Module: OtusHelper

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

Instance Method Summary collapse

Methods included from RecordNavigationHelper

for

Instance Method Details

#add_aggregate_geo_json(otu, target) ⇒ Object 



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# File 'app/helpers/otus_helper.rb', line 373

def add_aggregate_geo_json(otu, target)
  h = target

  if g = aggregate_geo_json(otu, h)
    g['properties'] = {'aggregate': true}
    g['properties']['target'] = geojson_target_for_otu(otu)

    h['features'].push g
  end

  h
end

#add_distribution_geo_json(otu, target, seen_shapes = nil) ⇒ Object 



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# File 'app/helpers/otus_helper.rb', line 435

def add_distribution_geo_json(otu, target, seen_shapes = nil)
  h = target
  o = otu

  # internal target
  t = geojson_target_for_otu(otu)

  o.current_field_occurrences.where(is_absent: [nil, false]).each do |f|
    shape_key = seen_shapes && f.collecting_event&.geo_json_shape_key
    g = build_geo_json_feature_deduped(seen_shapes&.fetch(:field_occurrences), shape_key) do |skip_geometry|
      field_occurrence_to_geo_json_feature(f, skip_geometry:)
    end
    next unless g
    g['properties']['target'] = t
    h['features'].push g
  end

  o.current_collection_objects.each do |c|
    shape_key = seen_shapes && c.collecting_event&.geo_json_shape_key
    g = build_geo_json_feature_deduped(seen_shapes&.fetch(:collection_objects), shape_key) do |skip_geometry|
      collection_object_to_geo_json_feature(c, skip_geometry:)
    end
    next unless g
    g['properties']['target'] = t
    h['features'].push g
  end

  o.asserted_distributions.without_is_absent.each do |a|
    shape_key = seen_shapes && [a.asserted_distribution_shape_type, a.asserted_distribution_shape_id]
    g = build_geo_json_feature_deduped(seen_shapes&.fetch(:asserted_distributions), shape_key) do |skip_geometry|
      asserted_distribution_to_geo_json_feature(a, skip_geometry:)
    end
    next unless g
    g['properties']['target'] = t
    h['features'].push g
  end

  ba_ids = ::Queries::BiologicalAssociation::Filter.new(otu_query: { otu_id: [o.id] }).all.pluck(:id)
  unless ba_ids.empty?
    ::AssertedDistribution
      .where(
        asserted_distribution_object_type: 'BiologicalAssociation',
        asserted_distribution_object_id: ba_ids
      )
      .without_is_absent
      .each do |a|
        shape_key = seen_shapes && [a.asserted_distribution_shape_type, a.asserted_distribution_shape_id]
        g = build_geo_json_feature_deduped(seen_shapes&.fetch(:asserted_distributions), shape_key) do |skip_geometry|
          asserted_distribution_to_geo_json_feature(a, skip_geometry:)
        end
        next unless g
        g['properties']['target'] = t
        h['features'].push g
      end

    bag_ids = ::BiologicalAssociationsGraph
      .joins(:biological_associations_biological_associations_graphs)
      .where(biological_associations_biological_associations_graphs: { biological_association_id: ba_ids })
      .select(:id)

    unless bag_ids.empty?
      ::AssertedDistribution
        .where(
          asserted_distribution_object_type: 'BiologicalAssociationsGraph',
          asserted_distribution_object_id: bag_ids
        )
        .without_is_absent
        .each do |a|
          shape_key = seen_shapes && [a.asserted_distribution_shape_type, a.asserted_distribution_shape_id]
          g = build_geo_json_feature_deduped(seen_shapes&.fetch(:asserted_distributions), shape_key) do |skip_geometry|
            asserted_distribution_to_geo_json_feature(a, skip_geometry:)
          end
          next unless g
          g['properties']['target'] = t
          h['features'].push g
        end
    end
  end

  [
    [o.depictions, 'Depiction', :depiction_object_id],
    [o.conveyances, 'Conveyance', :conveyance_object_id],
    [o.observations, 'Observation', :observation_object_id],
  ].each do |related_records, object_type, _id_method|
    related_ids = related_records.map(&:id)
    next if related_ids.empty?

    ::AssertedDistribution
      .where(
        asserted_distribution_object_type: object_type,
        asserted_distribution_object_id: related_ids
      )
      .without_is_absent
      .each do |a|
        shape_key = seen_shapes && [a.asserted_distribution_shape_type, a.asserted_distribution_shape_id]
        g = build_geo_json_feature_deduped(seen_shapes&.fetch(:asserted_distributions), shape_key) do |skip_geometry|
          asserted_distribution_to_geo_json_feature(a, skip_geometry:)
        end
        next unless g
        g['properties']['target'] = t
        h['features'].push g
      end
  end

  o.type_materials.includes(:protonym).each do |e|
    next unless type_material_is_primary_type(e) && o.taxon_name.cached_is_valid

    shape_key = seen_shapes && e.collection_object&.collecting_event&.geo_json_shape_key
    g = build_geo_json_feature_deduped(seen_shapes&.fetch(:type_materials), shape_key) do |skip_geometry|
      type_material_to_geo_json_feature(e, skip_geometry:)
    end
    next unless g
    g['properties']['target'] = t
    h['features'].push g
  end

  h
end

#aggregate_geo_json(otu, target, cached_map_type = 'CachedMapItem::WebLevel1') ⇒ Object

