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 1668

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 parent_id.blank?
    if 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 1652

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 1624

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 1608

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 1638

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 1691

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.to_i > 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 (it is nevertheless deemed to be subspecific if, before 1985, it was either adopted as the valid name or was treated as a senior homonym).')
  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 1643

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 1615

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?
  # MJY Why?
  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 1629

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 1660

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 1680

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