Module: Export::Coldp::Files::NameRelation

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

Overview

nameID relatedNameID type referenceID remarks

Constant Summary collapse

BLOCKED =

These concepts do not really fit with the CoL Name/NameRelation data model or are represented in a different way TODO: SupressedSynony misspelled in TW models, which probably should be SupressedSynonym

%w{
  TaxonNameRelationship::Typification
  TaxonNameRelationship::CurrentCombination
  TaxonNameRelationship::Combination
  TaxonNameRelationship::Combination::Family
  TaxonNameRelationship::Combination::Genus
  TaxonNameRelationship::Combination::Subgenus
  TaxonNameRelationship::Combination::Species
  TaxonNameRelationship::Combination::Subspecies
  TaxonNameRelationship::Combination::Variety
  TaxonNameRelationship::Combination::Subvariety
  TaxonNameRelationship::Combination::Series
  TaxonNameRelationship::Combination::Subseries
  TaxonNameRelationship::Combination::Section
  TaxonNameRelationship::Combination::Subsection
  TaxonNameRelationship::Combination::Form
  TaxonNameRelationship::Combination::Subform
  TaxonNameRelationship::OriginalCombination
  TaxonNameRelationship::OriginalCombination::Original
  TaxonNameRelationship::OriginalCombination::OriginalGenus
  TaxonNameRelationship::OriginalCombination::OriginalSubgenus
  TaxonNameRelationship::OriginalCombination::OriginalSpecies
  TaxonNameRelationship::OriginalCombination::OriginalSubspecies
  TaxonNameRelationship::OriginalCombination::OriginalVariety
  TaxonNameRelationship::OriginalCombination::OriginalSubvariety
  TaxonNameRelationship::OriginalCombination::OriginalForm
  TaxonNameRelationship::OriginalCombination::OriginalSubform
  TaxonNameRelationship::SourceClassifiedAs
  TaxonNameRelationship::Iczn::Invalidating
  TaxonNameRelationship::Iczn::Invalidating::Suppression::Total
  TaxonNameRelationship::Iczn::Invalidating::Misapplication
  TaxonNameRelationship::Iczn::Invalidating::Synonym
  TaxonNameRelationship::Iczn::Invalidating::Synonym::Subjective
  TaxonNameRelationship::Iczn::Invalidating::Usage
  TaxonNameRelationship::Iczn::PotentiallyValidating
  TaxonNameRelationship::Iczn::Validating
  TaxonNameRelationship::Iczn::Validating::UncertainPlacement
  TaxonNameRelationship::Icnp::Accepting
  TaxonNameRelationship::Icnp::Unaccepting
  TaxonNameRelationship::Icnp::Unaccepting::Synonym
  TaxonNameRelationship::Icnp::Unaccepting::SupressedSynonym
  TaxonNameRelationship::Icnp::Unaccepting::Usage
  TaxonNameRelationship::Icn::Accepting
  TaxonNameRelationship::Icn::Unaccepting
  TaxonNameRelationship::Icn::Unaccepting::Synonym
  TaxonNameRelationship::Icn::Unaccepting::Synonym::Heterotypic
  TaxonNameRelationship::Icn::Unaccepting::Usage
  TaxonNameRelationship::Icvcn::Accepting
  TaxonNameRelationship::Icvcn::Accepting::UncertainPlacement
  TaxonNameRelationship::Icvcn::Unaccepting
  TaxonNameRelationship::Hybrid
}.freeze

Class Method Summary collapse

Class Method Details

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



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# File 'lib/export/coldp/files/name_relation.rb', line 79

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

    csv << %w{
      nameID
      relatedNameID
      type
      referenceID
      modified
      modifiedBy
      remarks
    }

    rels = taxon_name_relationships(otus)
    rels.length

    rels.each do |tnr|

      next if ::Export::Coldp.skipped_combinations.include?(tnr.subject_taxon_name_id)

      unless tnr.type.constantize.nomen_uri.blank?
        csv << [
          tnr.subject_taxon_name_id,                                       # nameID
          tnr.object_taxon_name_id,                                        # relatedNameID
          tnr.type.constantize.nomen_uri,                                  # type
          tnr.a_source_id,                                                 # referenceID
          Export::Coldp.modified(tnr[:updated_at]),                        # modified
          Export::Coldp.modified_by(tnr[:updated_by_id], project_members), # modified_by
          nil,                                                             # remarks
        ]
      end
    end
  end
  sources = []

  sources = Source.with(name_scope: rels)
    .joins(:citations)
    .joins("JOIN name_scope ns on ns.id = citations.citation_object_id AND citations.citation_object_type = 'TaxonNameRelationship'")
    .distinct

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

.taxon_name_relationships(otus) ⇒ Object

TODO: This is the original set, but it doesn’t quite feel right.



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# File 'lib/export/coldp/files/name_relation.rb', line 67

def self.taxon_name_relationships(otus)

  # TODO: Join in proper name methods, don't rely on OTU scope
  a = TaxonNameRelationship.with(otu_scope: otus.select(:id, :taxon_name_id))
    .joins("JOIN taxon_names obj_tn on obj_tn.id = taxon_name_relationships.object_taxon_name_id")
    .joins("JOIN otu_scope on otu_scope.taxon_name_id = obj_tn.id")
    .left_joins(:sources)
    .where.not(taxon_name_relationships: {type: BLOCKED})
    .group('taxon_name_relationships.id')
    .select("taxon_name_relationships.*, MAX(sources.id) a_source_id")
end