Module: Protonym::SoftValidationExtensions::Instance

Included in:
Protonym
Defined in:
app/models/protonym/soft_validation_extensions.rb

Instance Method Summary collapse

Instance Method Details

#sv_author_is_not_required ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1582

def sv_author_is_not_required
  if self.verbatim_author && (!self.taxon_name_author_roles.empty? || (self.source && self.verbatim_author == self.source.authority_name))
    soft_validations.add(
      :verbatim_author, 'Verbatim author is not required, it is derived from the source and taxon name author roles',
      success_message: 'Verbatim author was deleted',
      failure_message:  'Failed to delete verbatim author')
  end
end

#sv_duplicate_nomen_nudum ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1667

def sv_duplicate_nomen_nudum
  if self.id == self.cached_valid_taxon_name_id && self.cached_is_valid == false
    if !self.cached_secondary_homonym_alternative_spelling.nil?
      possible_available = Protonym.where(cached_secondary_homonym_alternative_spelling: self.cached_secondary_homonym_alternative_spelling).not_self(self).with_project(self.project_id).any?
      soft_validations.add(:base, "An available protonym with the same original combination,  #{self.cached_html}, exits.") if possible_available
    elsif !self.cached_primary_homonym_alternative_spelling.nil?
      possible_available = Protonym.where(cached_primary_homonym_alternative_spelling: self.cached_primary_homonym_alternative_spelling).not_self(self).with_project(self.project_id).any?
      soft_validations.add(:base, "An available protonym with the same name,  #{self.cached_html}, exits.") if possible_available
    end
  end
end

#sv_extant_children ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1523

def sv_extant_children
  unless self.parent_id.blank?
    if self.is_fossil?
      taxa = Protonym.where(parent_id: self.id)
      z = 0
      unless taxa.empty?
        taxa.each do |t|
          soft_validations.add(:base, "Extinct taxon #{self.cached_html} has extant children") if !t.is_fossil? && t.id == t.cached_valid_taxon_name_id && z == 0
          z = 1
        end
      end
    end
  end
end

#sv_family_is_invalid ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1383

def sv_family_is_invalid
  if persisted? && is_family_rank? && is_available?
    tg = type_genus
    if tg && (!TaxonNameRelationship.where_subject_is_taxon_name(tg).homonym_or_suppressed.empty? ||
        !TaxonNameClassification.where_taxon_name(tg).with_type_string('TaxonNameClassification::Iczn::Available::Invalid::Homonym').empty? )
      if self.id == self.lowest_rank_coordinated_taxon.id
        if TaxonNameClassification.where_taxon_name(self).with_type_base('TaxonNameClassification::Iczn::Available::Invalid').empty?
          soft_validations.add(:base, "Missing relationship: #{self.cached_html_name_and_author_year} is invalid due to the homonymy or suppression of its type genus")
        end
      end
    end
  end
end

#sv_family_is_invalid_no_substitute ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1397

def sv_family_is_invalid_no_substitute
  if persisted? && is_family_rank? && self.id == self.lowest_rank_coordinated_taxon.id
    if !TaxonNameClassification.where_taxon_name(self).with_type_base('TaxonNameClassification::Iczn::Available::Invalid').empty?
      if self.iczn_set_as_synonym_of.nil?
        soft_validations.add(:base, 'Missing relationship: The name is invalid, but a substitute name is not selected')
      end
    end
  end
end

#sv_fix_add_nominotypical_sub ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1286

def sv_fix_add_nominotypical_sub
  return false if list_of_coordinated_names.collect{|r| r.id}.include?(parent_id)
  rank  = rank_string
  p     = self.parent
  prank = p.rank_string
  if (rank =~ /Family/ && prank =~ /Family/) || (rank =~ /Genus/ && prank =~ /Genus/) || (rank =~ /Species/ && prank =~ /Species/)
    begin
      Protonym.transaction do
        if rank =~ /Family/ && prank =~ /Family/
          name = Protonym.family_group_base(self.parent.name)
          case self.rank_class.rank_name
          when 'subfamily'
            name += 'inae'
          when 'tribe'
            name += 'ini'
          when 'subtribe'
            name += 'ina'
          end
        else
          name = p.name
        end

        t = Protonym.new(name: name, rank_class: rank, verbatim_author: p.verbatim_author, year_of_publication: p.year_of_publication, source: p.source, parent: p)
        t.save
        t.soft_validate
        t.fix_soft_validations
      end
    rescue ActiveRecord::RecordInvalid # naked rescue is very bad
      return false
    end
    return true
  end
end

#sv_fix_author_is_not_required ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1591

def sv_fix_author_is_not_required
  self.update_column(:verbatim_author, nil)
  return true
end

#sv_fix_coordinated_names_author ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 659

def sv_fix_coordinated_names_author
  return false if !self.verbatim_author.nil? || !self.taxon_name_author_roles.empty?
  list_of_coordinated_names.each do |t|
    if self.verbatim_author.nil? && !t.verbatim_author.nil?
      self.update_column(:verbatim_author, t.verbatim_author)
      return true
    end
  end
  return false
end

#sv_fix_coordinated_names_etymology ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 952

def sv_fix_coordinated_names_etymology
  fixed = false
  return false unless self.etymology.blank?
  list_of_coordinated_names.each do |t|
    if !t.etymology.blank?
      self.etymology = t.etymology
      fixed = true
    end
  end
  if fixed
    begin
      Protonym.transaction do
        self.save
      end
      return true
    rescue
      return false
    end
  end
end

#sv_fix_coordinated_names_gender ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 699

def sv_fix_coordinated_names_gender
  return false unless self.gender_class.nil?
  list_of_coordinated_names.each do |t|
    unless t.gender_class.nil?
      c = self.taxon_name_classifications.create(type: t.gender_class.to_s)
      return true if c.id
    end
  end
  return false
end

#sv_fix_coordinated_names_original_form ⇒ Object 



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

def sv_fix_coordinated_names_original_form
  fixed = false
  return false unless self.original_form.nil?
  list_of_coordinated_names.each do |t|
    if !t.original_form.nil?
      self.original_form = t.original_form
      fixed = true
    end
  end
  if fixed
    begin
      Protonym.transaction do
        self.save
      end
      return true
    rescue
      return false
    end
  end
end

#sv_fix_coordinated_names_original_genus ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 740

def sv_fix_coordinated_names_original_genus
  fixed = false
  return false unless self.original_genus.nil?
  list_of_coordinated_names.each do |t|
    if !t.original_genus.nil?
      self.original_genus = t.original_genus
      fixed = true
    end
  end
  if fixed
    begin
      Protonym.transaction do
        self.save
      end
      return true
    rescue
      return false
    end
  end
end

#sv_fix_coordinated_names_original_species ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 800

def sv_fix_coordinated_names_original_species
  fixed = false
  return false unless self.original_species.nil?
  list_of_coordinated_names.each do |t|
    if !t.original_species.nil?
      self.original_species = t.original_species
      fixed = true
    end
  end
  if fixed
    begin
      Protonym.transaction do
        self.save
      end
      return true
    rescue
      return false
    end
  end
end

