb', line 232

def paper_history_author_year_tag(taxon_name)
  return nil if taxon_name.nil? || taxon_name.cached_author_year.nil?

  body =  case taxon_name.type
          when 'Combination'
            current_author_year(taxon_name)
          when 'Protonym'
            original_author_year(taxon_name)
          else
            'HYBRID NOT YET HANDLED'
          end
end

#paper_history_in_taxon_name(t, c, i) ⇒ Object

# @return [String, nil]

#    return the citation author/year if differeing from the taxon name author year



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# File 'app/helpers/taxon_names/paper_catalog_helper.rb', line 271

def paper_history_in_taxon_name(t, c, i)
  if c
    a = history_author_year_tag(t)   # TODO: probably label
    b = source_author_year_tag(c.source)

    if a != b || i.from_relationship?
      ' in ' +  b
    end
  end
end

#paper_history_other_name(catalog_item, reference_taxon_name) ⇒ String?

Returns a parenthesized line item containing relationship and related name.

Returns:

  • (String, nil) —

    a parenthesized line item containing relationship and related name



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# File 'app/helpers/taxon_names/paper_catalog_helper.rb', line 284

def paper_history_other_name(catalog_item, reference_taxon_name)
  if catalog_item.from_relationship?
    other_str = nil

    if catalog_item.other_name == reference_taxon_name
      other_str = full_original_taxon_name_tag(catalog_item.other_name)
    else
      other_str = [
        original_taxon_name_tag(catalog_item.other_name) || 'MISSING',
        (original_author_year(catalog_item.other_name) || 'MISSING')
      ].join(' ')
    end
    " (#{catalog_item.object.subject_status_tag} #{other_str})".html_safe
  end
end

#paper_history_statuses(nomenclature_catalog_entry_item) ⇒ Object

# @return [String, nil]

#   A brief summary of the validity of the name (e.g. 'Valid')
#     ... think this has to be refined, it doesn't quite make sense to show multiple status per relationship



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# File 'app/helpers/taxon_names/paper_catalog_helper.rb', line 188

def paper_history_statuses(nomenclature_catalog_entry_item)
  i = nomenclature_catalog_entry_item
  s = i.base_object.taxon_name_classifications_for_statuses
  return nil if (s.empty? || !i.is_first) # is_subsequent?
  return nil if i.from_relationship?

  (' (' +
   s.collect{|tnc|
     tnc.classification_label + (tnc.citations.load.any? ? (' in ' + citations_tag(tnc)).html_safe : '')
   }.join('; ')
  ).html_safe +
  ')'

end

#paper_history_subject_original_citation(catalog_item) ⇒ Object

# @return [String, nil]

#   the taxon name author year for the citation in question
#   if the same as the author/year for the catalog_item taxon name then this
#   only renders the pages in that citation



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# File 'app/helpers/taxon_names/paper_catalog_helper.rb', line 249

def paper_history_subject_original_citation(catalog_item)
  return nil if !catalog_item.from_relationship? || catalog_item.object.subject_taxon_name.origin_citation.blank?
  return nil if catalog_item.from_relationship?
  t = catalog_item.object.subject_taxon_name
  c = t.origin_citation

  a = history_author_year_tag(t)
  b = source_author_year_tag(c.source)

  body =  [
    (a != b ?  source_author_year_tag(c.source) : nil) #,
    #history_pages(c)
  ].compact.join.html_safe

  unless body.blank?
    ': ' + body
  end
  #    content_tag(:span, body, class: :history__subject_original_citation) unless body.blank?
end

#paper_history_taxon_name(taxon_name, r, c, target = nil) ⇒ Object 



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# File 'app/helpers/taxon_names/paper_catalog_helper.rb', line 181

def paper_history_taxon_name(taxon_name, r, c, target = nil)
  original_taxon_name_tag(taxon_name)
end

#paper_history_type_material(entry_item) ⇒ Object

TODO: always displayed inline, consider target



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# File 'app/helpers/taxon_names/paper_catalog_helper.rb', line 110

def paper_history_type_material(entry_item)
  return nil if entry_item.object_class != 'Protonym' || !entry_item.is_first # is_subsequent?

