Module: OtusHelper

Includes:
RecordNavigationHelper
Defined in:
app/helpers/otus_helper.rb

Instance Method Summary collapse

Methods included from RecordNavigationHelper

for

Instance Method Details

Stub a smart link to browse OTUs

Parameters:

  • object (an instance of TaxonName or Otu) —

    if TaxonName is provided JS UI will disambiguate if more options are possible



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# File 'app/helpers/otus_helper.rb', line 235

def browse_otu_link(object)
  return nil if object.nil?
  otu = object.metamorphosize
  content_tag(:div, '', 'data-taxon-name' => object_tag(otu), 'data-redirect' => 'true', 'data-id' => otu.id, 'data-klass' => object.class.base_class.name.to_s, 'data-otu-button' => 'true')
end

#dwc_gallery_data(otu, dwc_occurrence_id: [], pagination_headers: true) ⇒ Hash

Returns { dwc_occurrence_id: [ image1, image2 ... ], ... }.

Returns:

  • (Hash) —

    { dwc_occurrence_id: [ image1, image2 ... ], ... }



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# File 'app/helpers/otus_helper.rb', line 336

def dwc_gallery_data(otu, dwc_occurrence_id: [], pagination_headers: true)
  a = DwcOccurrence.scoped_by_otu(otu)
    .select(:id, :dwc_occurrence_object_id, :dwc_occurrence_object_type)

  dwc_ids = [dwc_occurrence_id].flatten.compact.uniq

  if dwc_ids.any?
    a = a.where(id: dwc_ids)
  end

  a = a.page(params[:page]).per(params[:per])

  # Somehwhat of a janky pattern, probably needs to be
  # moved into Controller.
  assign_pagination(a) if pagination_headers

  b = Image.with(dwc_scope: a)
    .joins('JOIN depictions d on d.image_id = images.id' )
    .joins("JOIN dwc_scope on d.depiction_object_id = dwc_scope.dwc_occurrence_object_id AND d.depiction_object_type = 'CollectionObject' AND dwc_scope.dwc_occurrence_object_type = 'CollectionObject'")
    .select('images.*, dwc_scope.id dwc_id')
    .distinct

  r = {}
  b.find_each do |o|
    r[o.dwc_id] ||= []
    r[o.dwc_id].push o
  end
  r
end

#label_for_otu(otu) ⇒ Object 



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# File 'app/helpers/otus_helper.rb', line 78

def label_for_otu(otu)
  return nil if otu.nil?
  if otu.taxon_name
    if otu.taxon_name.is_combination?

      if otu.name?
        [
          otu.name,
          label_for_taxon_name(otu.taxon_name)
        ].compact.join(' == ').html_safe
      else
        label_for_taxon_name(otu.taxon_name) + ' [c]'
      end

    else # protonym
      if otu.taxon_name.is_valid?

        [ label_for_taxon_name(otu.taxon_name),
          otu.name
        ].compact.join(' ')

      else # invalid taxon name
        [
          [ label_for_taxon_name(otu.taxon_name),
            otu.name
          ].compact.join(' '),

          [ label_for_taxon_name(otu.taxon_name.valid_taxon_name),
            otu.name
          ].compact.join(' ')
        ].join(' now ')

      end
    end

  else
    otu.name
  end
end

#next_records(otu) ⇒ Array

Returns of OTUs.

Returns:

  • (Array) —

    of OTUs



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# File 'app/helpers/otus_helper.rb', line 252

def next_records(otu)
  if otu.taxon_name_id
    o = []
    t = otu.taxon_name.next_sibling
    unless t.nil?
      while o.empty?
        break if t.nil?
        o = t.otus.to_a
        t = t.next_sibling
      end
    end
    o
  else
    super
  end
end

#otu_autocomplete_selected_tag(otu) ⇒ String

DEPRECATE

Returns:

  • (String) —

    no HTML inside 



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# File 'app/helpers/otus_helper.rb', line 211

def otu_autocomplete_selected_tag(otu)
  return nil if otu.nil? || (otu.new_record? && !otu.changed?) # probably get rid of this
  label_for_otu(otu)
#   [otu.name,
#    Utilities::Strings.nil_wrap('[',taxon_name_autocomplete_selected_tag(otu.taxon_name), ']')&.html_safe
#   ].compact.join(' ')
end

#otu_autocomplete_tag(otu, term = nil) ⇒ Object Also known as: otu_autoselect_tag 



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# File 'app/helpers/otus_helper.rb', line 118

def otu_autocomplete_tag(otu, term = nil)
  return nil if otu.nil?
  mark_tag(otu_tag(otu), term)
end

#otu_autoselect_info(otu) ⇒ Object

TODO: alias proper

HTML label for the autoselect dropdown (left-justified).