#sv_fix_coordinated_names_original_subgenus ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 770

def sv_fix_coordinated_names_original_subgenus
  fixed = false
  return false unless self.original_subgenus.nil?
  list_of_coordinated_names.each do |t|
    if !t.original_subgenus.nil?
      self.original_subgenus = t.original_subgenus
      fixed = true
    end
  end
  if fixed
    begin
      Protonym.transaction do
        self.save
      end
      return true
    rescue
      return false
    end
  end
end

#sv_fix_coordinated_names_original_subspecies ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 830

def sv_fix_coordinated_names_original_subspecies
  fixed = false
  return false unless self.original_subspecies.nil?
  list_of_coordinated_names.each do |t|
    if !t.original_subspecies.nil?
      self.original_subspecies = t.original_subspecies
      fixed = true
    end
  end
  if fixed
    begin
      Protonym.transaction do
        self.save
      end
      return true
    rescue
      return false
    end
  end
end

#sv_fix_coordinated_names_original_variety ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 860

def sv_fix_coordinated_names_original_variety
  fixed = false
  return false unless self.original_variety.nil?
  list_of_coordinated_names.each do |t|
    if !t.original_variety.nil?
      self.original_variety = t.original_variety
      fixed = true
    end
  end
  if fixed
    begin
      Protonym.transaction do
        self.save
      end
      return true
    rescue
      return false
    end
  end
end

#sv_fix_coordinated_names_page ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 631

def sv_fix_coordinated_names_page
  fixed = false
  return false if self.origin_citation.nil? || !self.origin_citation.pages.nil?
  list_of_coordinated_names.each do |t|
    if !t.origin_citation.nil? && !t.origin_citation.pages.nil? && self.origin_citation.source_id == t.origin_citation.source_id
      self.origin_citation.pages = t.origin_citation.pages
      fixed = true
    end
  end
  if fixed
    begin
      Protonym.transaction do
        self.origin_citation.save
      end
      return true
    rescue
      return false
    end
  end
end

#sv_fix_coordinated_names_part_of_speech ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 720

def sv_fix_coordinated_names_part_of_speech
  return false unless self.part_of_speech_class.nil?
  list_of_coordinated_names.each do |t|
    unless t.part_of_speech_class.nil?
      c = self.taxon_name_classifications.create(type: t.part_of_speech_class.to_s)
      return true if c.id
    end
  end
  return false
end

#sv_fix_coordinated_names_roles ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 982

def sv_fix_coordinated_names_roles
  return false unless self.taxon_name_author_roles.empty?
  list_of_coordinated_names.each do |t|
    if !t.taxon_name_author_roles.empty?
      t.taxon_name_author_roles.each do |r|
        TaxonNameAuthor.create(person_id: r.person_id, role_object: self, position: r.position)
      end
      return true
    end
  end
  return false
end

#sv_fix_coordinated_names_source ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 596

def sv_fix_coordinated_names_source
  fixed = false
  pg = nil
  return false unless self.source.nil?
    list_of_coordinated_names.each do |t|
      if !t.source.nil?
        self.source = t.source
        pg = t.origin_citation.pages
        fixed = true
      end
    end
    if fixed
    begin
      Protonym.transaction do
        self.source.save
        self.origin_citation.update_column(:pages, pg)
      end
      return true
    rescue
      return false
    end
  end
end

#sv_fix_coordinated_names_type_genus ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1040

def sv_fix_coordinated_names_type_genus
  fixed = false
  return false unless self.type_genus.nil?
  list_of_coordinated_names.each do |t|
    if !t.type_genus.nil?
      self.type_genus = t.type_genus
      fixed = true
    end
  end
  if fixed
    begin
      Protonym.transaction do
        self.type_genus.save
      end
      return true
    rescue
      return false
    end
  end
end

#sv_fix_coordinated_names_type_species ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 921

def sv_fix_coordinated_names_type_species
  fixed = false
  tr = nil
  return false unless self.type_species.nil?
  list_of_coordinated_names.each do |t|
    if !t.type_species.nil? && fixed == false
      tr = TaxonNameRelationship.new(type: t.type_species_relationship.type, subject_taxon_name_id: t.type_species_relationship.subject_taxon_name_id, object_taxon_name_id: self.id)
      fixed = true
    end
  end
  if fixed
    begin
      TaxonNameRelationship.transaction do
        tr.save
      end
      return true
    rescue
      return false
    end
  end
end

#sv_fix_coordinated_names_type_species_type ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1007

def sv_fix_coordinated_names_type_species_type
  sttnr = self.type_taxon_name_relationship
  return false if sttnr.nil?
  fixed = false
  list_of_coordinated_names.each do |t|
    tttnr = t.type_taxon_name_relationship
    if !tttnr.nil? && sttnr.type != tttnr.type && sttnr.type.safe_constantize.descendants.collect{|i| i.to_s}.include?(tttnr.type.to_s)
      self.type_taxon_name_relationship.type = t.type_taxon_name_relationship.type
      fixed = true
    end
  end
  if fixed
    begin
      Protonym.transaction do
        self.type_taxon_name_relationship.save
      end
      return true
    rescue
      return false
    end
  end
end

#sv_fix_coordinated_names_type_specimen ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1070

def sv_fix_coordinated_names_type_specimen
  fixed = false
  return false unless self.get_primary_type.empty?
  list_of_coordinated_names.each do |t1|
    types2 = t1.get_primary_type
    if !types2.empty?
      new_type_material = []
      types2.each do |t|
        new_type_material.push({type_type: t.type_type, protonym_id: self.id, collection_object_id: t.collection_object_id, source: t.source})
      end
      self.type_materials.build(new_type_material)
      fixed = true
    end
  end
  if fixed
    begin
      Protonym.transaction do
        self.save
      end
      return true
    rescue
      return false
    end
  end
end

#sv_fix_coordinated_names_year ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 677

def sv_fix_coordinated_names_year
  return false if !self.year_of_publication.nil? || !self.source.try(:year).nil?
  list_of_coordinated_names.each do |t|
    if self.year_of_publication.nil? && !t.year_of_publication.nil?
      self.update_column(:year_of_publication, t.year_of_publication)
      return true
    end
  end
  return false
end

#sv_fix_missing_otu ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1651

def sv_fix_missing_otu
  if is_available? && otus.empty?
    otus.create(taxon_name_id: id)
    return true
  end
  return false
end

#sv_fix_misspelling_author_is_not_required ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1623

def sv_fix_misspelling_author_is_not_required
  self.update_column(:verbatim_author, nil)
  return true
end

#sv_fix_misspelling_roles_are_not_required ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1607

def sv_fix_misspelling_roles_are_not_required
  self.taxon_name_author_roles.each do |r|
    r.destroy
  end
  return true
end

#sv_fix_misspelling_year_is_not_required ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1637

def sv_fix_misspelling_year_is_not_required
  self.update_column(:year_of_publication, nil)
  return true
end

#sv_fix_presence_of_combination ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1690

def sv_fix_presence_of_combination
  begin
    TaxonName.transaction do
      c = Combination.new
      safe_self_and_ancestors.each do |i|
        case i.rank
          when 'genus'
            c.genus = i
          when 'subgenus'
            c.subgenus = i
          when 'species'
            c.species = i
          when 'subspecies'
            c.subspecies = i
        end
      end
      c.save
    end
  rescue
  end
end

