Module: ObservationMatrices::Export::OtuContentsHelper

Includes:
Lib::DistributionHelper
Defined in:
app/helpers/observation_matrices/export/otu_contents_helper.rb

Instance Method Summary collapse

Instance Method Details

#content_type_material(t) ⇒ Object 



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# File 'app/helpers/observation_matrices/export/otu_contents_helper.rb', line 232

def content_type_material(t)
  return nil if t.type != 'Protonym'

  # Species type
  if t.is_species_rank?
    types = t.get_primary_type
    if types.any?
      return types.collect{|i| type_material_catalog_label(i)}.join('. ')
    else
      return nil
    end
  else
    if type_taxon_name_relationship = t&.type_taxon_name_relationship
      str = citations_tag(type_taxon_name_relationship)
      [ ' ' + type_taxon_name_relationship_label(t.type_taxon_name_relationship),
        (type_taxon_name_relationship.citations&.load&.any? ?  ' in ' : nil),
        str
      ].compact.join #.html_safe
    else
      nil
    end
  end
end

#get_otu_contents(options = {}) ⇒ Object 



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# File 'app/helpers/observation_matrices/export/otu_contents_helper.rb', line 5

def get_otu_contents(options = {})
  opt = {otus: []}.merge!(options)

  m = opt[:observation_matrix]

  otus = Otu.select('otus.*, observation_matrix_rows.id AS row_id').
    joins('INNER JOIN observation_matrix_rows ON observation_matrix_rows.observation_object_id = otus.id').
    where("observation_matrix_rows.observation_object_type = 'Otu'").
    where('observation_matrix_rows.observation_matrix_id = (?)', m.id).
    order(:observation_object_id) # Doesn't facilitate mixed object types

  otu_rows = {}

  otus.each do |i|
    otu_rows[i.id] = i.row_id
  end

  otu_ids = otu_rows.keys

  content_hash = {}
  content_columns = {}

  if options[:taxon_name] == 'true'
    protonyms = Protonym.select('taxon_names.*, otus.name AS otu_name, observation_matrix_rows.id AS row_id').
      joins(:otus).joins('INNER JOIN observation_matrix_rows ON observation_matrix_rows.observation_object_id = otus.id').
      where("observation_matrix_rows.observation_object_type = 'Otu'").
      where('otus.id IN (?)', otu_ids).where('observation_matrix_rows.observation_matrix_id = (?)', m.id).
      order(:observation_object_id)

    content_columns['Taxon name'] = true
    content_columns['Authority'] = true

    protonyms.each do |p|
      ##### csv << ['row_' + p.row_id.to_s, 'Taxon name', [p.otu_name, p.cached_html].compact.join(': ') ]
      content_hash['row_' + p.row_id.to_s] ||= {}
      content_hash['row_' + p.row_id.to_s]['Taxon name'] = [p.otu_name, p.cached_html].compact.join(': ')
      content_hash['row_' + p.row_id.to_s]['Authority'] = p.cached_author_year
    end
  end

  if options[:include_nomenclature] == 'true'
    protonyms = Protonym.select('taxon_names.*, observation_matrix_rows.id AS row_id').
      joins(:otus).joins('INNER JOIN observation_matrix_rows ON observation_matrix_rows.observation_object_id = otus.id').
      where("observation_matrix_rows.observation_object_type = 'Otu'").
      where('otus.id IN (?)', otu_ids).where('observation_matrix_rows.observation_matrix_id = (?)', m.id).
      order(:observation_object_id)

    protonyms.each do |p|
      h = p.nomeclatural_history
      unless h.empty?
        st = []
        h.each do |h|
          st.push( [h[:name], h[:author_year], h[:statuses]].join(' '))
        end
        content_columns['Nomenclature'] = true

        content_hash['row_' + p.row_id.to_s] ||= {}
        content_hash['row_' + p.row_id.to_s]['Nomenclature'] = st.join('<br>')
      end
    end

