Class: Protonym

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

Overview

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 collapse

Attributes inherited from TaxonName

#also_create_otu, #cached, #cached_author_year, #cached_classified_as, #cached_html, #cached_misspelling, #cached_original_combination, #cached_original_combination_html, #cached_primary_homonym, #cached_primary_homonym_alternative_spelling, #cached_secondary_homonym, #cached_secondary_homonym_alternative_spelling, #etymology, #feminine_name, #masculine_name, #name, #neuter_name, #no_cached, #parent_id, #project_id, #rank_class, #type, #verbatim_author, #verbatim_name, #year_of_publication

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_etymology, #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_page, #sv_fix_coordinated_names_part_of_speech, #sv_fix_coordinated_names_roles, #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_otu, #sv_fix_misspelling_roles_are_not_required, #sv_fix_misspelling_year_is_not_required, #sv_fix_type_placement1, #sv_fix_year_is_not_required, #sv_homotypic_synonyms, #sv_missing_etymology, #sv_missing_gender, #sv_missing_original_genus, #sv_missing_otu, #sv_missing_part_of_speech, #sv_missing_roles, #sv_missing_substitute_name, #sv_missing_type_genus, #sv_missing_type_species, #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_etymology, #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_page, #sv_validate_coordinated_names_part_of_speech, #sv_validate_coordinated_names_roles, #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_name, #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_html_original_name_and_author_year, #cached_name_and_author_year, #cached_year, calculated_invalid, calculated_valid, #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_author_and_year, #get_cached_classified_as, #get_cached_misspelling, #get_full_name, #get_full_name_html, #icn_author_and_year, #iczn_author_and_year, #is_ambiguously_invalid?, #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, #nomeclatural_history, #nomenclature_date, #normalized_genus, #not_binomial?, not_leaves, #original_author_year, #out_of_scope_combinations, out_of_scope_combinations, parent, #parent_is_set?, #part_of_speech_class, #part_of_speech_instance, #part_of_speech_name, #previous_sibling, #rank, #rank_string, #reified_id, #related_taxon_names, #relationship_invalid?, #safe_self_and_ancestors, select_optimized, #set_cached_author_year, #set_cached_classified_as, #set_cached_is_valid, #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_parent_is_valid_name, #sv_homotypic_synonyms, #sv_hybrid_name_relationships, #sv_incomplete_combination, #sv_missing_classifications, #sv_missing_confidence_level, #sv_missing_etymology, #sv_missing_original_publication, #sv_missing_relationships, #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_for, #fix_soft_validations, #soft_fixed?, #soft_valid?, #soft_validate, #soft_validated?, #soft_validations, #soft_validators

Methods included from Shared::HasPapertrail

#attribute_updated, #attribute_updater

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

#dwc_occurrence_id, #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

Instance Attribute Details

#is_available ⇒ Boolean (readonly)

Returns memoize `#is_avaiable?`.

Returns:

  • (Boolean) —

    memoize `#is_avaiable?`



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# File 'app/models/protonym.rb', line 20

def is_available
  @is_available
end

Class Method Details

.family_group_base(name_string) ⇒ Object 



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# File 'app/models/protonym.rb', line 151

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 156

def self.family_group_name_at_rank(name_string, rank_string)
  if name_string == Protonym.family_group_base(name_string)
    name_string
  else
    Protonym.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 166

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 147

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_placements ⇒ Array 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 188

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_descendants ⇒ Array

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 305

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 624

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 637

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_class ⇒ Object (protected) 



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# File 'app/models/protonym.rb', line 857

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_otu ⇒ Object (protected) 



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# File 'app/models/protonym.rb', line 886

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

#genus_suggested_gender ⇒ Object 



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# File 'app/models/protonym.rb', line 601

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_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 263

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_combination ⇒ Object 



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# File 'app/models/protonym.rb', line 652

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 ICVCN 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_html ⇒ Object 



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# File 'app/models/protonym.rb', line 751

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])').gsub(') (sic)', ' (sic))')
    v = w.join(' ')
  end
  v = v.gsub(') [sic]', ' [sic])').gsub(') (sic)', ' (sic))') if !v.blank?

  v = Utilities::Italicize.taxon_name(v)
  v = '† ' + v if !v.blank? && is_fossil?
  v
end

#get_primary_type ⇒ TypeMaterial, []

Returns ?!.

Returns:



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

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_name ⇒ Protonym

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 247

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_alternate_original? ⇒ Boolean

Same as is_original_name?!