#sv_fix_type_placement1 ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1218

def sv_fix_type_placement1
  self.type_of_taxon_names.each do |t|
    coordinated = t.lowest_rank_coordinated_taxon
    if self.parent_id != coordinated.id
      #          if t.id != coordinated.id && self.parent_id != coordinated.id
      begin
        Protonym.transaction do
          self.parent_id = coordinated.id
          self.save
        end
        return true
      rescue
        return false
      end
    end
  end
end

#sv_fix_year_is_not_required ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1577

def sv_fix_year_is_not_required
  self.update_column(:year_of_publication, nil)
  return true
end

#sv_homotypic_synonyms ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1339

def sv_homotypic_synonyms
  unless !is_valid? # unavailable_or_invalid?
    if self.id == self.lowest_rank_coordinated_taxon.id
      possible_synonyms = []
      if rank_string =~ /Species/
        primary_types = self.get_primary_type
        unless primary_types.empty?
          p                 = primary_types.collect {|t| t.collection_object_id}
          possible_synonyms = Protonym.with_type_material_array(p).without_taxon_name_classification_array(TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID).not_self(self).with_project(self.project_id)
        end
      elsif rank_string =~ /Family/ && self.name == Protonym.family_group_base(self.name)
        # do nothing
      else
        type = self.type_taxon_name
        unless type.nil?
          possible_synonyms = Protonym.with_type_of_taxon_names(type.id).not_self(self).with_project(self.project_id)
        end
      end

      possible_synonyms = reduce_list_of_synonyms(possible_synonyms)
      possible_synonyms.each do |s|
        soft_validations.add(:base, "Missing relationship: #{self.rank_class.rank_name} #{self.cached_html} should be a synonym of #{s.cached_html} #{s.cached_author_year} since they share the same type")
      end
    end
  end
end

#sv_missing_etymology ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1499

def sv_missing_etymology
  if self.etymology.nil? && self.rank_string =~ /(Genus|Species)/ && is_available?
    z = TaxonName.
        where(name: name, project_id: project_id).where.not(etymology: nil).
        group(:etymology).
        count(:etymology)

    if z.empty?
      z = TaxonName.where(name: name).where.not(etymology: nil).group(:etymology).count(:etymology)
      other_project = ' in different projects'
    else
      other_project = ''
    end

    if z.empty?
      soft_validations.add(:etymology, 'Etymology is missing')
    else
      z1 = z.sort_by {|k, v| -v}
      t = z1[0][1] == 1 ? 'time' : 'times'
      soft_validations.add(:etymology, "Etymology is missing. Previously used etymology for similar name#{other_project}: '#{z1[0][0]}' (#{z1[0][1]} #{t})")
    end
  end
end

#sv_missing_gender ⇒ Object 



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

def sv_missing_gender
  if is_genus_rank? && self.gender_class.nil? && !self.cached_misspelling && is_available?
    g = genus_suggested_gender
    soft_validations.add(:base, "Gender is not specified#{ g.nil? ? '' : ' (possible gender is ' + g + ')'}")
  end
end

#sv_missing_infrasubspecific_status ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1478

def sv_missing_infrasubspecific_status
  if nomenclatural_code == :iczn && (self.cached_original_combination&.include?(' var. ') || self.cached_original_combination&.include?(' f. ')) && self.cached_nomenclature_date&.year > 1960 && is_available?(refresh = true)
    soft_validations.add(:base, 'Missing status. The name described as variety or form after 1960 should be treated as infrasubspecific.')
  end
end

#sv_missing_original_genus ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1472

def sv_missing_original_genus
  if is_genus_or_species_rank? && self.original_genus.nil? && !not_binominal?
    soft_validations.add(:base, 'Missing relationship: Original genus is not selected')
  end
end

#sv_missing_otu ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1642

def sv_missing_otu
  if is_available? && otus.empty? && rank_string != 'NomenclaturalRank'
    soft_validations.add(
      :year_of_publication, 'Missing OTU',
      success_message: 'OTU was created',
      failure_message:  'Failed to create OTU')
  end
end

#sv_missing_part_of_speech ⇒ Object 



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

def sv_missing_part_of_speech
  if is_species_rank? && self.part_of_speech_class.nil? && !has_misspelling_relationship? && is_available?

    z = TaxonNameClassification.
        joins(:taxon_name).
        where(taxon_names: { name: name, project_id: project_id }).
        where("taxon_name_classifications.type LIKE 'TaxonNameClassification::Latinized::PartOfSpeech%'").
        group(:type).
        count(:type)

    if z.empty?
      z = TaxonNameClassification.
          joins(:taxon_name).
          where(taxon_names: { name: name}).
          where("taxon_name_classifications.type LIKE 'TaxonNameClassification::Latinized::PartOfSpeech%'").
          group(:type).
          count(:type)
      other_project = ' in different projects'
    else
      other_project = ''
    end

    if z.empty?
      soft_validations.add(:base, 'Part of speech is not specified. Please select if the name is a noun or an adjective.')
    else
      l = []
      z.each do |key, value|
        l << (value == 1 ? " as '#{key.constantize.label}' #{value.to_s} time" : " as '#{key.constantize.label}' #{value.to_s} times")
      end
      soft_validations.add(:base, "Part of speech is not specified. The name was previously used#{other_project}" + l.join('; '))
    end
  end
end

#sv_missing_roles ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1546

def sv_missing_roles
  if self.taxon_name_author_roles.empty? && !has_misspelling_relationship? && !name_is_misapplied? && is_family_or_genus_or_species_rank?
    soft_validations.add(:base, 'Taxon name author role is not selected')
  end
end

#sv_missing_substitute_name ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 453

def sv_missing_substitute_name
  if !self.iczn_set_as_homonym_of.nil? || !TaxonNameClassification.where_taxon_name(self).with_type_string('TaxonNameClassification::Iczn::Available::Invalid::Homonym').empty?
    if self.iczn_set_as_synonym_of.nil? && is_available?
      soft_validations.add(:base, 'Missing relationship: The name is a homonym, but a substitute name is not selected')
    end
  end
end

#sv_missing_type_genus ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 447

def sv_missing_type_genus
  if is_family_rank? && self.type_genus.nil? && is_available?
    soft_validations.add(:base, 'Missing relationship: Type genus is not selected')
  end
end

#sv_missing_type_species ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 441

def sv_missing_type_species
  if is_genus_rank? && self.type_species.nil? && is_available?
    soft_validations.add(:base, 'Missing relationship: Type species is not selected')
  end
end

#sv_misspelling_author_is_not_required ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1614

def sv_misspelling_author_is_not_required
  if self.verbatim_author && self.source && taxon_name_relationships.with_type_array(TAXON_NAME_RELATIONSHIP_NAMES_MISSPELLING_AND_MISAPPLICATION).any?
    soft_validations.add(
      :verbatim_author, 'Verbatim author is not required for misspellings and misapplications',
      success_message: 'Verbatim author was deleted',
      failure_message:  'Failed to delete verbatim author')
  end
end

