Class: Protonym

Inherits:
TaxonName show all
Extended by:
SoftValidationExtensions::Klass
Includes:
Becomes, SoftValidationExtensions::Instance
Defined in:
app/models/protonym.rb

Overview

Force the loading of TaxonNameRelationships in all worlds. This allows us to edit without restarting in development. Dir[Rails.root.to_s + '/app/models/taxon_name_relationship/*/.rb'].sort.each {|file| require_dependency file }

A monomial TaxonName, a record implies a first usage. This follows Pyle's concept almost exactly.

We inject a lot of relationship helper methods here, in this format.

subject                      object
Aus      original_genus of   bus
aus      type_species of     Bus

Defined Under Namespace

Modules: Becomes, SoftValidationExtensions

Constant Summary collapse

FAMILY_GROUP_ENDINGS =
%w{ini ina inae idae oidae odd ad oidea}.freeze

Constants included from SoftValidationExtensions::Klass

SoftValidationExtensions::Klass::VALIDATIONS

Constants inherited from TaxonName

TaxonName::ALTERNATE_VALUES_FOR, TaxonName::COMBINATION_ELEMENTS, TaxonName::NOMEN_VALID, TaxonName::NOT_LATIN, TaxonName::NO_CACHED_MESSAGE, TaxonName::SPECIES_EPITHET_RANKS

Constants included from SoftValidation

SoftValidation::ANCESTORS_WITH_SOFT_VALIDATIONS

Instance Attribute Summary

Attributes inherited from TaxonName

#also_create_otu, #cached_classified_as, #foo, #no_cached

Class Method Summary collapse

Instance Method Summary collapse

Methods included from Becomes

#becomes_combination, #becomes_test_classifications, #becomes_test_for_original_genus, #becomes_test_for_original_relationships, #becomes_test_for_other_relationships, #becomes_test_for_relationship, #becomes_test_for_similarity, #convertable_to_combination?

Methods included from SoftValidationExtensions::Instance

#sv_author_is_not_required, #sv_extant_children, #sv_family_is_invalid, #sv_family_is_invalid_no_substitute, #sv_fix_add_nominotypical_sub, #sv_fix_author_is_not_required, #sv_fix_coordinated_names_author, #sv_fix_coordinated_names_gender, #sv_fix_coordinated_names_original_form, #sv_fix_coordinated_names_original_genus, #sv_fix_coordinated_names_original_species, #sv_fix_coordinated_names_original_subgenus, #sv_fix_coordinated_names_original_subspecies, #sv_fix_coordinated_names_original_variety, #sv_fix_coordinated_names_part_of_speach, #sv_fix_coordinated_names_source, #sv_fix_coordinated_names_type_genus, #sv_fix_coordinated_names_type_species, #sv_fix_coordinated_names_type_species_type, #sv_fix_coordinated_names_type_specimen, #sv_fix_coordinated_names_year, #sv_fix_misspelling_author_is_not_required, #sv_fix_misspelling_roles_are_not_required, #sv_fix_misspelling_year_is_not_required, #sv_fix_year_is_not_required, #sv_homotypic_synonyms, #sv_missing_author, #sv_missing_etymology, #sv_missing_gender, #sv_missing_original_genus, #sv_missing_part_of_speach, #sv_missing_roles, #sv_missing_substitute_name, #sv_missing_type_genus, #sv_missing_type_species, #sv_missing_year, #sv_misspelling_author_is_not_required, #sv_misspelling_roles_are_not_required, #sv_misspelling_year_is_not_required, #sv_original_combination_relationships, #sv_parent_priority, #sv_potential_family_homonyms, #sv_potential_genus_homonyms, #sv_potential_species_homonyms, #sv_primary_types, #sv_primary_types_repository, #sv_protonym_to_combination, #sv_single_sub_taxon, #sv_source_not_older_then_description, #sv_species_gender_agreement, #sv_species_gender_agreement_not_required, #sv_type_placement, #sv_type_placement1, #sv_validate_coordinated_names_author, #sv_validate_coordinated_names_gender, #sv_validate_coordinated_names_original_form, #sv_validate_coordinated_names_original_genus, #sv_validate_coordinated_names_original_species, #sv_validate_coordinated_names_original_subgenus, #sv_validate_coordinated_names_original_subspecies, #sv_validate_coordinated_names_original_variety, #sv_validate_coordinated_names_part_of_speach, #sv_validate_coordinated_names_source, #sv_validate_coordinated_names_type_genus, #sv_validate_coordinated_names_type_species, #sv_validate_coordinated_names_type_species_type, #sv_validate_coordinated_names_type_specimen, #sv_validate_coordinated_names_year, #sv_validate_parent_rank, #sv_year_is_not_required