def otu_autoselect_tag(otu, term = nil) return nil if otu.nil? mark_tag(otu_tag(otu), term) end



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# File 'app/helpers/otus_helper.rb', line 132

def otu_autoselect_info(otu)
  return [] if otu.taxon_name_id.blank?
  r = [ ]

  t = otu.taxon_name

  if t && t.is_protonym?
    if t.is_genus_or_species_rank?
      r.push taxon_name_original_combination_tag(t)
    end

  # if !t.is_valid?
  #   r.push taxon_name_now_tag(t.valid_taxon_name)
  # end
  else
    r.push t.type
  end
  r
end

#otu_common_names_label(common_names, term = nil) ⇒ Object 



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# File 'app/helpers/otus_helper.rb', line 179

def otu_common_names_label(common_names, term = nil)
  return nil if common_names.nil? || common_names.empty?

  if term.empty?
    return common_names.map(&:name).sort.join(', ')
  end

  prefix_matches = []
  wildcard_matches = []
  non_matches = []

  term = term.downcase
  # Regexp.escape turns each space into '\\ '.
  wildcard_term = Regexp.escape(term).gsub(/(\\ )+/, '.*')

  common_names.each do |o|
    name = o.name.downcase
    if name.start_with?(term)
      prefix_matches << name
    elsif name =~ /#{wildcard_term}/
      wildcard_matches << name
    else
      non_matches << name
    end
  end

  (prefix_matches.sort + wildcard_matches.sort + non_matches.sort).join(', ')
end

#otu_extended_autocomplete_tag(target, otu, common_names, term) ⇒ Object

Used exclusively in /api/v1/otus/autocomplete



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# File 'app/helpers/otus_helper.rb', line 162

def otu_extended_autocomplete_tag(target, otu, common_names, term)
  if target.kind_of?(Otu)
    t = otu_tag(target)
  else # TaxonName
    a = [ tag.span( full_taxon_name_tag(target).html_safe, class: :otu_tag_taxon_name, title: target.id) ]
    a.push taxon_name_type_short_tag(target)
    t = tag.span( a.compact.join(' ').html_safe, class: :otu_tag )
  end

  if common_names.present? && otu.present? &&
     (common_names_label = otu_common_names_label(common_names, term)).present?
    tag.span( "#{common_names_label} (#{t})".html_safe )
  else
    t
  end
end

#otu_key_inventory(otu) ⇒ Object 



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# File 'app/helpers/otus_helper.rb', line 378

def otu_key_inventory(otu)
  return {
    observation_matrices: {
      scoped: serialize_matrices(otu.in_scope_observation_matrices),
      in: serialize_matrices(otu.observation_matrices)
    },
    leads: {
      scoped: otu.leads
        .where(parent_id: nil, is_public: true)
        .where('leads.is_virtual IS NOT TRUE')
        .select(:id, :text)
        .map { |l| { id: l.id, text: l.text } },

      in: Lead.public_root_leads_for_leaf_otus(otu)
        .select(:id, :text)
        .map { |l| { id: l.id, text: l.text } }
    }
  }
end

#otu_link(otu) ⇒ Object 



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# File 'app/helpers/otus_helper.rb', line 219

def otu_link(otu)
  return nil if otu.nil?
  link_to(otu_tag_elements(otu).join(' ').html_safe, otu)
end

#otu_tag(otu) ⇒ Object

a.push content_tag(:span, b.join(' ').html_safe, class: :otu_taxon_name) a.push taxon_name_type_short_tag(otu.taxon_name).html_safe end

tag.span( a.flatten.compact.join(' ').html_safe, class: :otu_tag )

end



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# File 'app/helpers/otus_helper.rb', line 27

def otu_tag(otu)
  return nil if otu.nil?
  return  tag.span(otu.name, class: :otu_tag) unless otu.taxon_name.present?

  if otu.taxon_name.is_combination?
    if otu.name?
      tag.span(
        [ h(otu.name),
          tag.span(otu.taxon_name.cached_html&.html_safe, class: :otu_tag_taxon_name)
        ].join(' ' + tag.em('==') + ' ').html_safe,
      class: :otu_tag
      )
    else
      tag.span(
        (tag.span(otu.taxon_name.cached_html&.html_safe, class: :otu_tag_taxon_name) + ' ' + TaxonNamesHelper::COMBINATION_MARK).html_safe,
        class: :otu_tag
      )
    end

  else # protonym
    if otu.taxon_name.is_valid?
      if otu.name
        tag.span(
          [ tag.span(otu.taxon_name.cached_html&.html_safe, class: :otu_tag_taxon_name),
            h(otu.name)
          ].compact.join('&nbsp;').html_safe,
        class: :otu_tag
        )
      else
        tag.span(
          tag.span(full_taxon_name_tag(otu.taxon_name), class: :otu_tag_taxon_name),
          class: :otu_tag
        )
      end