#sv_misspelling_roles_are_not_required ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1596

def sv_misspelling_roles_are_not_required
  #DD: do not use .has_misspelling_relationship?
  misspellings = taxon_name_relationships.with_type_array(TAXON_NAME_RELATIONSHIP_NAMES_MISSPELLING_AND_MISAPPLICATION).any?
  if !self.taxon_name_author_roles.empty? && self.source && misspellings
    soft_validations.add(
      :base, 'Taxon name author role is not required for misspellings and misapplications',
      success_message: 'Roles were deleted',
      failure_message:  'Fail to delete roles')
  end
end

#sv_misspelling_year_is_not_required ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1628

def sv_misspelling_year_is_not_required
  if self.year_of_publication && taxon_name_relationships.with_type_array(TAXON_NAME_RELATIONSHIP_NAMES_MISSPELLING_AND_MISAPPLICATION).any?
    soft_validations.add(
      :year_of_publication, 'Year is not required for misspellings and misapplications',
      success_message: 'Year was deleted',
      failure_message:  'Failed to delete year')
  end
end

#sv_original_combination_relationships ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1484

def sv_original_combination_relationships
  relationships = self.original_combination_relationships
  unless relationships.empty?
    relationships = relationships.sort_by{|r| r.type_class.order_index }
    ids = relationships.collect{|r| r.subject_taxon_name_id}
    if !ids.include?(self.id)
      if (list_of_coordinated_names.collect{|r| r.id} & ids).empty?
        soft_validations.add(:base, "Missing relationship: The original rank of #{self.cached_html} is not specified in the original combination.")
      end
    elsif ids.last != self.id
      soft_validations.add(:base, "Invalid original combination relationship: #{self.cached_html} should be moved to the lowest rank")
    end
  end
end

#sv_parent_priority ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1320

def sv_parent_priority
  if self.rank_class
    rank_group = self.rank_class.parent
    parent = self.parent

    if !is_higher_rank? && parent && rank_group == parent.rank_class.parent
      unless !is_valid? #  unavailable_or_invalid?
        date1 = self.cached_nomenclature_date
        date2 = parent.cached_nomenclature_date
        unless date1.nil? || date2.nil?
          if date1 < date2
            soft_validations.add(:base, "#{self.rank_class.rank_name.capitalize} #{self.cached_html_name_and_author_year} should not be older than parent #{parent.rank_class.rank_name} #{parent.cached_html_name_and_author_year}")
          end
        end
      end
    end
  end
end

#sv_person_vs_year_of_publication ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1552

def sv_person_vs_year_of_publication
  if self.cached_nomenclature_date
    year = self.cached_nomenclature_date&.year
    self.taxon_name_author_roles.each do |r|
      person = r.person
      if person.year_died && year > person.year_died + 2
        soft_validations.add(:base, "The year of description does not fit the years of #{person.last_name}'s life (#{person.year_born}–#{person.year_died})")
      elsif person.year_born && year > person.year_born + 105
        soft_validations.add(:base, "The year of description does not fit the years of #{person.last_name}'s life (#{person.year_born}–#{person.year_died})")
      elsif person.year_born && year < person.year_born + 10
        soft_validations.add(:base, "The year of description does not fit the years of #{person.last_name}'s life (#{person.year_born}–#{person.year_died})")
      end
    end
  end
end

#sv_potential_family_homonyms ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1366

def sv_potential_family_homonyms
  if persisted? && is_family_rank? && is_available?
    if TaxonNameRelationship.where_subject_is_taxon_name(self).homonym_or_suppressed.empty?
      if self.id == self.lowest_rank_coordinated_taxon.id
        name2 = self.cached_primary_homonym_alternative_spelling ? self.cached_primary_homonym_alternative_spelling : nil
        possible_primary_homonyms_alternative_spelling = name2 ? Protonym.with_primary_homonym_alternative_spelling(name2).without_homonym_or_suppressed.without_taxon_name_classification_array(TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID).not_self(self).with_base_of_rank_class('NomenclaturalRank::Iczn::FamilyGroup').with_project(self.project_id) : []
        list2 = reduce_list_of_synonyms(possible_primary_homonyms_alternative_spelling)
        if !list2.empty?
          list2.each do |s|
            soft_validations.add(:base, "Missing relationship: #{self.cached_html_name_and_author_year} should be a homonym or duplicate of #{s.cached_html_name_and_author_year}")
          end
        end
      end
    end
  end
end

#sv_potential_genus_homonyms ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1407

def sv_potential_genus_homonyms
  if persisted? && is_genus_rank? && is_available?
    if TaxonNameRelationship.where_subject_is_taxon_name(self).homonym_or_suppressed.empty?
      if self.id == self.lowest_rank_coordinated_taxon.id
        name1 = self.cached_primary_homonym ? self.cached_primary_homonym : nil
        possible_primary_homonyms = name1 ? Protonym.with_primary_homonym(name1).without_taxon_name_classification_array(TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID).without_homonym_or_suppressed.not_self(self).with_base_of_rank_class('NomenclaturalRank::Iczn::GenusGroup').with_project(self.project_id) : []
        list1 = reduce_list_of_synonyms(possible_primary_homonyms)
        if !list1.empty?
          list1.each do |s|
            soft_validations.add(:base, "Missing relationship: #{self.cached_html_name_and_author_year} should be a homonym or duplicate of #{s.cached_html_name_and_author_year}") if s.nomenclatural_code == self.nomenclatural_code
          end
        end
      end
    end
  end
end

#sv_potential_species_homonyms ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1424