  # Species type
  if entry_item.object.is_species_rank?
    types = entry_item.object.get_primary_type
    if types.any?
      return types.collect{|t| type_material_catalog_label(t)}.join('. ')
    else
      return nil
    end
  else
    if type_taxon_name_relationship = entry_item.base_object&.type_taxon_name_relationship
      str = citations_tag(type_taxon_name_relationship)

      [ ' ' + type_taxon_name_relationship_label(entry_item.base_object.type_taxon_name_relationship),
        (type_taxon_name_relationship.citations&.load&.any? ?  ' in ' : nil),
        str
      ].compact.join.html_safe
    else
      nil
    end
  end
end

#paper_line_tag(nomenclature_catalog_entry_item, reference_taxon_name, target = :browse_nomenclature_task_path) ⇒ Object

TODO: rename reference_taxon_name



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# File 'app/helpers/taxon_names/paper_catalog_helper.rb', line 160

def paper_line_tag(nomenclature_catalog_entry_item, reference_taxon_name, target = :browse_nomenclature_task_path)
  i = nomenclature_catalog_entry_item

  t = i.base_object
  c = i.citation
  r = reference_taxon_name

  [
    paper_history_taxon_name(t, r, c, target),        # the subject, or protonym
    paper_history_author_year(t, c),                  ## author year of the subject, or protonym
    paper_history_subject_original_citation(i),       ##
    paper_history_other_name(i, r),                   # The TaxonNameRelaltionship
    paper_history_in_taxon_name(t, c, i),             ##  citation for related name
    paper_history_pages(c),                           ##  pages for citation of related name
    paper_history_statuses(i),                        # TaxonNameClassification summary
    # history_citation_notes(c),                      # Notes on the citation
    paper_history_topics(c),                          # Topics on the citation
    # history_type_material(i), # TODO: could still be OK here
  ].compact.join.html_safe
end

#paper_repositories(entry_item) ⇒ Array

Returns of [acronym, name] pairs.

Returns:

  • (Array) —

    of [acronym, name] pairs



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# File 'app/helpers/taxon_names/paper_catalog_helper.rb', line 95

def paper_repositories(entry_item)
  return nil if entry_item.object_class != 'Protonym' || !entry_item.is_first || !entry_item.object.is_species_rank?
  types = entry_item.object.get_primary_type
  repositories = []
  if types.any?
    types.each do |t|
      if r = t.collection_object.repository
        repositories.push [r.acronym, r.name]
      end
    end
  end
  repositories.uniq
end

#recursive_catalog_tag(taxon_name, data = { body: '', sources: [], supplementary_distribution: ::Catalog::Distribution::Entry.new([]), repositories: [], options: OPTIONS}, depth = 0) ⇒ Hash

The body format is “chronological”, i.e. each citation

Returns:

  • (Hash) —

    like { body: HTML, sources: [], repositories; [] }



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# File 'app/helpers/taxon_names/paper_catalog_helper.rb', line 28

def recursive_catalog_tag(taxon_name, data = { body: '', sources: [], supplementary_distribution: ::Catalog::Distribution::Entry.new([]), repositories: [], options: OPTIONS}, depth = 0 )

  data[:body] << [
    paper_header_prefix(taxon_name, data[:options]),
    full_taxon_name_tag(taxon_name),
    "\n\n"].join

    cat = ::Catalog::Nomenclature::Entry.new(taxon_name)
    data[:sources].push(cat.sources)

    # type of primary name
    #  if t = paper_history_type_material(c)
    #    body << [depth_string, 'Type: ', t].join.html_safe + tag.br
    #  end

    # synonymy
    cat.ordered_by_nomenclature_date.each do |c|
      data[:body] << [ paper_catalog_li_tag(c, cat.object, :browse_nomenclature_task_path), "\n\n"].join.html_safe

      if t = paper_history_type_material(c)
        data[:body] << ['[.type]**Type:** ', t, "\n\n"].join
        if r = paper_repositories(c)
          data[:repositories].push r
        end
      end
    end

    # distribution is only calculated for species level here!!
    d = paper_distribution_entry(taxon_name)
    if d && d.items.any?
      data[:body] << ['[.distribution]**Distribution:** ', d.to_s, "\n\n"].join
      data[:supplementary_distribution].items += d.items
    end

   data[:body] << "\n"

   taxon_name.children.that_is_valid.order(:cached).each do |t|
     recursive_catalog_tag(t, data, depth + 1)
   end

  data
end

#recursive_catalog_tag2(taxon_name, body = '', depth = 0) ⇒ Object

!! Unused Scaffold by by unique synonyms



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# File 'app/helpers/taxon_names/paper_catalog_helper.rb', line 137

def recursive_catalog_tag2(taxon_name, body = '', depth = 0)
  body << '== ' + full_taxon_name_tag(taxon_name) + '<br>'.html_safe
  taxon_name.children.that_is_valid.order(:cached).each do |t|

    t.children.that_is_invalid.order(:cached).each do |i|
      #        body << ['&nbsp;&nbsp;' * (depth + 3), '= '].join.html_safe + full_original_taxon_name_tag(i) + '<br>'.html_safe
      body << '=== ' + (full_original_taxon_name_tag(i) + "\n").html_safe
    end
    recursive_catalog_tag(t, body, depth + 1)
  end
  body.html_safe
end