  end

  if options[:include_contents] == 'true'
    contents = Content.select('contents.*, controlled_vocabulary_terms.name, observation_matrix_rows.id AS row_id').
      joins(:topic).joins('INNER JOIN observation_matrix_rows ON observation_matrix_rows.observation_object_id = contents.otu_id').
      where("observation_matrix_rows.observation_object_type = 'Otu'").
      where('contents.otu_id IN (?)', otu_ids).where('observation_matrix_rows.observation_matrix_id = (?)', m.id).
      order(:otu_id, :topic_id)

    contents.each do |i|
      content_columns[i.name] = true
      content_hash['row_' + i.row_id.to_s] ||= {}
      content_hash['row_' + i.row_id.to_s][i.name] = i.text
    end
  end

  if options[:include_autogenerated_description] == 'true'
    otus = Otu.select('otus.*, observation_matrix_rows.id AS row_id').
      joins('INNER JOIN observation_matrix_rows ON observation_matrix_rows.observation_object_id = otus.id').
      where("observation_matrix_rows.observation_object_type = 'Otu'").
      where('observation_matrix_rows.observation_matrix_id = (?)', m.id).
      order(:observation_object_id)

    otus.each do |o|
      description = Tools::Description::FromObservationMatrix.new(project_id: m.project_id, observation_matrix_id: m.id, otu_id: o.id)
      content_columns['Description'] = true

      content_hash['row_' + o.row_id.to_s] ||= {}
      content_hash['row_' + o.row_id.to_s]['Description'] = description.generated_description
      ##### csv << ['row_' + o.row_id.to_s, 'Description', description.generated_description ]
    end
  end

  if options[:include_distribution] == 'true'
    ###### ad = AssertedDistribution.select('asserted_distributions.*, geographic_areas.name, observation_matrix_rows.id AS row_id').
    #  joins(:geographic_area).joins('INNER JOIN observation_matrix_rows ON observation_matrix_rows.observation_object_id = asserted_distributions.otu_id').
    #  where("observation_matrix_rows.observation_object_type = 'Otu'").
    #  where('asserted_distributions.otu_id IN (?)', otu_ids).where('observation_matrix_rows.observation_matrix_id = (?)', m.id).
    #  order(:otu_id, :geographic_area_id)
    #otu_ad = {}
    #ad.each do |i|
    #  otu_ad[i.row_id] = [] if otu_ad[i.row_id].nil?
    #  otu_ad[i.row_id].append(i.name)
    #end
    #otu_ad.each do |key, value|
    #  ##### csv << ['row_' + key.to_s, 'Distribution', value.join(', ') ]
    #end
    #
    protonyms = Protonym.select('taxon_names.*, observation_matrix_rows.id AS row_id').
      joins(:otus).joins('INNER JOIN observation_matrix_rows ON observation_matrix_rows.observation_object_id = otus.id').
      where("observation_matrix_rows.observation_object_type = 'Otu'").
      where('otus.id IN (?)', otu_ids).where('observation_matrix_rows.observation_matrix_id = (?)', m.id).
      order(:observation_object_id)
    protonyms.each do |p|
      content_columns['Distribution'] = true

      content_hash['row_' + p.row_id.to_s] ||= {}
      content_hash['row_' + p.row_id.to_s]['Distribution'] = paper_distribution_entry(p)
    end
  end

  if options[:include_type] == 'true'
    protonyms = Protonym.select('taxon_names.*, observation_matrix_rows.id AS row_id').
      joins(:otus).joins('INNER JOIN observation_matrix_rows ON observation_matrix_rows.observation_object_id = otus.id').
      where("observation_matrix_rows.observation_object_type = 'Otu'").
      where('otus.id IN (?)', otu_ids).where('observation_matrix_rows.observation_matrix_id = (?)', m.id).
      order(:observation_object_id)
    #p_ids = {}
    protonyms.each do |p|
      content_columns['Type'] = true