def sv_potential_species_homonyms
  if persisted? && is_species_rank? && is_available?
    if TaxonNameRelationship.where_subject_is_taxon_name(self).homonym_or_suppressed.empty?
      if self.id == self.lowest_rank_coordinated_taxon.id
        name1 = self.cached_primary_homonym ? self.cached_primary_homonym : nil
        possible_primary_homonyms = name1 ? Protonym.with_primary_homonym(name1).without_taxon_name_classification_array(TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID).without_homonym_or_suppressed.not_self(self).with_base_of_rank_class('NomenclaturalRank::Iczn::SpeciesGroup').with_project(self.project_id) : []
        list1 = reduce_list_of_synonyms(possible_primary_homonyms)
        if !list1.empty?
          list1.each do |s|
            soft_validations.add(
              :base, "Missing relationship: #{self.cached_html_name_and_author_year} should be a primary homonym or duplicate of #{s.cached_html_name_and_author_year}")
            #  fix: :sv_fix_add_relationship('iczn_set_as_primary_homonym_of'.to_sym, s.id),
            #  success_message: 'Primary homonym relationship was added',
            #  failure_message: 'Fail to add a relationship')
          end
        else
          name2 = self.cached_primary_homonym_alternative_spelling ? self.cached_primary_homonym_alternative_spelling : nil
          possible_primary_homonyms_alternative_spelling = name2 ? Protonym.with_primary_homonym_alternative_spelling(name2).without_homonym_or_suppressed.without_taxon_name_classification_array(TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID).not_self(self).with_base_of_rank_class('NomenclaturalRank::Iczn::SpeciesGroup').with_project(self.project_id) : []
          list2 = reduce_list_of_synonyms(possible_primary_homonyms_alternative_spelling)
          if !list2.empty?
            list2.each do |s|
              soft_validations.add(:base, "Missing relationship: #{self.cached_html_name_and_author_year} could be a primary homonym of #{s.cached_html_name_and_author_year} (alternative spelling)")
            end
          else
            name3 = self.cached_secondary_homonym ? self.cached_secondary_homonym : nil
            possible_secondary_homonyms = name3 ? Protonym.with_secondary_homonym(name3).without_homonym_or_suppressed.without_taxon_name_classification_array(TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID).not_self(self).with_base_of_rank_class('NomenclaturalRank::Iczn::SpeciesGroup').with_project(self.project_id) : []
            list3 = reduce_list_of_synonyms(possible_secondary_homonyms)
            if !list3.empty?
              list3.each do |s|
                soft_validations.add(:base, "Missing relationship: #{self.cached_html_name_and_author_year} should be a secondary homonym or duplicate of #{s.cached_html_name_and_author_year}")
              end
            else
              name4 = self.cached_secondary_homonym ? self.cached_secondary_homonym_alternative_spelling : nil
              possible_secondary_homonyms_alternative_spelling = name4 ? Protonym.with_secondary_homonym_alternative_spelling(name4).without_homonym_or_suppressed.without_taxon_name_classification_array(TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID).not_self(self).with_base_of_rank_class('NomenclaturalRank::Iczn::SpeciesGroup').with_project(self.project_id) : []
              list4 = reduce_list_of_synonyms(possible_secondary_homonyms_alternative_spelling)
              if !list4.empty?
                list4.each do |s|
                  soft_validations.add(:base, "Missing relationship: #{self.cached_html_name_and_author_year} could be a secondary homonym of #{s.cached_html_name_and_author_year} (alternative spelling)")
                end
              end
            end
          end
        end
      end
    end
  end
end

#sv_potential_usage_duplicates ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1659

def sv_potential_usage_duplicates
  usage = TaxonNameRelationship::Iczn::Invalidating::Usage.where(subject_taxon_name_id: self.id).first
  return true if usage.nil?
  TaxonNameRelationship::Iczn::Invalidating::Usage.where(object_taxon_name_id: usage.object_taxon_name_id).not_self(usage).each do |tr|
    soft_validations.add(:base, "'#{name}' is a duplicate #{usage.subject_status + ' ' + usage.subject_status_connector_to_object} #{tr.object_taxon_name.cached_html}",) if usage.subject_taxon_name.name == tr.subject_taxon_name.name
  end
end

#sv_presence_of_combination ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1679

def sv_presence_of_combination
  if is_genus_or_species_rank? && is_valid? && self.id == self.lowest_rank_coordinated_taxon.id && !cached_original_combination.nil? && cached != cached_original_combination
    unless Combination.where("cached = ? AND cached_valid_taxon_name_id = ?", cached, cached_valid_taxon_name_id).any?
      soft_validations.add(
        :base, "Protonym #{self.cached_html} missing corresponding subsequent combination. Current classification of the taxon is different from original combination. (Fix will try to create a new combination if possible)",
        success_message: "Combination #{self.cached_html} was successfully create",
        failure_message:  'Failed to create a new combination')
    end
  end
end

#sv_primary_types ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1236

def sv_primary_types
  if is_species_rank? && is_available?
    if self.type_materials.primary.empty? && self.type_materials.syntypes.empty?
      soft_validations.add(:base, 'Primary type is not selected')
    elsif self.type_materials.primary.count > 1 || (!self.type_materials.primary.empty? && !self.type_materials.syntypes.empty?)
      soft_validations.add(:base, 'More than one of primary types are selected. Uncheck the specimens which are not primary types for this taxon')
    end
  end
end

#sv_primary_types_repository ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1246

def sv_primary_types_repository
  if is_species_rank?
    s = self.type_materials
    unless s.empty?
      s.primary.each do |t|
        soft_validations.add(:base, 'Primary type repository is not set') if t.collection_object.try(:repository).nil?
      end
      s.syntypes.each do |t|
        soft_validations.add(:base, 'Syntype repository is not set') if t.collection_object.try(:repository).nil?
      end
    end
  end
end

#sv_protonym_to_combination ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1538

def sv_protonym_to_combination
  if convertable_to_combination?
    soft_validations.add(
      :base, "Unavailable or Invalid #{self.cached_original_combination_html} could potentially be converted into a combination (Fix will try to convert protonym into combination)",
      success_message: "Protonym #{self.cached_original_combination_html} was successfully converted into a combination", failure_message:  'Failed to convert protonym into combination')
  end
end

#sv_single_sub_taxon ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1260

def sv_single_sub_taxon
  if self.rank_class
    rank = rank_string
    if rank != 'potentially_validating rank' && self.rank_class.nomenclatural_code == :iczn && %w(subspecies subgenus subtribe tribe subfamily).include?(self.rank_class.rank_name)
      sisters = self.parent.descendants.with_rank_class(rank).select{|t| t.id == t.cached_valid_taxon_name_id}
      if rank =~ /Family/
        z = Protonym.family_group_base(self.name)
        search_name = z.nil? ? nil : Protonym::FAMILY_GROUP_ENDINGS.collect{|i| z+i}
        a = sisters.collect{|i| Protonym.family_group_base(i.name) }
        sister_names = a.collect{|z| Protonym::FAMILY_GROUP_ENDINGS.collect{|i| z+i} }.flatten
      else
        search_name = [self.name]
        sister_names = sisters.collect{|i| i.name }
      end
      if search_name.include?(self.parent.name) && sisters.count == 1
        soft_validations.add(:base, "#{self.cached_html} is a single #{self.rank_class.rank_name} in the nominal #{self.parent.rank_class.rank_name} #{self.parent.cached_html}")
      elsif !sister_names.include?(self.parent.name) && !sisters.empty? && self.parent.name == Protonym.family_group_base(self.parent.name) && rank =~ /Family/
        # do nothing
      elsif !sister_names.include?(self.parent.name) && !sisters.empty?
        soft_validations.add(:base, "The parent #{self.parent.rank_class.rank_name} #{self.parent.cached_html} of this #{self.rank_class.rank_name} does not contain nominotypical #{self.rank_class.rank_name} #{Protonym.family_group_name_at_rank(self.parent.name, self.rank_class.rank_name)}",
                             success_message: "Nominotypical #{self.rank_class.rank_name} was added to nominal #{self.parent.rank_class.rank_name} #{self.parent.cached_html}", failure_message:  'Failed to create nomynotypical taxon')
      end
    end
  end
end

#sv_source_not_older_then_description ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 399

def sv_source_not_older_then_description
  if self.source && self.year_of_publication
    soft_validations.add(:base, 'The year of publication of the taxon and the year in the original reference do not match') if self.try(:source).try(:year) != self.year_of_publication
  end
end

