Module: Export::Coldp::Files::VernacularName

Defined in:
lib/export/coldp/files/vernacular_name.rb

Overview

taxon_id name - ORIGINAL LANGUAGE transliteration language country area sex reference_id modified modifiedBy

Class Method Summary collapse

Class Method Details

.area(common_name) ⇒ Object

[View source]

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# File 'lib/export/coldp/files/vernacular_name.rb', line 25

def self.area(common_name)
  common_name.geographic_area&.self_and_ancestors&.collect{|a| a.name}&.join('; ')
end

.generate(otus, project_members, reference_csv = nil) ⇒ Object

[View source]

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# File 'lib/export/coldp/files/vernacular_name.rb', line 44

def self.generate(otus, project_members, reference_csv = nil )
  ::CSV.generate(col_sep: "\t") do |csv|

    # TODO: Biocuration attributes on these two
    # sex

    csv << %w{
      taxonID
      name
      transliteration
      language
      country
      area
      referenceID
      modified
      modifiedBy
    }

    otus.joins(:common_names).each do |o|
      o.common_names.each do |n|
        sources = n.sources.load

        csv << [
          o.id,                                                          # taxon_id
          n.name,                                                        # name
          transliteration(n),                                            # transliteration
          n.language&.alpha_3_bibliographic,                             # language
          n.geographic_area&.level0&.iso_3166_a2,                        # country
          area(n),                                                       # area
          sources.collect{|a| a.id}.join(','),                           # reference_id
          Export::Coldp.modified(n[:updated_at]),                        # modified
          Export::Coldp.modified_by(n[:updated_by_id], project_members)  # modified_by
        ]

        Export::Coldp::Files::Reference.add_reference_rows(sources, reference_csv, project_members) if reference_csv && sources.any?
      end
    end
  end
end

.reference_id(common_name) ⇒ String?

“supporting the taxonomic concept” Potentially- all other Citations tied to OTU, what exactly supports a concept?

Not used internally within CoLDP, for reference only. TODO: confirm.

Returns:

  • (String, nil)
[View source]

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# File 'lib/export/coldp/files/vernacular_name.rb', line 38

def self.reference_id(common_name)
  i = common_name.sources.pluck(:id)
  return i.join(',') if i.any?
  nil
end

.sex(common_name) ⇒ Object

TODO: Map to biocuration attribute via URI

[View source]

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# File 'lib/export/coldp/files/vernacular_name.rb', line 30

def self.sex(common_name)
  nil
end

.transliteration(common_name) ⇒ String?

Returns the ‘English’ translation(s) if available.

Returns:

  • (String, nil) —

    the ‘English’ translation(s) if available

[View source]

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# File 'lib/export/coldp/files/vernacular_name.rb', line 16

def self.transliteration(common_name)
  n = common_name.alternate_values.where(type: 'AlternateValue::Translation', alternate_value_object_attribute: :name).load
  if n.any?
    n.collect{|a| a.language.name == 'English' ? a.language.name : nil}.compact.join('; ')
  else
    nil
  end
end