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

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

Overview

taxonID relatedTaxonID relatedTaxonScientificName type referenceID remarks

Class Method Summary collapse

Class Method Details

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



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# File 'lib/export/coldp/files/species_interaction.rb', line 59

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


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

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

    q = ::Queries::BiologicalAssociation::Filter.new({})
    q.otu_query = otus

    # TODO: expand for CollectionObject or FO occurrences later
    q.all.where(biological_association_subject_type: 'Otu', biological_association_object_type: 'Otu' ).find_each do |ba|

      taxon_id = taxon_id(ba)
      related_taxon_id = related_taxon_id(ba)
      sources = ba.sources.load
      reference_ids = sources.collect{|a| a.id}
      reference_id = reference_ids.first

      csv << [
        taxon_id,                                                       # taxonID
        related_taxon_id,                                               # relatedTaxonID
        related_taxon_scientific_name(related_taxon_id),                # relatedTaxonScientificName
        species_interaction_type(ba),                                   # type
        reference_id,                                                   # referenceID
        Export::Coldp.modified(ba[:update_at]),                         # modified
        Export::Coldp.modified_by(ba[:updated_by_id], project_members), # modified_by
        nil                                                             # remarks
      ]

      Export::Coldp::Files::Reference.add_reference_rows(sources, reference_csv, project_members) if reference_csv
    end
    # end
  end
end

.related_taxon_id(ba) ⇒ Object 



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# File 'lib/export/coldp/files/species_interaction.rb', line 22

def self.related_taxon_id(ba)
  object_otu = nil
  if ba.biological_association_object_type == "Otu"
    begin
      object_otu = Otu.find(ba.biological_association_object_id).id
    rescue ActiveRecord::RecordNotFound
      object_otu = nil
    end
  end
  object_otu
end

.related_taxon_scientific_name(otu_id) ⇒ Object 



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# File 'lib/export/coldp/files/species_interaction.rb', line 34

def self.related_taxon_scientific_name(otu_id)
  object_taxon_name = nil
  begin
    o = Otu.find(otu_id)
  rescue ActiveRecord::RecordNotFound
    return nil
  end
  if !o.taxon_name_id.nil?
    object_taxon_name = TaxonName.find(o.taxon_name_id).cached
  else
    unless o.name.nil?
      object_taxon_name = o.name
    end
  end
  object_taxon_name
end

.species_interaction_type(ba, inverted = false) ⇒ Object 



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# File 'lib/export/coldp/files/species_interaction.rb', line 51

def self.species_interaction_type(ba, inverted=false)
  species_interaction_type = BiologicalRelationship.find(ba.biological_relationship_id).name
  if inverted
    species_interaction_type = BiologicalRelationship.find(ba.biological_relationship_id).inverted_name
  end
  species_interaction_type
end

.taxon_id(ba) ⇒ Object 



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# File 'lib/export/coldp/files/species_interaction.rb', line 10

def self.taxon_id(ba)
  subject_otu = nil
  if ba.biological_association_subject_type == "Otu"
    begin
      subject_otu = Otu.find(ba.biological_association_subject_id).id
    rescue ActiveRecord::RecordNotFound
      subject_otu = nil
    end
  end
  subject_otu
end