Module: Export::Coldp::Files::TaxonConceptRelation

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

Overview

The target format for CoLDP is:

taxonID relatedTaxonID sourceID type referenceID remarks modified modifiedBy

TODO: This hasn’t been tested IRL.

Constant Summary collapse

MAP_TYPES = 
{
  "OtuRelationship::Intersecting" => "intersecting", # TODO: not included in CLB? http://api.checklistbank.org/vocab/TaxonConceptRelType
  "OtuRelationship::Disjoint" => "excludes",
  "OtuRelationship::Equal" => "equals",
  "OtuRelationship::ProperPartInverse" => "includes",
  "OtuRelationship::ProperPart" => "included in",
  "OtuRelationship::PartiallyOverlapping" => "overlaps",
}

Class Method Summary collapse

Class Method Details

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



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# File 'lib/export/coldp/files/taxon_concept_relation.rb', line 29

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

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

    a = OtuRelationship.with(otu_scope: otus.select(:id))
      .joins('JOIN otu_scope os1 on os1.id = otu_relationships.subject_otu_id')

    b = OtuRelationship.with(otu_scope: otus.select(:id))
      .joins('JOIN otu_scope os1 on os1.id = otu_relationships.object_otu_id')

    c = ::Queries.union(OtuRelationship, [a,b])

    c.each do |orel|
      sources = orel.sources.load
      reference_ids = sources.collect{|a| a.id}
      reference_id = reference_ids.first

      csv << [
        orel.subject_otu_id,                                             # taxonID
        orel.object_otu_id,                                              # relatedTaxonID
        nil,                                                             # sourceID
        type(orel),                                                      # type
        reference_id,                                                    # referenceID
        nil,                                                             # remarks
        Export::Coldp.modified(orel[:updated_at]),                       # modified
        Export::Coldp.modified_by(orel[:updated_by_id], project_members) # modified_by
      ]

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

.type(orel) ⇒ Object 



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

def self.type(orel)
  MAP_TYPES[orel.type]
end