Methods inherited from TaxonName

#all_taxon_name_relationships, #ancestor_at_rank, #ancestor_hash, #ancestor_protonyms, #ancestors_through_parents, #author_string, #cached_author, #cached_html_name_and_author_year, #cached_name_and_author_year, #cached_year, #check_for_children, #check_new_rank_class, #classification_invalid_or_unavailable?, #classification_valid?, #clear_cached, #combination_list_all, #combination_list_self, #combined_statuses, #descendant_protonyms, #descendants_at_rank, #first_possible_valid_taxon_name, #first_possible_valid_taxon_name_relationship, foo, #full_name_array, #full_name_hash, #gbif_status_array, #gender_class, #gender_instance, #gender_name, #genderized_name, #get_cached_classified_as, #get_cached_misspelling, #get_full_name, #get_full_name_html, #icn_author_and_year, #iczn_author_and_year, #is_candidatus?, #is_combination?, #is_fossil?, #is_hybrid?, #is_italicized?, #is_protonym?, #is_valid?, #list_of_invalid_taxon_names, #matrix_row_item, #name_in_gender, #name_is_misapplied?, #name_with_misspelling, #next_sibling, #nomenclature_date, #normalized_genus, #not_binomial?, not_leaves, #original_author_year, parent, #parent_is_set?, #part_of_speech_class, #part_of_speech_instance, #part_of_speech_name, #previous_sibling, #rank, #rank_class, #rank_class=, #rank_string, #related_taxon_names, #relationship_invalid?, #safe_self_and_ancestors, select_optimized, #set_cached_author_year, #set_cached_classified_as, #set_cached_valid_taxon_name_id, #set_cached_warnings, sort_by_rank, #statuses_from_classifications, #statuses_from_relationships, #sv_combination_duplicates, #sv_conflicting_subordinate_taxa, #sv_fix_cached_names, #sv_fix_missing_author, #sv_fix_missing_year, #sv_fix_parent_is_valid_name, #sv_homotypic_synonyms, #sv_hybrid_name_relationships, #sv_incomplete_combination, #sv_missing_author, #sv_missing_classifications, #sv_missing_confidence_level, #sv_missing_etymology, #sv_missing_original_publication, #sv_missing_relationships, #sv_missing_year, #sv_not_synonym_of_self, #sv_parent_is_valid_name, #sv_parent_priority, #sv_potential_homonyms, #sv_primary_types, #sv_single_sub_taxon, #sv_species_gender_agreement, #sv_two_unresolved_alternative_synonyms, #sv_type_placement, #sv_validate_coordinated_names, #sv_validate_name, #sv_validate_parent_rank, #synonyms, #taxon_name_classifications_for_statuses, #unavailable_or_invalid?, used_recently, used_recently_in_classifications, used_recently_in_relationships, #validate_one_root_per_project, #validate_parent_from_the_same_project, #validate_parent_is_set, #validate_source_type, with_taxon_name_relationship, #year_integer

Methods included from TaxonName::MatrixHooks

#coordinate_observation_matrix_row_items, #in_scope_observation_matrix_row_items, #out_of_scope_observation_matrix_row_items

Methods included from Shared::MatrixHooks::Dynamic

#dynamic_add_to_matrix_column_items, #dynamic_add_to_matrix_row_items, #dynamic_cleanup_in_scope_column_items, #dynamic_cleanup_in_scope_row_items, #dynamic_cleanup_out_of_scope_column_items, #dynamic_cleanup_out_of_scope_row_items, #dynamic_column_items_in, #dynamic_column_items_out, #dynamic_inspect_matrices, #dynamic_remove_from_matrix_column_items, #dynamic_remove_from_matrix_row_items, #dynamic_row_items_in, #dynamic_row_items_out, #dynamic_syncronize_matrices, #dynamic_update_matrix_column_items?, #dynamic_update_matrix_row_items?, #in_scope_observation_matrix_column_items, #in_scope_observation_matrix_row_items, #out_of_scope_observation_matrix_column_items, #out_of_scope_observation_matrix_row_items, #prepare_matrix_items

Methods included from Shared::MatrixHooks::Member

#member_add_matrix_columns, #member_add_matrix_rows, #member_add_to_matrix_items, #member_of_new_matrix_column_items, #member_of_new_matrix_row_items, #member_of_old_matrix_column_items, #member_of_old_matrix_row_items, #member_remove_from_matrix_items, #member_remove_matrix_columns, #member_remove_matrix_rows, #member_syncronize_matrices, #member_update_matrix_items?

Methods included from Shared::IsData

#errors_excepting, #full_error_messages_excepting, #identical, #is_community?, #is_destroyable?, #is_editable?, #is_in_use?, #is_in_users_projects?, #metamorphosize, #similar

Methods included from SoftValidation

#clear_soft_validations, #fix_soft_validations, #soft_fixed?, #soft_valid?, #soft_validate, #soft_validated?, #soft_validations

Methods included from Shared::AlternateValues

#all_values_for, #alternate_valued?

Methods included from Shared::Confidences

#reject_confidences

Methods included from Shared::Citations

#cited?, #mark_citations_for_destruction, #nomenclature_date, #origin_citation_source_id, #reject_citations, #requires_citation?, #sources_by_topic_id

Methods included from Shared::Depictions

#has_depictions?, #image_array=, #reject_depictions, #reject_images

Methods included from Shared::Notes

#concatenated_notes_string, #reject_notes

Methods included from Shared::Identifiers

#identified?, #next_by_identifier, #previous_by_identifier, #reject_identifiers

Methods included from Shared::Tags

#reject_tags, #tag_with, #tagged?, #tagged_with?

Methods included from Shared::HasRoles

#has_roles?

Methods included from Shared::DataAttributes

#import_attributes, #internal_attributes, #keyword_value_hash, #reject_data_attributes

Methods included from Housekeeping

#has_polymorphic_relationship?