      content_hash['row_' + p.row_id.to_s] ||= {}

      content_hash['row_' + p.row_id.to_s]['Type'] = content_type_material(p)
      #next unless p_ids[p.id].nil?
      #stype = p.type_species
      #csv << ['row_' + p.row_id.to_s, 'Type species', stype.cached_html_original_name_and_author_year ] unless stype.nil?
      #gtype = p.type_genus
      #csv << ['row_' + p.row_id.to_s, 'Type genus', gtype.cached_html_original_name_and_author_year ] unless gtype.nil?
      #p_ids[p.id] = true
    end
    # protonyms = Protonym.select('taxon_names.*, observation_matrix_rows.id AS row_id').
    #  joins(:otus).joins('INNER JOIN observation_matrix_rows ON observation_matrix_rows.observation_object_id = otus.id').
    #  where("observation_matrix_rows.observation_object_type = 'Otu'").
    #  where('otus.id IN (?)', otu_ids).where('observation_matrix_rows.observation_matrix_id = (?)', m.id).
    #  where("rank_class LIKE '%Species%'").
    #  order(:observation_object_id)
    #p_ids = {}
    #protonyms.each do |p|
    #  next unless p_ids[p.id].nil?
    #  type = p&.type_materials&.primary&.first&.collection_object&.repository&.name
    #  csv << ['row_' + p.row_id.to_s, 'Type repository', type ] unless type.nil?
    #  p_ids[p.id] = true
    #end
    #p_ids = {}
    #protonyms.each do |p|
    #  next unless p_ids[p.id].nil?
    #  type = type = p&.type_materials&.primary&.first&.type_type
    #  csv << ['row_' + p.row_id.to_s, 'Type status', type ] unless type.nil?
    #  p_ids[p.id] = true
    #end
    #p_ids = {}
    #protonyms.each do |p|
    #  next unless p_ids[p.id].nil?
    #  type = p&.type_materials&.primary&.first&.collection_object&.buffered_collecting_event
    #  csv << ['row_' + p.row_id.to_s, 'Type locality', type ] unless type.nil?
    #  p_ids[p.id] = true
    #end
  end

  if options[:include_depictions] == 'true'
    tw_url = 'https://sfg.taxonworks.org'
    im = Tools::ImageMatrix.new(
      project_id: m.project_id,
      otu_filter: otu_ids.join('|'),
      per: 1000000)
    descriptors = im.list_of_descriptors.values
    im.depiction_matrix.each do |object|
      list = ''
      object[1][:depictions].each_with_index do |depictions, index|
        depictions.each do |depiction|
          lbl = []
          cit = im.image_hash[depiction[:image_id]][:citations].collect{|i| i[:cached]}.join('')
          lbl.push(descriptors[index][:name]) unless descriptors[index][:name].blank?
          lbl.push(depiction[:caption]) unless depiction[:caption].blank?
          #lbl.push('<b>Citation:</b> ' + cit) unless cit.blank?
          img_attr = Image.find(depiction[:image_id]).attribution
          #lbl.push(attribution_tag(img_attr).gsub('&#169;', '')) unless img_attr.nil?
          lbl.push(attribution_nexml_label(img_attr)) unless img_attr.nil?
          lbl = lbl.compact.join('; ')

          if im.image_hash[depiction[:image_id]][:image_file_content_type] == 'image/tiff'
            href = im.image_hash[depiction[:image_id]][:medium_url]
          else
            href = im.image_hash[depiction[:image_id]][:original_url]
          end

          list += "<span class='tw_depiction'><br>"
          list += "#{tag.img(src: short_url(href), class: 'tw_image')}<br>"
          list += "<b>Label:</b> #{lbl}<br>" unless lbl.blank?
          list += "<b>Citation:</b> #{cit}<br>" unless cit.blank?
          list += "</span>"
        end
      end
      content_columns['Illustrations'] = true

      content_hash['row_' + otu_rows[object[1][:otu_id]].to_s] ||= {}

      content_hash['row_' + otu_rows[object[1][:otu_id]].to_s]['Illustrations'] = list unless list.blank?
      ##### csv << ['row_' + otu_rows[object[1][:otu_id]].to_s, 'Illustrations', list ] unless list.blank?
    end
  end

  ::CSV.generate(col_sep: "\t") do |csv|
    row = ['otu_id'] + content_columns.keys # Headers
    csv << row
    content_hash.each do |k,v|
      row = [k]
      content_columns.keys.each do |c|
        row << v[c]
      end
      csv << row
    end
  end.html_safe
end