TODO: cleanup



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# File 'app/helpers/otus_helper.rb', line 402

def aggregate_geo_json(otu, target, cached_map_type = 'CachedMapItem::WebLevel1')
  h = target

  if gj = otu.cached_map_geo_json(cached_map_type)

    i =
      {
        **gj,
        # 'type' => gj['type'],  # 'Feature',

        'properties' => {
          'base' => geojson_target_for_otu(otu),
          #     'shape' => {
          #       'type' => cached_map_type,
          #       'id' => 99999 }, # was nil
          'updated_at' => 'foo' # last updated at on CachedMapItem scope, possibly
        }
      }

    if gj.keys.include?('coordinates')
      i['coordinates'] = gj['coordinates'] # was 'coordinates' TODO: might not work
    elsif gj.keys.include?('geometries')
      i['geometries'] = gj['geometries'] # was 'coordinates' TODO: might not work
    end

    i

  else
    nil
  end

end

#browse_otu_link(object) ⇒ Object

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 147

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

#build_geo_json_feature_deduped(seen, shape_key) ⇒ Object (private)

Yields once with skip_geometry true or false depending on whether shape_key [shape_type, shape_id] has already been recorded in seen.

First occurrence of a shape: yields skip_geometry=false (full geometry fetched). The shape is recorded in seen only if the block returns a non-nil feature, so shapes that produce no feature (e.g. no geographic item) are never marked seen. Subsequent occurrences: yields skip_geometry=true (geometry skipped, nil in feature).

When seen or shape_key is nil (deduplication disabled or no shape available), yields skip_geometry=false unconditionally.



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# File 'app/helpers/otus_helper.rb', line 654

def build_geo_json_feature_deduped(seen, shape_key)
  if seen.nil? || shape_key.nil? || shape_key.first.nil?
    return yield(false)
  end

  key = "#{shape_key[0]}_#{shape_key[1]}"
  if seen.key?(key)
    yield(true)
  else
    g = yield(false)
    seen[key] = true if g
    g
  end
end

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

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

Returns:

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



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# File 'app/helpers/otus_helper.rb', line 581

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

#geojson_for_otu(otu) ⇒ Object 



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

def geojson_for_otu(otu)
  {
    'type' => 'FeatureCollection',
    'features' => [],
    'properties' => {
      'target' => geojson_target_for_otu(otu)
    }
  }
end

#geojson_target_for_otu(otu) ⇒ Object 



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# File 'app/helpers/otus_helper.rb', line 365

def geojson_target_for_otu(otu)
  {
    'id' => otu.id,
    'label' => label_for_otu(otu),
    'type' => 'Otu'
  }
end

#label_for_otu(otu) ⇒ Object 



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# File 'app/helpers/otus_helper.rb', line 60

def label_for_otu(otu)
  return nil if otu.nil?
  [ label_for_taxon_name(otu.taxon_name),
    otu.name
  ].compact.join(': ')
end

#next_records(otu) ⇒ Array

Returns of OTUs.

Returns:

  • (Array) —

    of OTUs



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# File 'app/helpers/otus_helper.rb', line 164

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

Returns no HTML inside .

Returns:

  • (String) —

    no HTML inside 



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# File 'app/helpers/otus_helper.rb', line 124

def otu_autocomplete_selected_tag(otu)
  return nil if otu.nil? || (otu.new_record? && !otu.changed?)
  [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 



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# File 'app/helpers/otus_helper.rb', line 55

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

#otu_autoselect_info(otu) ⇒ Object 



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# File 'app/helpers/otus_helper.rb', line 28

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_autoselect_tag(otu) ⇒ Object

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



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# File 'app/helpers/otus_helper.rb', line 7

def otu_autoselect_tag(otu)
  return nil if otu.nil?
  if otu.taxon_name&.is_combination?
    if otu.name.present?
      return [
        otu.name,
        '=',
        tag.span( otu.taxon_name.cached_html_name_and_author_year.html_safe, class: :klass),
        TaxonNamesHelper::COMBINATION_MARK
      ].compact.join(' ')
    else
      return tag.span( otu.taxon_name.cached_html_name_and_author_year.html_safe, class: :klass)
    end
  else
    return  [
      otu.taxon_name&.cached_html_name_and_author_year,
      otu.name
    ].compact.join(' ')
  end
end

#otu_cached_map(otu, target, cached_map_type = 'CachedMapItem::WebLevel1', cache = true, force = false) ⇒ Object

NOT USED Caching the cached map



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# File 'app/helpers/otus_helper.rb', line 388

def otu_cached_map(otu, target, cached_map_type = 'CachedMapItem::WebLevel1', cache = true, force = false)
  r = nil
  if force
    r = aggregate_geo_json(otu, target, cached_map_type)
  else
    # Check for map