Returns:

  • (Boolean) 


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# File 'app/models/protonym.rb', line 460

def has_alternate_original?
  cached_original_combination && (cached != cached_original_combination) ? true : false
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 436

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. '))

  return true if is_family_rank? && !(taxon_name_relationships.collect{|i| i.type} & TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM).empty?
  return true unless (taxon_name_classifications.collect{|i| i.type} & EXCEPTED_FORM_TAXON_NAME_CLASSIFICATIONS).empty?
  return true unless (taxon_name_relationships.collect{|i| i.type} & TAXON_NAME_RELATIONSHIP_NAMES_MISSPELLING).empty?
  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 455

def has_misspelling_relationship?
  taxon_name_relationships.with_type_array(TAXON_NAME_RELATIONSHIP_NAMES_MISSPELLING).any?
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 394

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?(refresh = false) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/models/protonym.rb', line 236

def is_available?(refresh = false)
  if !refresh
    @is_available ||= !has_misspelling_relationship? && !name_is_misapplied? && !classification_invalid_or_unavailable?
  else
    @is_available = !has_misspelling_relationship? && !name_is_misapplied? && !classification_invalid_or_unavailable?
  end
  @is_available
end

#is_family_or_genus_or_species_rank? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/models/protonym.rb', line 476

def is_family_or_genus_or_species_rank?
  FAMILY_AND_GENUS_AND_SPECIES_RANK_NAMES .include?(rank_string)
end

#is_family_rank? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/models/protonym.rb', line 480

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 472

def is_genus_or_species_rank?
  GENUS_AND_SPECIES_RANK_NAMES .include?(rank_string)
end

#is_genus_rank? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/models/protonym.rb', line 468

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 484

def is_higher_rank?
  HIGHER_RANK_NAMES.include?(rank_string)
end

#is_latin? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/models/protonym.rb', line 449

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 490

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 464

def is_species_rank?
  SPECIES_RANK_NAMES.include?(rank_string)
end

#list_of_coordinated_names ⇒ Object 



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# File 'app/models/protonym.rb', line 196

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(rank_string)
      if !!search_rank
        if search_rank =~ /Family/
          if self.cached_is_valid
            z = Protonym.family_group_base(self.name)
            search_name = z.nil? ? nil : Protonym::FAMILY_GROUP_ENDINGS.collect{|i| z+i}
          else
            search_name = nil
          end
        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?
      if !search_name.nil? && is_available?
        list = Protonym
          .ancestors_and_descendants_of(self)
          .with_rank_class_including(search_rank)
          .where(name: search_name)
          .not_self(self)
          .that_is_valid
      else
        list = []
      end
    else
      list = [r.object_taxon_name]
    end
  end
  return list
end

#lowest_rank_coordinated_taxon ⇒ Object

TODO, make back half of this raw SQL



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# File 'app/models/protonym.rb', line 293

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_latinized ⇒ Object (protected) 



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# File 'app/models/protonym.rb', line 867

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

#name_is_valid_format ⇒ Object (protected) 



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# File 'app/models/protonym.rb', line 882

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_spelling ⇒ Object 



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# File 'app/models/protonym.rb', line 507

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_name ⇒ Object (protected) 



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# File 'app/models/protonym.rb', line 890

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 851

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

#number_of_taxa_by_year ⇒ Object 



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# File 'app/models/protonym.rb', line 365

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_relationships ⇒ Object

return [Array]

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



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# File 'app/models/protonym.rb', line 407

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_elements ⇒ Hash 

genus: ["", 'Aus' ],
...
form: ['frm', 'aus']

Returns:

  • (Hash) 


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# File 'app/models/protonym.rb', line 678

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) # this is like '{genus: [nil, 'Aus']}
  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] = [nil, original_name]
    end
  end

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

  elements
end

#original_combination_infraspecific_element(elements = nil) ⇒ [rank_name, name]?

Returns Used in ColDP export.

Returns:

  • ([rank_name, name], nil) —

    Used in ColDP export



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

def original_combination_infraspecific_element(elements = nil)
  elements ||= original_combination_elements

  # TODO: consider plants/other codes?
  [:form, :variety, :subspecies].each do |r|
    return [r.to_s, elements[r].last] if elements[r]
  end
  nil
end

#original_combination_relationships_and_stubs ⇒ Array

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 417

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_name ⇒ String?

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 745

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

#predict_three_forms ⇒ Object 



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# File 'app/models/protonym.rb', line 565

def predict_three_forms
  exception = LATIN_ADJECTIVES[name]