Methods inherited from ApplicationRecord

transaction_with_retry

Class Method Details

.family_group_base(name_string) ⇒ Object


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# File 'app/models/protonym.rb', line 147

def self.family_group_base(name_string)
  name_string.match(/(^.*)(ini|ina|inae|idae|oidae|odd|ad|oidea)$/)
  $1 || name_string
end

.family_group_name_at_rank(name_string, rank_string) ⇒ Object


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# File 'app/models/protonym.rb', line 152

def self.family_group_name_at_rank(name_string, rank_string)
  if name_string == family_group_base(name_string)
    name_string
  else
    family_group_base(name_string) + Ranks.lookup(:iczn, rank_string).constantize.try(:valid_name_ending).to_s
  end
end

.names_at_rank_group_for_collection_objects(rank = 'speciesgroup') ⇒ Object

Parameters:

  • rank ('speciesgroup' or 'genusgroup' or 'family') (defaults to: 'speciesgroup')

    scope to names used in taxon determinations


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# File 'app/models/protonym.rb', line 162

def self.names_at_rank_group_for_collection_objects(rank = 'speciesgroup')
  h = ::TaxonNameHierarchy.arel_table
  t = ::TaxonName.arel_table
  t1 = ::TaxonName.arel_table.alias('tndet')
  d = ::TaxonDetermination.arel_table
  o = ::Otu.arel_table

  q = t.join(h, Arel::Nodes::InnerJoin).on(
    t[:id].eq(h[:ancestor_id])
  ).join(t1, Arel::Nodes::InnerJoin).on(
    h[:descendant_id].eq(t1[:id])
  ).join(o, Arel::Nodes::InnerJoin).on(
    t1[:id].eq(o[:id])
  ).join(d, Arel::Nodes::InnerJoin).on(
    o[:id].eq(d[:otu_id])
  )

  joins(q.join_sources).where(t[:rank_class].matches('%' + rank + '%').to_sql).distinct
end

.stub_root(project_id: nil, by: nil) ⇒ Protonym

Returns a name ready to become the root.

Returns:

  • (Protonym)

    a name ready to become the root


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# File 'app/models/protonym.rb', line 143

def self.stub_root(project_id: nil, by: nil)
  Protonym.new(name: 'Root', rank_class: 'NomenclaturalRank', parent_id: nil, project_id: project_id, by: by)
end

Instance Method Details

#all_generic_placementsArray of Strings

Returns genera where the species was placed.

Returns:

  • (Array of Strings)

    genera where the species was placed


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# File 'app/models/protonym.rb', line 184

def all_generic_placements
  valid_name = get_valid_taxon_name
  return nil unless valid_name.rank_string !=~/Species/
  descendants_and_self = valid_name.descendants + [self] + self.combinations
  relationships = TaxonNameRelationship.where_object_in_taxon_names(descendants_and_self).with_two_type_bases('TaxonNameRelationship::OriginalCombination::OriginalGenus', 'TaxonNameRelationship::Combination::Genus')
  (relationships.collect { |r| r.subject_taxon_name.name } + [self.ancestor_at_rank('genus').try(:name)]).uniq
end

#ancestors_and_descendantsArray

Returns all descendant and ancestor protonyms for this Protonym.

Returns:

  • (Array)

    all descendant and ancestor protonyms for this Protonym


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# File 'app/models/protonym.rb', line 310

def ancestors_and_descendants
  Protonym.ancestors_and_descendants_of(self).not_self(self).to_a
end

#build_original_combination_from_biodiversity(biodiversity_result, relationship_housekeeping = {}) ⇒ Boolean

Returns Wraps set_original_combination with result from Biodiversity parse !!You must can optionally pre-calculate a disambiguated protonym if you wish to use one.

Parameters:

  • biodiversity_result (Biodiversity.result)
  • relationship_housekeeping (Hash) (defaults to: {})

    like `22, created_by_id: 2`

Returns:

  • (Boolean)

    Wraps set_original_combination with result from Biodiversity parse !!You must can optionally pre-calculate a disambiguated protonym if you wish to use one.


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# File 'app/models/protonym.rb', line 597

def build_original_combination_from_biodiversity(biodiversity_result, relationship_housekeeping = {})
  br = biodiversity_result
  return false if br.nil?
  c = [br.disambiguated_combination, br.combination].first
  build_original_combinations(c, relationship_housekeeping)
  true
end

#build_original_combinations(combination, relationship_housekeeping) ⇒ Boolean

Parameters:

  • combination (Combination)
  • relationship_housekeeping (Hash)

    like `22, created_by_id: 2` builds, but does not save, original relationships for all corresponding protonyms in a combination !! Replaces existing relationship without checking identify if they are there!

Returns:

  • (Boolean)

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# File 'app/models/protonym.rb', line 610

def build_original_combinations(combination, relationship_housekeeping)
  return false if combination.nil?
  combination.protonyms_by_rank.each do |rank, p|
    send("original_#{rank}=", p)
  end

  if !relationship_housekeeping.empty?
    combination.protonyms_by_rank.each do |rank, p|
      r = send("original_#{rank}_relationship")
      r.write_attributes(relationship_housekeeping)
    end
  end
  true
end

#check_new_parent_classObject (protected)

TODO: move to Protonym


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# File 'app/models/protonym.rb', line 803

def check_new_parent_class
  if is_protonym? && parent_id != parent_id_was && !parent_id_was.nil? && nomenclatural_code == :iczn
    if old_parent = TaxonName.find_by(id: parent_id_was)
      if (rank_name == 'subgenus' || rank_name == 'subspecies') && old_parent.name == name
        errors.add(:parent_id, "The nominotypical #{rank_name} #{name} can not be moved out of the nominal #{old_parent.rank_name}")
      end
    end
  end
end

#create_otuObject (protected)


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# File 'app/models/protonym.rb', line 821

def create_otu
  Otu.create(by: self.creator, project: self.project, taxon_name_id: self.id)
end

#genus_suggested_genderObject


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# File 'app/models/protonym.rb', line 574

def genus_suggested_gender
  return nil unless rank_string =~/Genus/
  TAXON_NAME_CLASSIFICATION_GENDER_CLASSES.each do |g|
    g.possible_genus_endings.each do |e|
      return g.name.demodulize.underscore.humanize.downcase if self.name =~ /^[a-zA-Z]*#{e}$/
    end
  end
  nil
end

#get_author_and_yearString?