    # TODO: extend with synced check
    if a = CachedMap.where(project_id: sessions_current_project_id).where(otu_id: otu.id, cached_map_type:  )
    end
  end
end

#otu_common_names_label(common_names, term = nil) ⇒ Object 



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# File 'app/helpers/otus_helper.rb', line 93

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_distribution(otu, children = true, cutoff = 200) ⇒ Object

TODO:

  • make properties universal type: 'Model', id: id, label:
  • merge origin_otu_id: id to reference coordinate OTUs

target:

type: Otu
label:
id

base: # one level above target (or one level below shape?!) type:

id:

shape: # Either GeographicArea or Georeference type id

Returns:

  • Hash A GeoJSON collection of distribution data in x parts need a to_geo_json for each object

    :asserted_distributions
  with shape
  without shapes
:collection_objects
    with georeferences
    with GeographicAreas
:type material
    with georeferences
    with GeographicAreas


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# File 'app/helpers/otus_helper.rb', line 255

def otu_distribution(otu, children = true, cutoff = 200)
  return {} if otu.nil?
  otus = if children
    otu.coordinate_otus_with_children
  else
    Otu.coordinate_otus(otu.id)
  end

  h = geojson_for_otu(otu)

  if otu.taxon_name && otu.taxon_name.is_protonym? && !otu.taxon_name.is_species_rank?
    add_aggregate_geo_json(otu, h)
  else
    otus = if children
            otu.coordinate_otus_with_children
          else
            Otu.coordinate_otus(otu.id)
          end

    # Batch-load everything the downstream helpers touch.
    otus = otus.includes(
      :taxon_name,
      current_field_occurrences: [
        :identifiers,
        { collecting_event: [ :georeferences, :geographic_area, :geographic_items ] }
      ],
      current_collection_objects: [
        :identifiers,
        { collecting_event: [ :georeferences, :geographic_area, :geographic_items ] }
      ],
      asserted_distributions: { asserted_distribution_shape: :geographic_items },
      type_materials: [
        { collection_object: [
            :identifiers,
            { collecting_event: [ :georeferences, :geographic_area, :geographic_items ] }
          ] }
      ]
    )

    seen_shapes = {
      field_occurrences: {},
      collection_objects: {},
      asserted_distributions: {},
      type_materials: {}
    }

    otus.each do |o|
      add_distribution_geo_json(o, h, seen_shapes)
    end
  end

  h
end

#otu_distribution_is_absent(otu, descendants: false) ⇒ Hash

Returns GeoJSON FeatureCollection of absent FieldOccurrences and AssertedDistributions for the OTU, its coordinate OTUs, and ancestor taxon names (traversed via TaxonNameHierarchies).

Parameters:

  • descendants (Boolean) (defaults to: false) —

    when true, also include direct absents from descendant OTUs. Off by default: a descendant's absence does not propagate up to the OTU, and a sibling descendant's presence in the same region may contradict it. Use only when the caller wants a clade-wide visualization.

Returns:

  • (Hash) —

    GeoJSON FeatureCollection of absent FieldOccurrences and AssertedDistributions for the OTU, its coordinate OTUs, and ancestor taxon names (traversed via TaxonNameHierarchies).



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# File 'app/helpers/otus_helper.rb', line 317

def otu_distribution_is_absent(otu, descendants: false)
  return {} if otu.nil?

  h = geojson_for_otu(otu)
  seen_shapes = {
    field_occurrences: {},
    asserted_distributions: {}
  }

  otus = descendants ? otu.coordinate_otus_with_children : Otu.coordinate_otus(otu.id)

  otus.each do |o|
    t = geojson_target_for_otu(o)

    o.absent_and_ancestor_absent_field_occurrences.each do |f|
      shape_key = f.collecting_event&.geo_json_shape_key
      g = build_geo_json_feature_deduped(seen_shapes[:field_occurrences], shape_key) do |skip_geometry|
        field_occurrence_to_geo_json_feature(f, skip_geometry:)
      end
      next unless g
      g['properties']['target'] = t
      h['features'].push g
    end

    o.absent_and_ancestor_absent_asserted_distributions.each do |a|
      shape_key = [a.asserted_distribution_shape_type, a.asserted_distribution_shape_id]
      g = build_geo_json_feature_deduped(seen_shapes[:asserted_distributions], shape_key) do |skip_geometry|
        asserted_distribution_to_geo_json_feature(a, skip_geometry:)
      end
      next unless g
      g['properties']['target'] = t
      h['features'].push g
    end
  end

  h
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 76

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 623

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)
        .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 131

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

#otu_tag(otu) ⇒ Object 



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# File 'app/helpers/otus_helper.rb', line 48

def otu_tag(otu)
  return nil if otu.nil?
  a = otu_tag_elements(otu)
  a.push taxon_name_type_short_tag(otu.taxon_name)
  content_tag(:span, a.compact.join(' ').html_safe, class: :otu_tag)
end

#otu_tag_elements(otu) ⇒ Object 



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# File 'app/helpers/otus_helper.rb', line 67

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 140

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 158

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 153

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 136

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 202

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 207

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 185

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 554

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 611

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