  return exception unless exception.nil?
  m_name, f_name, n_name = nil, nil, nil
  case name
  when /(color|coloris)$/
    m_name, f_name, n_name = name, name, name
  when /is$/
    m_name, f_name, n_name = name, name, name[0..-3] + 'e'
  when /e$/
    m_name, f_name, n_name = name[0..-2] + 'is', name[0..-2] + 'is', name
  when /us$/
    m_name, f_name, n_name = name, name[0..-3] + 'a', name[0..-3] + 'um'
  when /er$/
    m_name, f_name, n_name = name, name[0..-3] + 'ra', name[0..-3] + 'rum'
  when /(ferum|gerum)$/
    m_name, f_name, n_name = name[0..-3], name[0..-3] + 'a', name
  when /(gera|fera)$/
    m_name, f_name, n_name = name[0..-2], name, name[0..-2] + 'um'
  when /(brum|frum|grum)$/
    m_name, f_name, n_name = name[0..-4] + 'er', name[0..-3] + 'a', name
  when /(bra|gra|fra)$/
    m_name, f_name, n_name = name[0..-3] + 'er', name, name[0..-2] + 'um'
  when /(um)$/
    m_name, f_name, n_name = name[0..-3] + 'us', name[0..-3] + 'a', name
  when /a$/
    m_name, f_name, n_name = name[0..-2] + 'us', name, name[0..-2] + 'um'
  when /(nor|ior|jor)$/
    m_name, f_name, n_name = name, name, name[0..-3] + 'us'
  else
    m_name, f_name, n_name = name, name, name
  end
  {masculine_name: m_name, feminine_name: f_name, neuter_name: n_name}
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 324

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) && r2.typical_use && RANKS.index(r1) > RANKS.index(parent_rank)
          r = r1
          break
        end
      end
      r = Ranks.lookup(ncode, 'genus') if r.nil?
    end
  else
    return nil
  end
  r.constantize
end

#reduce_list_of_synonyms(list) ⇒ Object 



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# File 'app/models/protonym.rb', line 494

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_cached ⇒ Object (protected) 



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# File 'app/models/protonym.rb', line 962

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_homonymy ⇒ Object (protected) 



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# File 'app/models/protonym.rb', line 972

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_misspelling ⇒ Object (protected)

all three in one update here



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# File 'app/models/protonym.rb', line 980

def set_cached_misspelling
  update_column(:cached_misspelling, get_cached_misspelling)
end

#set_cached_names_for_dependants ⇒ Object 



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# File 'app/models/protonym.rb', line 781

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|
      n = i.get_full_name
      columns_to_update = {
        cached: n,
        cached_html: i.get_full_name_html(n),
        cached_author_year: i.get_author_and_year,
        cached_nomenclature_date: i.nomenclature_date
      }

      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|
      n = j.get_full_name
      j.update_columns(
        cached: n,
        cached_html: j.get_full_name_html(n),
        cached_author_year: j.get_author_and_year,
        cached_nomenclature_date: j.nomenclature_date)
    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|
      n = i.get_full_name
      i.update_columns(
        cached: n,
        cached_html: i.get_full_name_html(n),
        cached_author_year: i.get_author_and_year,
        cached_nomenclature_date: i.nomenclature_date)
    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,
                       cached_nomenclature_date: i.nomenclature_date)
    end
  end
end

#set_cached_original_combination ⇒ Object (protected) 



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# File 'app/models/protonym.rb', line 984

def set_cached_original_combination
  update_column(:cached_original_combination, get_original_combination)
end

#set_cached_original_combination_html ⇒ Object (protected) 



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# File 'app/models/protonym.rb', line 988

def set_cached_original_combination_html
  update_column(:cached_original_combination_html, get_original_combination_html)
end

#set_cached_species_homonym ⇒ Object 



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# File 'app/models/protonym.rb', line 774

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 611

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_names ⇒ Object (protected)

this cannot be moved to soft_validation_extensions



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# File 'app/models/protonym.rb', line 936

def sv_cached_names # this cannot be moved to soft_validation_extensions
  is_cached = true
  is_cached = false if cached_author_year != get_author_and_year

  if is_cached && (
      cached_valid_taxon_name_id != get_valid_taxon_name.id ||
      cached_is_valid != !unavailable_or_invalid? || # Do not change this, we want the calculated value.
      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_nomenclature_date != nomenclature_date ||
      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',
      success_message: 'Cached values were updated',
      failure_message:  'Failed to update cached values') if !is_cached
end

#update_cached_original_combinations ⇒ Object 



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# File 'app/models/protonym.rb', line 766

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_lower ⇒ Object (protected) 



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# File 'app/models/protonym.rb', line 913

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_higher ⇒ Object (protected) 



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# File 'app/models/protonym.rb', line 928

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_class ⇒ Object (protected) 



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# File 'app/models/protonym.rb', line 909

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

#verbatim_author_with_closed_parens_when_present ⇒ Object (protected) 



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# File 'app/models/protonym.rb', line 875

def verbatim_author_with_closed_parens_when_present
  if verbatim_author.present? and nomenclatural_code != :icn  # workaround until basyonim field exists
    # Regex matches two possible, both params, or no params at start/end
    errors.add(:verbatim_author, 'Verbatim author is missing a parenthesis') unless verbatim_author =~ /\A\([^()]+\)\z|\A[^()]+\z/
  end
end

#verbatim_author_without_digits ⇒ Object (protected) 



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

def verbatim_author_without_digits
  errors.add(:verbatim_author, 'Verbatim author may not contain digits, a year may be present') if verbatim_author =~ /\d/
end