TODO: not true, has parens?!

a string, without parenthesis, that includes author and year

Returns:

  • (String, nil)

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# File 'app/models/protonym.rb', line 248

def get_author_and_year
  # times_called
  case rank_class.try(:nomenclatural_code)
    when :iczn
      ay = iczn_author_and_year
    when :icvcn
      ay = icn_author_and_year
    when :icnp
      ay = icn_author_and_year
    when :icn
      ay = icn_author_and_year
    else
      ay = ([author_string] + [year_integer]).compact.join(' ')
  end
  ay.blank? ? nil : ay
end

#get_genus_species(genus_option, self_option) ⇒ nil, ...

This method is currently only used for setting cached_primary_homonym

Returns:

  • (nil, false, String)

    !! Why both?


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# File 'app/models/protonym.rb', line 268

def get_genus_species(genus_option, self_option)
  return nil if rank_class.nil?
  genus = nil
  name1 = nil

  if is_species_rank? # self.rank_string =~ /Species/
    if genus_option == :original
      genus = original_genus
    elsif genus_option == :current
      genus = ancestor_at_rank('genus')
    else
      return false
    end

    genus = genus.name unless genus.blank?
    return nil if genus.blank?
  end

  if self_option == :self
    name1 = name
  elsif self_option == :alternative
    name1 = name_with_alternative_spelling
  end

  return nil if genus.nil? && name1.nil? # <- hitting this because Genus is never set
  [genus, name1].compact.join(' ')
  # (genus.to_s + ' ' + name1.to_s).squish
end

#get_original_combinationObject


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# File 'app/models/protonym.rb', line 625

def get_original_combination
  return verbatim_name if !GENUS_AND_SPECIES_RANK_NAMES.include?(rank_string) && !verbatim_name.nil?
  e = original_combination_elements
  return nil if e.none?

  # Weird, why?
  # DD: in ICTV the species name is "Potato spindle tuber viroid", the genus name is only used for classification...
  #
  # @proceps: then we should exclude or alter elements before we get to this point, not here, so that the renderer still works, exceptions at this point are bad
  # and this didn't do what you think it did, it's was returning an Array of two things
  return e[:species][1] if rank_class.to_s =~ /Icvcn/

  p = TaxonName::COMBINATION_ELEMENTS.inject([]){|ary, r| ary.push(e[r]) }

  s = p.flatten.compact.join(' ')
  s.blank? ? nil : s
end

#get_original_combination_htmlObject


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# File 'app/models/protonym.rb', line 704

def get_original_combination_html
  return  "\"<i>Candidatus</i> #{get_original_combination}\"" if is_candidatus?
  v = get_original_combination
  if !v.blank? && is_hybrid?
    w = v.split(' ')
    w[-1] = ('×' + w[-1]).gsub('×(', '').gsub(') [sic]', ' [sic])')
    v = w.join(' ')
  end
  v = v.gsub(') [sic]', ' [sic])') if !v.blank?
  v = Utilities::Italicize.taxon_name(v)
  v = '' + v if !v.blank? && is_fossil?
  v
end

#get_primary_typeTypeMaterial, []

Returns ?!.

Returns:


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# File 'app/models/protonym.rb', line 315

def get_primary_type
  return [] unless self.rank_class.parent.to_s =~ /Species/
  s = self.type_materials.syntypes
  p = self.type_materials.primary
  if s.empty? && p.count == 1
    p
  elsif p.empty? && !s.empty?
    s
  else
    []
  end
end

#get_valid_taxon_nameProtonym

Returns the accepted “valid” version of this name in the present classification.

Returns:

  • (Protonym)

    the accepted “valid” version of this name in the present classification


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# File 'app/models/protonym.rb', line 232

def get_valid_taxon_name
  v = first_possible_valid_taxon_name
  if v == self
    self
  elsif v.cached_valid_taxon_name_id == v.id
    v
  elsif !v.cached_valid_taxon_name_id.nil?
    v.valid_taxon_name
  else
    self
  end
end

#has_latinized_exceptions?Boolean

Returns whether this name has one of the TaxonNameClassifications that except it from being tested as latinized.

Returns:

  • (Boolean)

    whether this name has one of the TaxonNameClassifications that except it from being tested as latinized


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# File 'app/models/protonym.rb', line 446

def has_latinized_exceptions?
  # The second half of this handles classifications in memory, as required to save a non-latinized name (i.e. don't tune it to .any?)
  # !((type == 'Protonym') && (taxon_name_classifications.collect{|t| t.type} & EXCEPTED_FORM_TAXON_NAME_CLASSIFICATIONS).empty?)

  # Is faster than above?
  return true if rank_string =~ /Icnp/ && (name.start_with?('Candidatus ') || name.start_with?('Ca. '))
  taxon_name_classifications.each do |tc| # ! find_each
    return true if EXCEPTED_FORM_TAXON_NAME_CLASSIFICATIONS.include?(tc.type)
  end
  taxon_name_relationships.each do |tr|
    return true if TAXON_NAME_RELATIONSHIP_NAMES_MISSPELLING.include?(tr.type)
  end
  false
end

#has_misspelling_relationship?Boolean

Returns whether this name has one of the TaxonNameRelationships which justify wrong form of the name.