    else # invalid taxon name
      tag.span(
        [
          [ tag.span(full_taxon_name_tag(otu.taxon_name), class: [:otu_tag_taxon_name, :otu_tag_taxon_name_invalid]),
            ( otu.name ? h(otu.name) : nil )
          ].compact.join('&nbsp;'),

        tag.span(full_taxon_name_tag(otu.taxon_name.valid_taxon_name), class: :otu_tag_taxon_name)
        ].join(' ' + tag.em('now') + ' ').html_safe,
        class: :otu_tag
      )

    end
  end
end

#otu_tag_elements(otu) ⇒ Object 



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# File 'app/helpers/otus_helper.rb', line 153

def otu_tag_elements(otu)
  return nil if otu.nil?
  [
    ( otu.taxon_name ? tag.span(full_taxon_name_tag(otu.taxon_name).html_safe, class: :otu_tag_taxon_name, title: otu.taxon_name.id) : nil),
    ( otu.name ? content_tag(:span, otu.name, class: :otu_tag_otu_name, title: otu.id) : nil )
  ].compact
end

#otus_link_list_tag(otus) ⇒ Object 



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# File 'app/helpers/otus_helper.rb', line 228

def otus_link_list_tag(otus)
  otus.collect { |o| link_to(o.name, o) }.join(',')
end

#otus_radial(object) ⇒ Object 



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# File 'app/helpers/otus_helper.rb', line 246

def otus_radial(object)
  content_tag(:div, '', 'data-global-id' => object.to_global_id.to_s, 'data-otu-radial' => 'true')
end

#otus_radial_disambiguate(object) ⇒ Object 



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# File 'app/helpers/otus_helper.rb', line 241

def otus_radial_disambiguate(object)
  otu = object.metamorphosize
  content_tag(:div, '', 'data-taxon-name' => object_tag(otu), 'data-redirect' => 'false', 'data-id' => otu.id, 'data-klass' => object.class.base_class.name.to_s, 'data-otu-button' => 'true')
end

#otus_search_form ⇒ Object 



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# File 'app/helpers/otus_helper.rb', line 224

def otus_search_form
  render('/otus/quick_search_form')
end

#parent_records(otu) ⇒ Object 



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# File 'app/helpers/otus_helper.rb', line 290

def parent_records(otu)
  otu.taxon_name&.parent&.otus&.all || []
end

#parents_by_nomenclature(otu) ⇒ Object

See also otus#ancestor_otu_ids ?



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# File 'app/helpers/otus_helper.rb', line 295

def parents_by_nomenclature(otu)
  above = [ ]
  if otu.taxon_name_id
    TaxonName.ancestors_of(otu.taxon_name)
      .select('taxon_names.*, taxon_name_hierarchies.generations')
      .that_is_valid.joins(:otus)
      .distinct
      .reorder('taxon_name_hierarchies.generations DESC, taxon_names.cached_valid_taxon_name_id').each do |t|
        above.push [t.cached, t.otus.to_a] # TODO: to_a vs. pluck
      end
  end
  above
end

#previous_records(otu) ⇒ Array

Some OTUs don't have TaxonName, skip along until we hit one.

Returns:

  • (Array) —

    of OTUs



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# File 'app/helpers/otus_helper.rb', line 273

def previous_records(otu)
  if otu.taxon_name_id
    o = []
    t = otu.taxon_name.previous_sibling
    unless t.nil?
      while o.empty?
        break if t.nil?
        o = t.otus.to_a
        t = t.previous_sibling
      end
    end
    o
  else
    super
  end
end

#ranked_otu_table(otus) ⇒ Object 



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# File 'app/helpers/otus_helper.rb', line 309

def ranked_otu_table(otus)
  d = TaxonName.ranked_otus(otu_scope: otus, project_id: sessions_current_project_id)

  tbl = %w{otu_id order family genus species otu_name taxon_name taxon_name_author_year}
  output = StringIO.new
  output.puts ::CSV.generate_line(tbl, col_sep: "\t", encoding: Encoding::UTF_8)

  d.each do |o|
    output.puts ::CSV.generate_line(
      [
        o.id,
        o['order'],
        o['family'],
        o['genus'],
        o['species'],
        o.name,
        o.cached,
        o.cached_author_year
      ],
      col_sep: "\t", encoding: Encoding::UTF_8)
  end

  output.string
end

#serialize_matrices(scope) ⇒ Object 



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

def serialize_matrices(scope)
  scope
    .where(is_public: true)
    .map do |m|
      {
        id: m.id,
        name: m.name,
        is_media: m.is_media_matrix?
      }
    end
end