Module: Protonym::Becomes

Extended by:
ActiveSupport::Concern
Included in:
Protonym
Defined in:
app/models/protonym/becomes.rb

Overview

This module contains code that lets us convert Protonyms with very specific attributes into a Combination. It is used almost exclusively during an import.

Defined Under Namespace

Modules: ClassMethods

Instance Method Summary collapse

Instance Method Details

#becomes_combination ⇒ self, or self as Combination

Convert a Protonym into a Combination.

Returns:



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# File 'app/models/protonym/becomes.rb', line 97

def becomes_combination
  a, original_relationships, c = nil, nil, nil

  if b = convertable_to_combination?
    a, original_relationships = b
  else
    return self
  end

  begin
    Protonym.transaction do
      c = becomes!(Combination)

      c.assign_attributes(
        rank_class: nil,
        name: nil,
        verbatim_name: cached_original_combination,
        disable_combination_relationship_check: true
      )
      c.clear_cached

      # Destroy invalidating relationship, but note
      # what it references.
      o = a.object_taxon_name
      a_id = a.id
      a.destroy!

      taxon_name_relationships.each do |r|
        next if r.object_taxon_name_id == r.subject_taxon_name_id
        next if r.id == a_id
        r.update_column(:subject_taxon_name_id, o.id)
      end

      original_relationships.each do |i|
        atr = { type: i.type.gsub(/TaxonNameRelationship::OriginalCombination::Original/, 'TaxonNameRelationship::Combination::' ) }
        if i.object_taxon_name_id == i.subject_taxon_name_id
          atr[:subject_taxon_name_id] = o.id
        end

        i.update_columns(atr)
      end

      # Why?  Do something more specific, like
      c.save!
      c.disable_combination_relationship_check = false
      c
    end

  # Note: technically a.destroy could hit this, but that should never happen.
  rescue ActiveRecord::RecordInvalid => e
    errors.add(:base, 'Combination failed to save: ' + c.errors.full_messages.join('; '))
    c = becomes!(Protonym)
  rescue
    raise
  end

  c
  # TODO: This fixes ./spec/models/combination/combination_spec.rb:62. But is returning `self` (or `z`) when fails trustworthy?
  # self
end

#becomes_test_classifications ⇒ Object 



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# File 'app/models/protonym/becomes.rb', line 55

def becomes_test_classifications
  if taxon_name_classifications.any?
    errors.add(:base, 'Protonym has taxon name classifications, it can not be converted to combination.')
    false
  else
    true
  end
end

#becomes_test_for_original_genus ⇒ Object 



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# File 'app/models/protonym/becomes.rb', line 37

def becomes_test_for_original_genus
  if original_genus
    true
  else
    errors.add(:base, 'Protonym does not have original genus assigned.')
    false
  end
end

#becomes_test_for_original_relationships ⇒ Object 



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# File 'app/models/protonym/becomes.rb', line 73

def becomes_test_for_original_relationships
  r = original_combination_relationships.load
  if r.select{|r| r.subject_taxon_name_id == id}.empty?
    errors.add(:base, 'Protonym is missing original combination relationship to self.')
    false
  else
    r
  end
end

#becomes_test_for_other_relationships ⇒ Object 



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# File 'app/models/protonym/becomes.rb', line 64

def becomes_test_for_other_relationships
  if related_taxon_name_relationships.with_type_base('TaxonNameRelationship::Iczn').any? || related_taxon_name_relationships.with_type_base('TaxonNameRelationship::Typification').any?
    errors.add(:base, 'Protonym has additional taxon name relationships, it can not be converted to combination.')
    false
  else
    true
  end
end

#becomes_test_for_relationship ⇒ Object 



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# File 'app/models/protonym/becomes.rb', line 12

def becomes_test_for_relationship
  # a = TaxonNameRelationship::Iczn::Invalidating.where(subject_taxon_name: self).first ### This one returns all subclasses
  a = TaxonNameRelationship.where(subject_taxon_name: self, type: 'TaxonNameRelationship::Iczn::Invalidating').first
  if a.nil? || a.subject_taxon_name_id == a.object_taxon_name_id
    errors.add(:base, 'Required TaxonNameRelationship::Iczn::Invalidating relationship not found on this name.')
    false
  else
    if a.similar_homonym_string
      a
    else
      s = a.subject_taxon_name
      if !s.cached_secondary_homonym_alternative_spelling.blank?
        ids = TaxonName.where(cached_valid_taxon_name_id: s.cached_valid_taxon_name_id).pluck(:id)
        TaxonNameRelationship.where(subject_taxon_name: ids).where("type LIKE 'TaxonNameRelationship::Iczn::Invalidating::Synonym%'").each do |tr|
          o = tr.subject_taxon_name
          if !o.cached_secondary_homonym_alternative_spelling.blank? && s.cached_secondary_homonym_alternative_spelling == o.cached_secondary_homonym_alternative_spelling && s.cached_valid_taxon_name_id == o.cached_valid_taxon_name_id
            a.object_taxon_name_id = o.id
          end
        end
      end
      a
    end
  end
end

#becomes_test_for_similarity(invalidating_relationship) ⇒ Object 



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# File 'app/models/protonym/becomes.rb', line 46

def becomes_test_for_similarity(invalidating_relationship)
  if invalidating_relationship.similar_homonym_string
    true
  else
    errors.add(:base, 'Related invalid name is not similar enough to protonym to be treated as combination.')
    false
  end
end

#convertable_to_combination? ⇒ [taxon_name_relationship, original_relationships]

Returns:

  • ([taxon_name_relationship, original_relationships]) 


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# File 'app/models/protonym/becomes.rb', line 84

def convertable_to_combination?
  a = nil
  return false unless a = becomes_test_for_relationship
  return false unless becomes_test_for_similarity(a)
  return false unless becomes_test_for_original_genus
  return false unless becomes_test_classifications
  return false unless becomes_test_for_other_relationships
  return false unless original_relationships = becomes_test_for_original_relationships
  return [a, original_relationships]
end