Module: OtusHelper

Defined in:
app/helpers/otus_helper.rb

Instance Method Summary collapse

Instance Method Details

#add_aggregate_geo_json(otu, target) ⇒ Object 



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# File 'app/helpers/otus_helper.rb', line 200

def add_aggregate_geo_json(otu, target)
  h = target

  if g = aggregate_geo_json(otu, h)
    t = {
      'id' => otu.id,
      'type' => 'Otu',
      'label' => label_for_otu(otu)
    }

    g['properties'] = {'aggregate': true}

    g['properties']['target'] = t
    h['features'].push g
  end

  h
end

#add_distribution_geo_json(otu, target) ⇒ Object 



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# File 'app/helpers/otus_helper.rb', line 271

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

  # internal target
  t = {
    'id' => o.id,
    'type' => 'Otu',
    'label' => label_for_otu(otu)
  }

  o.current_collection_objects.each do |c|
    if g = collection_object_to_geo_json_feature(c)
      g['properties']['target'] = t
      h['features'].push g
    end
  end

  o.asserted_distributions.each do |a|
    if g = asserted_distribution_to_geo_json_feature(a)
      g['properties']['target'] = t
      h['features'].push g
    end
  end

  o.type_materials.each do |e|
    if g = type_material_to_geo_json_feature(e)
      g['properties']['target'] = t
      h['features'].push g
    end
  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 235

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' => {
          'type' => 'Otu',
          'id' => otu.id,
          'label' => label_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 61

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) ⇒ 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 331

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 10

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

#next_otus(otu) ⇒ Array

Returns of OTUs.

Returns:

  • (Array) —

    of OTUs



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

def next_otus(otu)
  if otu.taxon_name_id
    o = []
    t = otu.taxon_name.next_sibling
    unless t.nil?
      while o.empty?
        o = t&.otus.to_a
        break if t.nil?
        t = t.next_sibling
      end
    end
    o
  else
    Otu.where(project_id: otu.id).where('id > ?', otu.id).all
  end
end

#otu_autocomplete_selected_tag(otu) ⇒ String

Returns no HTML inside <input>.

Returns:

  • (String) —

    no HTML inside <input>



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# File 'app/helpers/otus_helper.rb', line 38

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_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 221

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

TODO:

* make properties universal
  type: 'Model',
  id: id,
  label: <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 169

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 = {
    'type' => 'FeatureCollection',
    'features' => [],
    'properties' => {
      'target' => { # Top level target
        'id' => otu.id,
        'label' => label_for_otu(otu),
        'type' => 'Otu'
      }
    }
  }

  if otu.taxon_name && otu.taxon_name.is_protonym? && !otu.taxon_name.is_species_rank?
    add_aggregate_geo_json(otu, h)
  else
    otus.each do |o|
      add_distribution_geo_json(o, h)
    end
  end

  h
end

#otu_extended_autocomplete_tag(target) ⇒ Object

Used exclusively in /api/v1/otus/autocomplete



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# File 'app/helpers/otus_helper.rb', line 26

def otu_extended_autocomplete_tag(target)
  if target.kind_of?(Otu)
    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)
    tag.span( a.compact.join(' ').html_safe, class: :otu_tag )
  end
end

#otu_key_inventory(otu, is_public: true) ⇒ Object 



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# File 'app/helpers/otus_helper.rb', line 361

def otu_key_inventory(otu, is_public: true)
  return {
    observation_matrices: {
      scoped: otu.in_scope_observation_matrices.where(is_public:).select(:id, :name).inject({}){|hsh, m| hsh[m.id] = m.name; hsh;} || {} ,
      in: otu.observation_matrices.where(is_public:).select(:id, :name).inject({}){|hsh, m| hsh[m.id] = m.name; hsh;} || {},
    },
    leads: {
      scoped: otu.leads.where(parent_id: nil, is_public:).select(:id, :text).inject({}){|hsh, m| hsh[m.id] = m.text; hsh;} || {},
      in:  otu.leads.where.not(parent_id: nil).where(is_public: true).select(:id, :text).inject({}){|hsh, m| hsh[m.id] = m.text; hsh;} || {},
    }
  }
end

#otu_link(otu) ⇒ Object 



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

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 3

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 17

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

#otus_link_list_tag(otus) ⇒ Object 



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# File 'app/helpers/otus_helper.rb', line 54

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 72

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 67

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 50

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

#parent_otus(otu) ⇒ Object 



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# File 'app/helpers/otus_helper.rb', line 116

def parent_otus(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 121

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_otus(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 99

def previous_otus(otu)
  if otu.taxon_name_id
    o = []
    t = otu.taxon_name.previous_sibling
    unless t.nil?
      while o.empty?
        o = t&.otus.to_a
        break if t.nil?
        t = t.previous_sibling
      end
    end
    o
  else
    Otu.where(project_id: otu.id).where('id < ?', otu.id).all
  end
end

#ranked_otu_table(otus) ⇒ Object 



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# File 'app/helpers/otus_helper.rb', line 305

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