Returns:

  • (Boolean)

    whether this name has one of the TaxonNameRelationships which justify wrong form of the name


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# File 'app/models/protonym.rb', line 470

def has_misspelling_relationship?
  taxon_name_relationships.each do |tr|
    return true if TAXON_NAME_RELATIONSHIP_NAMES_MISSPELLING.include?(tr.type)
  end
  false
end

#has_same_primary_type(taxon2) ⇒ Boolean

!! TODO: Should not be possible- fix the incoming data

Returns:

  • (Boolean)

    true if taxon2 has the same primary type


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# File 'app/models/protonym.rb', line 404

def has_same_primary_type(taxon2)
  return true unless rank_class.parent.to_s =~ /Species/

  taxon1_types = get_primary_type.sort_by{|i| i.id}
  taxon2_types = taxon2.get_primary_type.sort_by{|i| i.id}
  return true if taxon1_types.empty? && taxon2_types.empty? # both are empty !! If they are both empty then they don't have the same type, the have no types  !!
  return false if taxon1_types.empty? || taxon2_types.empty? # one is empty

  taxon1_types.map(&:collection_object_id) == taxon2_types.map(&:collection_object_id) # collect{|i| i.collection_object_id}
end

#is_available?Boolean

Returns:

  • (Boolean)

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# File 'app/models/protonym.rb', line 226

def is_available?
  !has_misspelling_relationship? && !name_is_misapplied? && !classification_invalid_or_unavailable?
end

#is_family_rank?Boolean

Returns:

  • (Boolean)

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# File 'app/models/protonym.rb', line 489

def is_family_rank?
  FAMILY_RANK_NAMES.include?(rank_string)
end

#is_genus_or_species_rank?Boolean

Returns:

  • (Boolean)

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# File 'app/models/protonym.rb', line 485

def is_genus_or_species_rank?
  is_species_rank? || is_genus_rank?
end

#is_genus_rank?Boolean

Returns:

  • (Boolean)

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# File 'app/models/protonym.rb', line 481

def is_genus_rank?
  GENUS_RANK_NAMES.include?(rank_string)
end

#is_higher_rank?Boolean

Returns:

  • (Boolean)

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# File 'app/models/protonym.rb', line 493

def is_higher_rank?
  HIGHER_RANK_NAMES.include?(rank_string)
end

#is_homonym_or_suppressed?Boolean

Returns:

  • (Boolean)

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# File 'app/models/protonym.rb', line 465

def is_homonym_or_suppressed?
end

#is_latin?Boolean

Returns:

  • (Boolean)

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# File 'app/models/protonym.rb', line 461

def is_latin?
  !NOT_LATIN.match(name) || has_latinized_exceptions?
end

#is_original_name?Boolean

Returns Boolean could also be determined by parens in cached_author year.

Returns:

  • (Boolean)

    Boolean could also be determined by parens in cached_author year


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# File 'app/models/protonym.rb', line 499

def is_original_name?
  cached_author_year =~ /\(/ ? false : true
end

#is_species_rank?Boolean

Returns:

  • (Boolean)

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# File 'app/models/protonym.rb', line 477

def is_species_rank?
  SPECIES_RANK_NAMES.include?(rank_string)
end

#list_of_coordinated_namesObject


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# File 'app/models/protonym.rb', line 192

def list_of_coordinated_names
  list = []
  if self.rank_string
    r = self.iczn_set_as_incorrect_original_spelling_of_relationship
    if r.blank?
      search_rank = NomenclaturalRank::Iczn.group_base(self.rank_string)
      if !!search_rank
        if search_rank =~ /Family/
          z = Protonym.that_is_valid.family_group_base(self.name)
          search_name = z.nil? ? nil : Protonym::FAMILY_GROUP_ENDINGS.collect{|i| z+i}
        else
          search_name = self.name
        end
      else
        search_name = nil
      end

      r = TaxonNameRelationship.where_subject_is_taxon_name(self).with_type_array(TAXON_NAME_RELATIONSHIP_NAMES_MISSPELLING)
      if !search_name.nil? && r.empty?
        list = Protonym.ancestors_and_descendants_of(self).not_self(self).
          with_rank_class_including(search_rank).
          where('name in (?)', search_name).
          as_subject_without_taxon_name_relationship_array(TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM)
          #as_subject_without_taxon_name_relationship_base('TaxonNameRelationship::Iczn::Invalidating::Synonym').
      else
        list = []
      end
    else
      list = [r.object_taxon_name]
    end
  end
  return list
end

#lowest_rank_coordinated_taxonObject

TODO, make back half of this raw SQL


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# File 'app/models/protonym.rb', line 298

def lowest_rank_coordinated_taxon
  list = [self] + list_of_coordinated_names
  if list.count == 1
    self
  else
    parents = list.collect{|i| i.parent.id}
    list.detect{|t| !parents.include?(t.id)}
  end
end

#name_is_latinizedObject (protected)


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# File 'app/models/protonym.rb', line 813

def name_is_latinized
  errors.add(:name, 'Name must be latinized, no digits or spaces allowed') if !is_latin?
end

#name_is_valid_formatObject (protected)


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# File 'app/models/protonym.rb', line 817

def name_is_valid_format
  rank_class.validate_name_format(self) if name.present? && rank_class && rank_class.respond_to?(:validate_name_format) && !has_latinized_exceptions?
end

