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# File 'app/helpers/observation_matrices/export/otu_contents_helper.rb', line 2
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)
otu_rows = {}
otus.each do |i|
otu_rows[i.id] = i.row_id
end
otu_ids = otu_rows.keys
CSV.generate do |csv|
csv << ['otu_id', 'topic', 'text']
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)
protonyms.each do |p|
csv << ['row_' + p.row_id.to_s, 'Taxon name', [p.otu_name, p.cached_html].compact.join(': ') ]
end
protonyms.each do |p|
csv << ['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|
history = p.nomeclatural_history
unless history.empty?
st = []
history.each do |h|
st.push( [h[:name], h[:author_year], h[:statuses]].join(' '))
end
csv << ['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|
csv << ['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)
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
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).
where("rank_class LIKE '%Family%' OR rank_class LIKE '%Genus%'").
order(:observation_object_id)
protonyms.each do |p|
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?
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)
protonyms.each do |p|
type = p&.type_materials&.primary&.first&.collection_object&.repository&.name
csv << ['row_' + p.row_id.to_s, 'Type repository', type ] unless type.nil?
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?
img_attr = Image.find(depiction[:image_id]).attribution
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>\n"
list += "#{tag.img(src: short_url(href), class: 'tw_image')}<br>\n"
list += "<b>Label:</b> #{lbl}<br>\n" unless lbl.blank?
list += "<b>Citation:</b> #{cit}<br>\n" unless cit.blank?
list += "</span>\n"
end
end
csv << ['row_' + otu_rows[object[1][:otu_id]].to_s, 'Illustrations', list ] unless list.blank?
end
end
end
end
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