#sv_species_gender_agreement ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 502

def sv_species_gender_agreement
  if is_species_rank?
    s = part_of_speech_name
    if !s.nil? && is_available?
      if %w{adjective participle}.include?(s)
        if !feminine_name.blank? && !masculine_name.blank? && !neuter_name.blank? && name != masculine_name && name != feminine_name && name != neuter_name
          soft_validations.add(:base, 'Species name does not match with either of three alternative forms')
        else
          forms = predict_three_forms
          if feminine_name.blank?
            soft_validations.add(:feminine_name, "The species name is marked as #{part_of_speech_name}, but the name spelling in feminine is not provided")
          else
            # e = species_questionable_ending(TaxonNameClassification::Latinized::Gender::Feminine, feminine_name)
            # soft_validations.add(:feminine_name, "Name has a non feminine ending: -#{e}") unless e.nil?
            soft_validations.add(:feminine_name, "Feminine form does not match with predicted: #{forms[:feminine_name]}") if feminine_name != forms[:feminine_name]
          end

          if masculine_name.blank?
            soft_validations.add(:masculine_name, "The species name is marked as #{part_of_speech_name}, but the name spelling in masculine is not provided")
          else
            # e = species_questionable_ending(TaxonNameClassification::Latinized::Gender::Masculine, masculine_name)
            # soft_validations.add(:masculine_name, "Name has a non masculine ending: -#{e}") unless e.nil?
            soft_validations.add(:masculine_name, "Masculine form does not match with predicted: #{forms[:masculine_name]}") if masculine_name != forms[:masculine_name]
          end

          if neuter_name.blank?
            soft_validations.add(:neuter_name, "The species name is marked as #{part_of_speech_name}, but the name spelling in neuter is not provided")
          else
            # e = species_questionable_ending(TaxonNameClassification::Latinized::Gender::Neuter, neuter_name)
            # soft_validations.add(:neuter_name, "Name has a non neuter ending: -#{e}") unless e.nil?
            soft_validations.add(:neuter_name, "Neuter form does not match with predicted: #{forms[:neuter_name]}") if neuter_name != forms[:neuter_name]
          end
        end
      end
    end
  end
end

#sv_species_gender_agreement_not_required ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 540

def sv_species_gender_agreement_not_required
  if is_species_rank? && ((!feminine_name.blank? || !masculine_name.blank? || !neuter_name.blank?)) && is_available?
    s = part_of_speech_name
    if !s.nil? && !%w{adjective participle}.include?(s)
      soft_validations.add(:feminine_name, 'Alternative spelling is not required for the name which is not adjective or participle.') unless feminine_name.blank?
      soft_validations.add(:masculine_name, 'Alternative spelling is not required for the name which is not adjective or participle.')  unless masculine_name.blank?
      soft_validations.add(:neuter_name, 'Alternative spelling is not required for the name which is not adjective or participle.')  unless neuter_name.blank?
    end
  end
end

#sv_type_placement ⇒ Object

def sv_fix_coordinated_names

  fixed = false
  gender = self.gender_class
  speech = self.part_of_speech_class

  list_of_coordinated_names.each do |t|
    if t.source.nil? && !t.source.nil?
      self.source = t.source
      fixed = true
    end

    if self.verbatim_author.nil? && !t.verbatim_author.nil?
      self.verbatim_author = t.verbatim_author
      fixed = true
    end

    if self.year_of_publication.nil? && !t.year_of_publication.nil?
      self.year_of_publication = t.year_of_publication
      fixed = true
    end

    t_gender = t.gender_class

    if gender.nil? && !t_gender.nil?
      self.taxon_name_classifications.build(type: t_gender.to_s)
      fixed = true
    end

    t_speech = t.part_of_speech_class

    if speech.nil? && speech != t_speech
      self.taxon_name_classifications.build(type: t_speech.to_s)
      fixed = true
    end

    if self.gender_class.nil? && !t.gender_class.nil?
      self.taxon_name_classifications.build(type: t.gender_class.to_s)
      fixed = true
    end

    if self.original_genus.nil? && !t.original_genus.nil?
      self.original_genus = t.original_genus
      fixed = true
    end

    if self.original_subgenus.nil? && !t.original_subgenus.nil?
      self.original_subgenus = t.original_subgenus
      fixed = true
    end

    if self.original_species.nil? && !t.original_species.nil?
      self.original_species = t.original_species
      fixed = true
    end

    if self.original_subspecies.nil? && !t.original_subspecies.nil?
      self.original_subspecies = t.original_subspecies
      fixed = true
    end

    if self.type_species.nil? && !t.type_species.nil?
      self.type_species = t.type_species
      fixed = true
    end

    if self.type_genus.nil? && !t.type_genus.nil?
      self.type_genus = t.type_genus
      fixed = true
    end

    types1 = self.get_primary_type
    types2 = t.get_primary_type
    if types1.empty? && !types2.empty?
      new_type_material = []
      types2.each do |t|
        new_type_material.push({type_type: t.type_type, protonym_id: t.protonym_id, collection_object_id: t.collection_object_id, source: t.source})
      end
      self.type_materials.build(new_type_material)
      fixed = true
    end

    sttnr = self.type_taxon_name_relationship
    tttnr = t.type_taxon_name_relationship
    unless sttnr.nil? || tttnr.nil?
      if sttnr.type != tttnr.type && sttnr.type.safe_constantize.descendants.collect{|i| i.to_s}.include?(tttnr.type.to_s)
        self.type_taxon_name_relationship.type = t.type_taxon_name_relationship.type
        fixed = true
      end
    end
  end

  if fixed
    begin
      Protonym.transaction do
        self.save
      end
    rescue
      return false
    end
  end
  return fixed
end



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1201

def sv_type_placement
  # type of this taxon is not included in this taxon
  if !!self.type_taxon_name
    soft_validations.add(:base, "#{self.rank_class.rank_name} #{self.cached_html} has the type #{self.type_taxon_name.rank_class.rank_name} #{self.type_taxon_name.cached_html} classified outside of this taxon") unless self.type_taxon_name.get_valid_taxon_name.ancestors.include?(TaxonName.find(self.cached_valid_taxon_name_id))
  end
end

#sv_type_placement1 ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1208

def sv_type_placement1
  # this taxon is a type, but not included in nominal taxon
  if !!self.type_of_taxon_names
    self.type_of_taxon_names.each do |t|
      soft_validations.add(:base, "#{self.rank_class.rank_name.capitalize} #{self.cached_html} is the type of #{t.rank_class.rank_name} #{t.cached_html} but it has a parent outside of #{t.cached_html}",
                           success_message: 'Parent for type species was updated', failure_message: 'Parent for type species was not updated') unless self.get_valid_taxon_name.ancestors.include?(TaxonName.find(t.cached_valid_taxon_name_id))
    end
  end
end

#sv_validate_coordinated_names_author ⇒ Object 



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

def sv_validate_coordinated_names_author
  s = self.verbatim_author
  list_of_coordinated_names.each do |t|
    soft_validations.add(:verbatim_author, "The author does not match with the author of the coordinate #{t.rank_class.rank_name}", success_message: 'Author was updated', failure_message:  'Failed to update author') unless s == t.verbatim_author
  end
end