#name_with_alternative_spellingObject


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# File 'app/models/protonym.rb', line 516

def name_with_alternative_spelling
  if rank_class.nil? || nomenclatural_code != :iczn
    # rank_string =~ /::Icn::/ # self.class != Protonym
    return nil
  elsif is_species_rank? # rank_string =~ /Species/
    n = name.squish # remove extra spaces and line brakes
    n = n.split(' ').last
    n = n[0..-4] + 'ae' if n =~ /^[a-z]*iae$/ # -iae > -ae in the end of word
    n = n[0..-6] + 'orum' if n =~ /^[a-z]*iorum$/ # -iorum > -orum
    n = n[0..-6] + 'arum' if n =~ /^[a-z]*iarum$/ # -iarum > -arum
    n = n[0..-3] + 'a' if n =~ /^[a-z]*um$/ # -um > -a
    n = n[0..-3] + 'a' if n =~ /^[a-z]*us$/ # -us > -a
    n = n[0..-3] + 'e' if n =~ /^[a-z]*is$/ # -is > -e
    n = n[0..-3] + 'ra' if n =~ /^[a-z]*er$/ # -er > -ra
    n = n[0..-7] + 'ensis' if n =~ /^[a-z]*iensis$/ # -iensis > -ensis
    n = n[0..-5] + 'ana' if n =~ /^[a-z]*iana$/ # -iana > -ana
    n = n.gsub('ae', 'e').
          gsub('oe', 'e').
          gsub('ai', 'i').
          gsub('ei', 'i').
          gsub('ej', 'i').
          gsub('ii', 'i').
          gsub('ij', 'i').
          gsub('jj', 'i').
          gsub('j', 'i').
          gsub('y', 'i').
          gsub('v', 'u').
          gsub('rh', 'r').
          gsub('th', 't').
          gsub('k', 'c').
          gsub('ch', 'c').
          gsub('tt', 't').
          gsub('bb', 'b').
          gsub('rr', 'r').
          gsub('nn', 'n').
          gsub('mm', 'm').
          gsub('pp', 'p').
          gsub('ss', 's').
          gsub('ff', 'f').
          gsub('ll', 'l').
          gsub('ct', 't').
          gsub('ph', 'f').
          gsub('-', '')
    n = n[0, 3] + n[3..-4].gsub('o', 'i') + n[-3, 3] if n.length > 6 # connecting vowel in the middle of the word (nigrocinctus vs. nigricinctus)
  elsif rank_string =~ /Family/
    n_base = Protonym.family_group_base(self.name)
    if n_base.nil? || n_base == self.name
      n = self.name
    else
      n = n_base + 'idae'
    end
  else
    n = self.name.squish
  end

  return n
end

#new_parent_taxon_nameObject (protected)


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# File 'app/models/protonym.rb', line 825

def new_parent_taxon_name
  r = self.iczn_uncertain_placement_relationship
  unless r.blank?
    if self.parent != r.object_taxon_name
      errors.add(:parent_id, "Taxon has a relationship 'incertae sedis' - delete the relationship before changing the parent")
    end
  end
end

#nominotypical_sub_of?(protonym) ⇒ boolean

Returns:

  • (boolean)

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# File 'app/models/protonym.rb', line 795

def nominotypical_sub_of?(protonym)
  is_genus_or_species_rank? && parent == protonym && parent.name == protonym.name
end

#number_of_taxa_by_yearObject


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# File 'app/models/protonym.rb', line 375

def number_of_taxa_by_year
  a = {}
  descendants.find_each do |z|
    year = z.year_integer
    year = 0 if year.nil?
    a[year] = {:valid => 0, :synonyms => 0} unless a[year]
    if z.rank_string == 'NomenclaturalRank::Iczn::SpeciesGroup::Species'
      if z.id == z.cached_valid_taxon_name_id
        a[year][:valid] = a[year][:valid] += 1
      elsif TaxonNameRelationship.where_subject_is_taxon_name(z.id).with_type_array(TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM).any?
        a[year][:synonyms] = a[year][:synonyms] += 1
      end
    end
  end
  for i in 1758..Time.now.year do
    a[i] = {:valid => 0, :synonyms => 0} unless a[i]
  end
  b = a.sort.to_h
  CSV.generate do |csv|
    csv << ['year', 'valid species', 'synonyms']
    b.keys.each do |i|
      csv << [i, b[i][:valid], b[i][:synonyms]]
    end
  end
end

#original_combination_class_relationshipsObject

return [Array]

TaxonNameRelationship classes that are applicable to this name, as deterimined by Rank

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# File 'app/models/protonym.rb', line 417

def original_combination_class_relationships
  relations = []
  TaxonNameRelationship::OriginalCombination.descendants.each do |r|
    relations.push(r) if r.valid_object_ranks.include?(self.rank_string)
  end
  relations
end

#original_combination_elementsObject


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# File 'app/models/protonym.rb', line 643

def original_combination_elements
  elements = { }
  return elements if rank.blank?

  this_rank = rank.to_sym

  # Why this?
  #   We need to apply gender to "internal" names for original combinations, everything
  #   but the last name
  # DD: if we have subspecies, the species name should be used not in the original form,
  # but the form correlated with the present genus gender
  # TODO: get SQL based ordering for original_combination_relationships, hard coded

  # order the relationships
  r = original_combination_relationships.reload.sort{|a,b| ORIGINAL_COMBINATION_RANKS.index(a.type) <=> ORIGINAL_COMBINATION_RANKS.index(b.type) }

  # get gender from first
  gender = original_genus&.gender_name # r.first.subject_taxon_name.gender_name

  # apply gender to everything but the last
  total = r.count - 1
  r.each_with_index do |j, i|
    if j.type =~ /enus/ || i == total
      g = nil
    else
      g = gender
    end
    elements.merge! j.combination_name(g)
  end

  # what is point of this? Do we get around this check by requiring self relationships? (species aus has species relationship to self)
  # DD: we do not require it, it is optional
  if !r.empty? && r.collect{|i| i.subject_taxon_name}.last.lowest_rank_coordinated_taxon.id != lowest_rank_coordinated_taxon.id
    if elements[this_rank].nil?
      elements[this_rank] = [original_name]
    end
  end

  if elements.any?
    if !elements[:genus] && !not_binomial?
      if original_genus
        elements[:genus] = "[#{original_genus&.name}]"
      else
        elements[:genus] = '[GENUS NOT SPECIFIED]'
      end
    end
    # If there is no :species, but some species group, add element
    elements[:species] = '[SPECIES NOT SPECIFIED]' if !elements[:species] && ( [:subspecies, :variety, :form] & elements.keys ).size > 0
  end

  elements
end

#original_combination_relationships_and_stubsArray

Returns A relationships for each possible original combination relationship.

