Class: Protonym

Inherits:
TaxonName
  • Object
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

Instance Attribute Summary collapse

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_missing_otu, #sv_fix_misspelling_author_is_not_required, #sv_fix_misspelling_roles_are_not_required, #sv_fix_misspelling_year_is_not_required, #sv_fix_presence_of_combination, #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_person_vs_year_of_publication, #sv_potential_family_homonyms, #sv_potential_genus_homonyms, #sv_potential_species_homonyms, #sv_potential_usage_duplicates, #sv_presence_of_combination, #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

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 155

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 160

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 170

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 151

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 219

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 336

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

TODO: likley belongs in lib/vendor/biodiversity.rb

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 664

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 677

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 897

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 926

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 640

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 294

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 692

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 791

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) if is_genus_or_species_rank?
  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 341

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 278

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 500

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 471

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_or_misapplication_relationship? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/models/protonym.rb', line 495

def has_misspelling_or_misapplication_relationship?
  taxon_name_relationships.with_type_array(TAXON_NAME_RELATIONSHIP_NAMES_MISSPELLING_AND_MISAPPLICATION).any?
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 490

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 429

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 267

def is_available?(refresh = false)
  if !refresh
    @is_available ||= !has_misspelling_or_misapplication_relationship? && !classification_unavailable?
  else
    @is_available = !has_misspelling_or_misapplication_relationship? && !classification_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 516

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 520

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 512

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 508

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 524

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 484

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

#is_original_name? ⇒ Boolean

Returns Boolean.

Returns:

  • (Boolean) —

    Boolean



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# File 'app/models/protonym.rb', line 529

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 504

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 227

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 324

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 907

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 922

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 546

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$/ # -iana > -ana
    n = n.gsub('ae', 'e') if n =~ /^[a-z]*ae[a-z]+$/ # -ae-
    n = n.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 930

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 an 'Incertae sedis' relationship, which prevent the parent modifications, change the relationship to 'Source classified as' before updating the parent")
    end
  end
end

#nominotypical_sub_of?(protonym) ⇒ boolean

Returns:

  • (boolean) 


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# File 'app/models/protonym.rb', line 891

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

#number_of_taxa_by_year ⇒ Object

temporary method to get a number of taxa described by year



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# File 'app/models/protonym.rb', line 398

def number_of_taxa_by_year
  file_name = '/tmp/taxa_by_year' + '_' + Time.now.to_i.to_s + '.csv'
  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.cached_is_valid
        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.open(file_name, 'w') do |csv|
    #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 442

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 718

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_binominal?
      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 773

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 452

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 monominal, as originally rendered, with parens if subgenus.

Returns:

  • (String, nil) —

    a monominal, as originally rendered, with parens if subgenus



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# File 'app/models/protonym.rb', line 785

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 604

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 355

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
  return nil if r.nil?
  r.constantize
end

#reduce_list_of_synonyms(list) ⇒ Object 



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# File 'app/models/protonym.rb', line 533

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.cached_nomenclature_date
    unless date1.nil?
      list1.reject!{|s| date1 < (s.cached_nomenclature_date ? s.cached_nomenclature_date : Time.utc(1))}
    end
  end
  list1
end

#set_cached ⇒ Object (protected) 



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# File 'app/models/protonym.rb', line 1003

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 1013

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 1021

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 821

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 1025

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 1029

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 814

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 650

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 is a very expensive soft validation, it should be fragemented into individual parts likely. It should also not be necessary by default our code should be good enough to handle these issues in the long run. DD: rules for cached tend to evolve, what was good in the past, may not be true today MJY: If the meaning of cached changes then it should be removed, not changed.



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# File 'app/models/protonym.rb', line 977

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
is_cached = false if cached_author != get_author
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

#synonymize_with(protonym) ⇒ Object

A convenience method to make this name a low-level synonym of another. Presently limited in scope to names that share rank (not rank group)



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# File 'app/models/protonym.rb', line 193

def synonymize_with(protonym)
  return false if protonym.nil?
  return false if protonym.rank_class.to_s != rank_class.to_s

  begin
    case nomenclatural_code
    when  :iczn
      TaxonNameRelationship::Iczn::Invalidating::Synonym.create!(subject_taxon_name: self, object_taxon_name: protonym)
    when :icn
      TaxonNameRelationship::Icn::Unaccepting::Synonym.create!(subject_taxon_name: self, object_taxon_name: protonym)
    when :icnp
      TaxonNameRelationship::Icnp::Unaccepting::Synonym.create!(subject_taxon_name: self, object_taxon_name: protonym)
    when :icvnc
      TaxonNameRelationship::Icnp::Unaccepting::SupressedSynony.create!(subject_taxon_name: self, object_taxon_name: protonym)
    else
      return false
    end
  rescue ActiveRecord::RecordInvalid
    return false
  end

end

#update_cached_original_combinations ⇒ Object 



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# File 'app/models/protonym.rb', line 806

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 943

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 958

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 939

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

#validate_same_nomenclatural_code ⇒ Object (protected) 



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# File 'app/models/protonym.rb', line 966

def validate_same_nomenclatural_code
  if parent&.nomenclatural_code && nomenclatural_code != parent.nomenclatural_code
    errors.add(:rank_class, "The parent nomenclatural code (#{parent.nomenclatural_code.to_s.upcase}) is not matching to the nomenclatural code (#{nomenclatural_code.to_s.upcase}) of this taxon")
  end
end

#verbatim_author_with_closed_parens_when_present ⇒ Object (protected) 



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# File 'app/models/protonym.rb', line 915

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 911

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