Module: Export::Coldp::Files::SpeciesInteraction

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

Class Method Summary collapse

Class Method Details

.biological_association_indices(otus) ⇒ Object 



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

def self.biological_association_indices(otus)
  b = BiologicalAssociationIndex
    .with(otus:)
    .joins("JOIN otus on otus.id = biological_association_indices.subject_id and biological_association_indices.subject_type = 'Otu'")
    .left_joins(biological_association: [:sources])
    .group('biological_association_id, subject_id, object_label, relationship_name, biological_association_indices.id, biological_associations.updated_at, biological_associations.updated_by_id, sources.id')
    .order('biological_association_id, sources.cached_nomenclature_date')
    .select(
      %w{
       biological_association_indices.id
       subject_id
       object_label
       relationship_name
       MAX(sources.id)\ AS\ source_id
       sources.cached_nomenclature_date
       biological_associations.updated_at
       biological_associations.updated_by_id
      }.join(', ')
    )
end

.biological_relationships(otus) ⇒ Object 



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# File 'lib/export/coldp/files/species_interaction.rb', line 50

def self.biological_relationships(otus)
  BiologicalRelationship.where(project_id: otus.first.project_id)
end

.checklistbank_vocab ⇒ Object 



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

def self.checklistbank_vocab
  url = URI.parse("https://api.checklistbank.org/vocab/speciesinteractiontype")
  response = Net::HTTP.get_response(url)

  if response.is_a?(Net::HTTPSuccess)
    data = JSON.parse(response.body)
  else
    {}
  end
end

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



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# File 'lib/export/coldp/files/species_interaction.rb', line 54

def self.generate(otus, project_members, reference_csv = nil )

  # We could skip non-standard vocabulary using this, but for now we just let it ride.
  # cvb = checklistbank_vocab

  # TODO: Support/encourage use of  Global URI Identifiers on BiologicalRelationships
  #
  #   Use those identifers as a proxy for type.
  #
  # br = biological_relationships(otus)
  # br_lookup = br.inject({}){|hsh, a| hsh['name'] = hsh['uri']; hsh}
  #

  CSV.generate(col_sep: "\t") do |csv|

    csv << %w{
      taxonID
      relatedTaxonID
      relatedTaxonScientificName
      type
      referenceID
      modified
      modifiedBy
      remarks
    }

    a = biological_association_indices(otus)

    a.find_each(batch_size: 2000) do |bai|
      csv << [
        bai.subject_id,                                                 # taxonID
        nil,                                                            # relatedTaxonID
        bai.object_label,                                               # relatedTaxonScientificName
        bai.relationship_name,                                          # type
        bai.source_id,                                                  # referenceID
        Export::Coldp.modified(bai[:updated_at]),                         # modified
        Export::Coldp.modified_by(bai[:updated_by_id], project_members), # modified_by
        nil                                                             # remarks
      ]
    end

    sources = Source.with(a: ).joins('JOIN a on a.source_id = sources.id')
    Export::Coldp::Files::Reference.add_reference_rows(sources, reference_csv, project_members) if reference_csv

  end
end