#sv_validate_coordinated_names_etymology ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 943

def sv_validate_coordinated_names_etymology
  return true unless is_available?
  list_of_coordinated_names.each do |t|
    if self.etymology != t.etymology
      soft_validations.add(:etymology, "The etymology does not match with the etymology of the coordinate #{t.rank_class.rank_name}", success_message: 'Etymology was updated', failure_message:  'Etymology was not updated')
    end
  end
end

#sv_validate_coordinated_names_gender ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 688

def sv_validate_coordinated_names_gender
  return true unless is_available?
  return true unless is_genus_rank?
  s = self.gender_class
  list_of_coordinated_names.each do |t|
    if s != t.gender_class
      soft_validations.add(:base, "The gender status does not match with that of the coordinate #{t.rank_class.rank_name}", success_message: 'Gender was updated', failure_message:  'Failed to update gender')
    end
  end
end

#sv_validate_coordinated_names_original_form ⇒ Object 



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

def sv_validate_coordinated_names_original_form
  return true if !is_species_rank? || has_misspelling_relationship?
  list_of_coordinated_names.each do |t|
    if self.original_form.try(:name) != t.original_form.try(:name)
      soft_validations.add(:base, "The original form does not match with the original form of coordinate #{t.rank_class.rank_name}", success_message: 'Original form was updated', failure_message:  'Failed to update original form')
    end
  end
end

#sv_validate_coordinated_names_original_genus ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 731

def sv_validate_coordinated_names_original_genus
  return true if !is_genus_or_species_rank? || !is_valid?
  list_of_coordinated_names.each do |t|
    if self.original_genus.try(:name) != t.original_genus.try(:name)
      soft_validations.add(:base, "The original genus does not match with the original genus of coordinate #{t.rank_class.rank_name}", success_message: 'Original genus was updated', failure_message:  'Failed to update original genus')
    end
  end
end

#sv_validate_coordinated_names_original_species ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 791

def sv_validate_coordinated_names_original_species
  return true if !is_species_rank? || has_misspelling_relationship?
  list_of_coordinated_names.each do |t|
    if self.original_species.try(:name) != t.original_species.try(:name)
      soft_validations.add(:base, "The original species does not match with the original species of coordinate #{t.rank_class.rank_name}", success_message: 'Original species was updated', failure_message:  'Failed to update original species')
    end
  end
end

#sv_validate_coordinated_names_original_subgenus ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 761

def sv_validate_coordinated_names_original_subgenus
  return true if !is_genus_or_species_rank? || has_misspelling_relationship?
  list_of_coordinated_names.each do |t|
    if self.original_subgenus.try(:name) != t.original_subgenus.try(:name)
      soft_validations.add(:base, "The original subgenus does not match with the original subgenus of coordinate #{t.rank_class.rank_name}", success_message: 'Original subgenus was updated', failure_message:  'Failed to update original subgenus')
    end
  end
end

#sv_validate_coordinated_names_original_subspecies ⇒ Object 



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

def sv_validate_coordinated_names_original_subspecies
  return true if !is_species_rank? || has_misspelling_relationship?
  list_of_coordinated_names.each do |t|
    if self.original_subspecies.try(:name) != t.original_subspecies.try(:name)
      soft_validations.add(:base, "The original subspecies does not match with the original subspecies of coordinate #{t.rank_class.rank_name}", success_message: 'Original subspecies was updated', failure_message:  'Failed to update original subspecies')
    end
  end
end

#sv_validate_coordinated_names_original_variety ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 851

def sv_validate_coordinated_names_original_variety
  return true if !is_species_rank? || has_misspelling_relationship?
  list_of_coordinated_names.each do |t|
    if self.original_variety.try(:name) != t.original_variety.try(:name)
      soft_validations.add(:base, "The original variety does not match with the original variety of coordinate #{t.rank_class.rank_name}", success_message: 'Original variety was updated', failure_message:  'Failed to update original variety')
    end
  end
end

#sv_validate_coordinated_names_page ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 620

def sv_validate_coordinated_names_page
  return true unless is_valid?
  s = self.origin_citation
  list_of_coordinated_names.each do |t|
    ts = t.origin_citation
    if s && ts && s.source_id == ts.source_id && (s.pages != ts.pages || (s.pages.nil? && !ts.pages.nil?))
      soft_validations.add(:base, "The original publication page does not match with the original publication page of the coordinate #{t.rank_class.rank_name}", success_message: 'Original publication pages were updated', failure_message: 'Original publication pages were not updated')
    end
  end
end

#sv_validate_coordinated_names_part_of_speech ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 710

def sv_validate_coordinated_names_part_of_speech
  return true unless is_available?
  return true unless is_species_rank?
  list_of_coordinated_names.each do |t|
    if self.part_of_speech_class != t.part_of_speech_class
      soft_validations.add(:base, "The part of speech status does not match with that of the coordinate #{t.rank_class.rank_name}", success_message: 'Part of speech was updated', failure_message:  'Failed to update part of speech')
    end
  end
end

#sv_validate_coordinated_names_roles ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 973

def sv_validate_coordinated_names_roles
  return true unless is_valid?
  list_of_coordinated_names.each do |t|
    if self.taxon_name_author_roles.collect{|i| i.person_id} != t.taxon_name_author_roles.collect{|i| i.person_id}
      soft_validations.add(:base, "The author roles do not match with the author roles of the coordinate #{t.rank_class.rank_name}", success_message: 'Author roles were updated', failure_message:  'Author roles were not updated')
    end
  end
end