Returns:

  • (Array)

    A relationships for each possible original combination relationship


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# File 'app/models/protonym.rb', line 427

def original_combination_relationships_and_stubs
  # TODO: figure out where to really put this, likely in one big sort
  display_order = [ :original_genus, :original_subgenus, :original_species, :original_subspecies, :original_variety, :original_subvariety, :original_form, :original_subform ]

  defined_relations = self.original_combination_relationships.all
  created_already   = defined_relations.collect{|a| a.class}
  new_relations     = []

  original_combination_class_relationships.each do |r|
    new_relations.push( r.new(object_taxon_name: self) ) if !created_already.include?(r)
  end

  (new_relations + defined_relations).sort{|a,b|
    display_order.index(a.class.inverse_assignment_method) <=> display_order.index(b.class.inverse_assignment_method)
  }
end

#original_nameString?

Returns a monomial, as originally rendered, with parens if subgenus.

Returns:

  • (String, nil)

    a monomial, as originally rendered, with parens if subgenus


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# File 'app/models/protonym.rb', line 698

def original_name
  n = verbatim_name.nil? ? name_with_misspelling(nil) : verbatim_name
  n = "(#{n})" if n && rank_name == 'subgenus'
  n
end

#predicted_child_rank(child_string) ⇒ Object

taxon_name.predicted_children_rank('Cicadellidae') >> NomenclaturalRank::Iczn::FamilyGroup::Family


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# File 'app/models/protonym.rb', line 329

def predicted_child_rank(child_string)
  return nil if child_string.blank?
  parent_rank = rank_class.to_s
  parent_rank_name = rank_name
  ncode = nomenclatural_code

  return nil if ncode.nil? # Happens with some names like "Root"

  if child_string == child_string.downcase
    if !is_species_rank?
      r = Ranks.lookup(ncode, 'species')
    elsif parent_rank_name == 'species'
      r = Ranks.lookup(ncode, 'subspecies')
    elsif parent_rank_name == 'subspecies'
      r = Ranks.lookup(ncode, 'variety')
    elsif parent_rank_name == 'variety'
      r = Ranks.lookup(ncode, 'form')
    elsif parent_rank_name == 'form'
      r = Ranks.lookup(ncode, 'subform')
    else
      return nil
    end
  elsif child_string == child_string.capitalize
    if rank_name == 'genus'
      r = Ranks.lookup(ncode, 'subgenus')
    else
      Ranks.lookup(ncode, 'family').constantize.valid_parents.each do |r1|
        r2 = r1.constantize
        if !r2.valid_name_ending.blank? && child_string.end_with?(r2.valid_name_ending) && RANKS.index(r1) > RANKS.index(parent_rank)
          r = r1
          break
        end
      end
      r = Ranks.lookup(ncode, 'genus') if r.nil?
    end
  else
    return nil

#      RANKS.index(rank_string) <= RANKS.index(parent.rank_string)
#      Ranks.lookup(:iczn, 'species')
# .valid_name_ending
#FAMILY_AND_ABOVE_RANK_NAMES
  end
  r.constantize
end

#reduce_list_of_synonyms(list) ⇒ Object


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# File 'app/models/protonym.rb', line 503

def reduce_list_of_synonyms(list)
  return [] if list.empty?
  list1 = list.select{|s| s.id == s.lowest_rank_coordinated_taxon.id}
  list1.reject!{|s| self.cached_valid_taxon_name_id == s.cached_valid_taxon_name_id} unless list1.empty?
  unless list1.empty?
    date1 = self.nomenclature_date
    unless date1.nil?
      list1.reject!{|s| date1 < (s.year_of_publication ? s.nomenclature_date : Time.utc(1))}
    end
  end
  list1
end

#set_cachedObject (protected)


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# File 'app/models/protonym.rb', line 871

def set_cached
  super
  set_cached_names_for_dependants
  set_cached_original_combination
  set_cached_original_combination_html
  set_cached_homonymy
  set_cached_species_homonym if is_species_rank?
  set_cached_misspelling
end

#set_cached_homonymyObject (protected)


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# File 'app/models/protonym.rb', line 881

def set_cached_homonymy
  update_columns(
    cached_primary_homonym: get_genus_species(:original, :self),
    cached_primary_homonym_alternative_spelling: get_genus_species(:original, :alternative)
  )
end

#set_cached_misspellingObject (protected)

all three in one update here


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# File 'app/models/protonym.rb', line 889

def set_cached_misspelling
  update_column(:cached_misspelling, get_cached_misspelling)
end

#set_cached_names_for_dependantsObject


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# File 'app/models/protonym.rb', line 733

def set_cached_names_for_dependants
  dependants = []
  related_through_original_combination_relationships = []
  combination_relationships = []

  TaxonName.transaction_with_retry do
    if is_genus_or_species_rank?
      dependants = Protonym.unscoped.descendants_of(self).to_a
      related_through_original_combination_relationships = TaxonNameRelationship.where_subject_is_taxon_name(self).with_type_contains('OriginalCombination')
      combination_relationships = TaxonNameRelationship.where_subject_is_taxon_name(self).with_type_contains('::Combination')
    end