#sv_validate_coordinated_names_source ⇒ Object

def sv_validate_coordinated_names

  return true unless is_available?
  r = self.iczn_set_as_incorrect_original_spelling_of_relationship
  list_of_coordinated_names.each do |t|
    soft_validations.add(:base, "The original publication does not match with the original publication of the coordinated #{t.rank_class.rank_name}",
                         fix: :sv_fix_coordinated_names, success_message: 'Original publication was updated') if self.source && t.source && self.source.id != t.source.id
    soft_validations.add(:verbatim_author, "The author does not match with the author of the coordinated #{t.rank_class.rank_name}",
                         fix: :sv_fix_coordinated_names, success_message: 'Author was updated') unless self.verbatim_author == t.verbatim_author
    soft_validations.add(:year_of_publication, "The year of publication does not match with the year of the coordinated #{t.rank_class.rank_name}",
                         fix: :sv_fix_coordinated_names, success_message: 'Year was updated') unless self.year_of_publication == t.year_of_publication
    soft_validations.add(:base, "The gender status does not match with the gender of the coordinated #{t.rank_class.rank_name}",
                         fix: :sv_fix_coordinated_names, success_message: 'Gender was updated') if rank_string =~ /Genus/ && self.gender_class != t.gender_class && !has_misspelling_relationship?
    soft_validations.add(:base, "The part of speech status does not match with the part of speech of the coordinated #{t.rank_class.rank_name}",
                         fix: :sv_fix_coordinated_names, success_message: 'Gender was updated') if rank_string =~ /Species/ && self.part_of_speech_class != t.part_of_speech_class && !has_misspelling_relationship?
    soft_validations.add(:base, "The original genus does not match with the original genus of coordinated #{t.rank_class.rank_name}",
                         fix: :sv_fix_coordinated_names, success_message: 'Original genus was updated') if self.original_genus != t.original_genus && r.blank?
    soft_validations.add(:base, "The original subgenus does not match with the original subgenus of the coordinated #{t.rank_class.rank_name}",
                         fix: :sv_fix_coordinated_names, success_message: 'Original subgenus was updated') if self.original_subgenus != t.original_subgenus && r.blank?
    soft_validations.add(:base, "The original species does not match with the original species of the coordinated #{t.rank_class.rank_name}",
                         fix: :sv_fix_coordinated_names, success_message: 'Original species was updated') if self.original_species != t.original_species && r.blank?
    soft_validations.add(:base, "The type species does not match with the type species of the coordinated #{t.rank_class.rank_name}",
                         fix: :sv_fix_coordinated_names, success_message: 'Type species was updated') if self.type_species != t.type_species && !has_misspelling_relationship?
    soft_validations.add(:base, "The type genus does not match with the type genus of the coordinated #{t.rank_class.rank_name}",
                         fix: :sv_fix_coordinated_names, success_message: 'Type genus was updated') if self.type_genus != t.type_genus && !has_misspelling_relationship?
    soft_validations.add(:base, "The type specimen does not match with the type specimen of the coordinated #{t.rank_class.rank_name}",
                         fix: :sv_fix_coordinated_names, success_message: 'Type specimen was updated') if !self.has_same_primary_type(t) && !has_misspelling_relationship?
    sttnr = self.type_taxon_name_relationship
    tttnr = t.type_taxon_name_relationship
    unless sttnr.nil? || tttnr.nil?
      soft_validations.add(:base, "The type species relationship does not match with the type species relationship of the coordinated #{t.rank_class.rank_name}",
                           fix: :sv_fix_coordinated_names, success_message: 'Type species relationship was updated') unless sttnr.type == tttnr.type
    end
  end
end



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# File 'app/models/protonym/soft_validation_extensions.rb', line 586

def sv_validate_coordinated_names_source
  return true unless is_valid?
  s = self.source
  list_of_coordinated_names.each do |t|
    if ((s && t.source && s.id != t.source.id) || (s.nil? && t.source))
      soft_validations.add(:base, "The original publication does not match with the original publication of the coordinate #{t.rank_class.rank_name}", success_message: 'Original publication was updated', failure_message:  'Failed to update original publication')
    end
  end
end

#sv_validate_coordinated_names_type_genus ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1030

def sv_validate_coordinated_names_type_genus
  return true unless is_valid?
  return true unless is_family_rank?
  list_of_coordinated_names.each do |t|
    if self.type_genus != t.type_genus
      soft_validations.add(:base, "The type genus does not match with the type genus of the coordinate #{t.rank_class.rank_name}", success_message: 'Type genus was updated', failure_message:  'Failed to update type genus')
    end
  end
end

#sv_validate_coordinated_names_type_species ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 911

def sv_validate_coordinated_names_type_species
  return true unless is_valid?
  return true unless is_genus_rank?
  list_of_coordinated_names.each do |t|
    if self.type_species != t.type_species
      soft_validations.add(:base, "The type species does not match with the type species of the coordinate #{t.rank_class.rank_name}", success_message: 'Type species was updated', failure_message:  'Failed to update type species')
    end
  end
end

#sv_validate_coordinated_names_type_species_type ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 995

def sv_validate_coordinated_names_type_species_type
  return true unless is_genus_rank?
  sttnr = self.type_taxon_name_relationship
  return true if sttnr.nil?
  list_of_coordinated_names.each do |t|
    tttnr = t.type_taxon_name_relationship
    if !tttnr.nil? && sttnr.type != tttnr.type
      soft_validations.add(:base, "The type species relationship does not match with the type species relationship of the coordinate #{t.rank_class.rank_name}", success_message: 'Type species relationship was updated', failure_message:  'Failed to update type species relationship')
    end
  end
end

#sv_validate_coordinated_names_type_specimen ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1061

def sv_validate_coordinated_names_type_specimen
  return true if !is_species_rank? || !is_valid?
  list_of_coordinated_names.each do |t|
    if !self.has_same_primary_type(t)
      soft_validations.add(:base, "The type specimen does not match with the type specimen of the coordinate #{t.rank_class.rank_name}", success_message: 'Type specimen was updated', failure_message:  'Failed to update type specimen')
    end
  end
end

#sv_validate_coordinated_names_year ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 670

def sv_validate_coordinated_names_year
  s = self.year_of_publication
  list_of_coordinated_names.each do |t|
    soft_validations.add(:year_of_publication, "The year of publication does not match with the year of the coordinate #{t.rank_class.rank_name}", success_message: 'Year was updated', failure_message:  'Failed to update year') unless s == t.year_of_publication
  end
end

#sv_validate_name ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 405

def sv_validate_name
  correct_name_format = false

  if rank_class
    # TODO: name these Regexp somewhere
    # TODO: move pertinent checks to base of nomenclature Classes to manage them there
    if (name =~ /^[a-zA-Z]*$/) || # !! should reference NOT_LATIN
        (nomenclatural_code == :iczn && name =~ /^[a-zA-Z]-[a-zA-Z]*$/) ||
        (nomenclatural_code == :icnp && name =~ /^[a-zA-Z]-[a-zA-Z]*$/) ||
        (nomenclatural_code == :icn && name =~  /^[a-zA-Z]*-[a-zA-Z]*$/) ||
        (nomenclatural_code == :icn && name =~  /^[a-zA-Z]*\s×\s[a-zA-Z]*$/) ||
        (nomenclatural_code == :icn && name =~  /^[a-zA-Z]*\s×[a-zA-Z]*$/) ||
        (nomenclatural_code == :icn && name =~  /^×[a-zA-Z]*$/) ||
        (nomenclatural_code == :icvcn)
      correct_name_format = true
    end

    unless correct_name_format
      icvcn_species = (nomenclatural_code == :icvcn && self.rank_string =~ /Species/) ? true : nil
      if is_available? && icvcn_species.nil?
        soft_validations.add(:name, 'Name should not have spaces or special characters, unless it has a status of misspelling or original misspelling')
      end
    end
  end
end

#sv_validate_parent_rank ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 431

def sv_validate_parent_rank
  if self.rank_class && self.id == self.cached_valid_taxon_name_id
    if rank_string == 'NomenclaturalRank' || self.parent&.rank_string == 'NomenclaturalRank' || !!self.iczn_uncertain_placement_relationship
      true
    elsif !self.rank_class&.valid_parents.include?(self.parent&.rank_string)
      soft_validations.add(:rank_class, "The rank #{self.rank_class&.rank_name} is not compatible with the rank of parent (#{self.parent&.rank_class&.rank_name}). The name should be marked as 'Incertae sedis'")
    end
  end
end

#sv_year_is_not_required ⇒ Object 



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# File 'app/models/protonym/soft_validation_extensions.rb', line 1568

def sv_year_is_not_required
  if !self.year_of_publication.nil? && self.source && self.year_of_publication == self.source.year
    soft_validations.add(
      :year_of_publication, 'Year of publication is not required, it is derived from the source',
      success_message: 'Year was deleted',
      failure_message: 'Failed to delete year')
  end
end