   #  dependants.push(self) # combination does hit here

    # Combination can hit here
    classified_as_relationships = TaxonNameRelationship.where_object_is_taxon_name(self).with_type_contains('SourceClassifiedAs')

    dependants.each do |i|
      columns_to_update = {
        cached: i.get_full_name,
        cached_html: i.get_full_name_html
      }

      if i.is_species_rank?
        columns_to_update[:cached_secondary_homonym] = i.get_genus_species(:current, :self)
        columns_to_update[:cached_secondary_homonym_alternative_spelling] = i.get_genus_species(:current, :alternative)
      end

      i.update_columns(columns_to_update)
    end

    related_through_original_combination_relationships.collect{|i| i.object_taxon_name}.uniq.each do |i|
      i.update_cached_original_combinations
    end

    # Update values in Combinations
    combination_relationships.collect{|i| i.object_taxon_name}.uniq.each do |j|
      j.update_columns(
        cached: j.get_full_name,
        cached_html: j.get_full_name_html,
        cached_author_year: j.get_author_and_year)
    end

    classified_as_relationships.collect{|i| i.subject_taxon_name}.uniq.each do |i|
      i.update_column(:cached_classified_as, i.get_cached_classified_as)
    end

    classified_as_relationships.collect{|i| i.object_taxon_name}.uniq.each do |i|
      i.update_columns(
        cached: i.get_full_name,
        cached_html: i.get_full_name_html,
        cached_author_year: i.get_author_and_year)
    end

    misspelling_relationships = TaxonNameRelationship.where_object_is_taxon_name(self).with_type_array(TAXON_NAME_RELATIONSHIP_NAMES_MISSPELLING_AND_MISAPPLICATION)
    misspelling_relationships.collect{|i| i.subject_taxon_name}.uniq.each do |i|
      i.update_columns(cached_author_year: i.get_author_and_year)
    end
  end
end

#set_cached_original_combinationObject (protected)


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# File 'app/models/protonym.rb', line 893

def set_cached_original_combination
  update_column(:cached_original_combination, get_original_combination)
end

#set_cached_original_combination_htmlObject (protected)


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# File 'app/models/protonym.rb', line 897

def set_cached_original_combination_html
  update_column(:cached_original_combination_html, get_original_combination_html)
end

#set_cached_species_homonymObject


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# File 'app/models/protonym.rb', line 726

def set_cached_species_homonym
  update_columns(
    cached_secondary_homonym: get_genus_species(:current, :self),
    cached_secondary_homonym_alternative_spelling: get_genus_species(:current, :alternative)
  )
end

#species_questionable_ending(taxon_name_classification_class, tested_name) ⇒ Object


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# File 'app/models/protonym.rb', line 584

def species_questionable_ending(taxon_name_classification_class, tested_name)
  return nil unless is_species_rank?
  taxon_name_classification_class.questionable_species_endings.each do |e|
    return e if tested_name =~ /^[a-z]*#{e}$/
  end
  nil
end

#sv_cached_namesObject (protected)

Validate whether cached names need to be rebuilt.

TODO: this is kind of pointless, we generate all the values need for cached, names, at that point the cached values should just be persisted The logic here also duplicates the tracking needed for building cached names.

Refactor this to single methods, one each to validate cached name?


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# File 'app/models/protonym.rb', line 912

def sv_cached_names
  is_cached = true
  is_cached = false if cached_author_year != get_author_and_year

  if is_cached && cached_html != get_full_name_html ||
    cached_misspelling != get_cached_misspelling ||
    cached_original_combination != get_original_combination ||
    cached_original_combination_html != get_original_combination_html ||
    cached_primary_homonym != get_genus_species(:original, :self) ||
    cached_primary_homonym_alternative_spelling != get_genus_species(:original, :alternative) ||
    rank_string =~ /Species/ &&
      (cached_secondary_homonym != get_genus_species(:current, :self) ||
        cached_secondary_homonym_alternative_spelling != get_genus_species(:current,
                                                                           :alternative))
    is_cached = false
  end

  soft_validations.add(
    :base, 'Cached values should be updated',
    fix: :sv_fix_cached_names, success_message: 'Cached values were updated'
  ) if !is_cached
end

#update_cached_original_combinationsObject


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# File 'app/models/protonym.rb', line 718

def update_cached_original_combinations
  update_columns(
    cached_original_combination: get_original_combination,
    cached_original_combination_html: get_original_combination_html,
    cached_primary_homonym: get_genus_species(:original, :self),
    cached_primary_homonym_alternative_spelling: get_genus_species(:original, :alternative))
end

#validate_child_rank_is_equal_or_lowerObject (protected)


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# File 'app/models/protonym.rb', line 848

def validate_child_rank_is_equal_or_lower
  if parent && !rank_class.blank? && rank_string != 'NomenclaturalRank'
    if rank_class_changed?
      a = children.where(type: 'Protonym').pluck(:rank_class)
      v = RANKS.index(rank_string)
      a.each do |b|
        if v >= RANKS.index(b)
          errors.add(:rank_class, "The rank of this taxon (#{rank_name}) should be higher than the ranks of children")
          break
        end
      end
    end
  end
end

#validate_parent_rank_is_higherObject (protected)


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# File 'app/models/protonym.rb', line 863

def validate_parent_rank_is_higher
  if parent && !rank_class.blank? && rank_string != 'NomenclaturalRank'
    if RANKS.index(rank_string) <= RANKS.index(parent.rank_string)
      errors.add(:parent_id, "The parent rank (#{parent.rank_class.rank_name}) is not higher than the rank (#{rank_name}) of this taxon")
    end
  end
end

#validate_rank_class_classObject (protected)


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# File 'app/models/protonym.rb', line 844

def validate_rank_class_class
  errors.add(:rank_class, 'Rank not found') unless RANKS.include?(rank_string)
end