Class: Taxonifi::Model::Name

Inherits:
Base
  • Object
show all
Defined in:
lib/taxonifi/model/name.rb

Overview

A taxonomic name.

Direct Known Subclasses

IcznName

Constant Summary collapse

@@ATTRIBUTES =

An Array, contains assignable properties in Taxonifi::Model::Name#new()

[:name, :rank, :year, :parens, :author, :related_name ]

Constants inherited from Base

Base::ATTRIBUTES

Instance Attribute Summary collapse

Attributes inherited from Base

#id, #properties, #row_number

Instance Method Summary collapse

Methods inherited from Base

#add_properties, #add_property, #ancestor_ids, #ancestors, #build, #delete_property, #replace_property

Methods included from SharedClassMethods

included

Constructor Details

#initialize(options = {}) ⇒ Name

Returns a new instance of Name.



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# File 'lib/taxonifi/model/name.rb', line 43

def initialize(options = {})
  super
  opts = {
    id: nil
  }.merge!(options)

  @parent = nil
  @authors ||= []

  build(@@ATTRIBUTES, opts)
  assign_author_year(opts)


  @id = opts[:id] 
  @parent = opts[:parent] if (!opts[:parent].nil? && opts[:parent].class == Taxonifi::Model::Name)
  @original_description_reference = opts[:original_description_reference] if (!opts[:original_description_reference].nil? && opts[:original_description_reference].class == Taxonifi::Model::Ref)

  true
end

Instance Attribute Details

#author ⇒ Object

String, authors as originally read



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# File 'lib/taxonifi/model/name.rb', line 14

def author
  @author
end

#author_year_index ⇒ Object

Return a Taxonifi::Model::AuthorYear representing author/year !! Identical to method in Taxonifi::Model::Ref !! Not necessarily unique.



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# File 'lib/taxonifi/model/name.rb', line 41

def author_year_index
  @author_year_index
end

#authors ⇒ Object

An Array of Taxonifi::Model::Person Optionally parsed/index



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# File 'lib/taxonifi/model/name.rb', line 38

def authors
  @authors
end

#name ⇒ Object

String



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# File 'lib/taxonifi/model/name.rb', line 8

def name
  @name
end

#original_description_reference ⇒ Object

A Taxonifi::Model::Reference The original description.



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# File 'lib/taxonifi/model/name.rb', line 31

def original_description_reference
  @original_description_reference
end

#parens ⇒ Object

Boolean, true if parens present (i.e. not in original combination)



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# File 'lib/taxonifi/model/name.rb', line 20

def parens
  @parens
end

#parent ⇒ Object

A Taxonifi::Model::Name



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# File 'lib/taxonifi/model/name.rb', line 23

def parent
  @parent
end

#rank ⇒ Object

String



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# File 'lib/taxonifi/model/name.rb', line 11

def rank
  @rank
end

#related_name ⇒ Object

A Taxonifi::Model::Name A general purpose relationship, typically used to indicate synonymy.



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# File 'lib/taxonifi/model/name.rb', line 27

def related_name
  @related_name
end

#year ⇒ Object

String, year as originally read



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# File 'lib/taxonifi/model/name.rb', line 17

def year
  @year
end

Instance Method Details

#add_author_year(string) ⇒ Object

Returns an Array of Taxonifi::Model::Person



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# File 'lib/taxonifi/model/name.rb', line 64

def add_author_year(string) # :yields: Array of Taxonifi::Model::Person
  auth_yr = Taxonifi::Splitter::Builder.build_author_year(string)
  @year = auth_yr.year
  @authors = auth_yr.people
end

#author_year ⇒ Object

Returns a formatted string, including parens for the name TODO: rename to reflect parens



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# File 'lib/taxonifi/model/name.rb', line 124

def author_year
  au = author_year_string
  return nil if au.nil?
  (self.parens == true) ? "(#{au})" : au
end

#author_year_string ⇒ Object

Return the author year string.



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# File 'lib/taxonifi/model/name.rb', line 132

def author_year_string
  # Build based on People 

  auth = nil
  if authors.size > 0
    case authors.size
    when 1
      auth = self.author
    when 2 
      auth = authors.map(&:last_name).join(" & ")
    when 2...100
      auth =  authors[0..-1].map(&:last_name).join(", ") + " & " + authors.last.last_name
    end
    # Build based on string
  else
    auth = self.author
  end
  au = [auth, self.year].compact.join(", ")
  return nil if au.size == 0
  au
end

#derive_authors_year ⇒ Object

Translates the String representation of author year to an Array of People. Used in indexing, when comparing Name microtations to Ref microcitations.



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# File 'lib/taxonifi/model/name.rb', line 72

def derive_authors_year
  add_author_year(author_year_string) 
end

#display_name ⇒ Object

Return a String, the human readable version of this name (genus, subgenus, species, subspecies, variety author, year)



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# File 'lib/taxonifi/model/name.rb', line 155

def display_name
  [nomenclator_name, author_year].compact.join(" ")
end

#generate_author_year_index ⇒ Object

Generate and return (String) the author year index.



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# File 'lib/taxonifi/model/name.rb', line 265

def generate_author_year_index
  @author_year_index = Taxonifi::Model::AuthorYear.new(people: @authors, year: @year).compact_index
end

#genus_group? ⇒ Boolean

TODO: test Returne True of False based on @rank

Returns:

  • (Boolean) 


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# File 'lib/taxonifi/model/name.rb', line 277

def genus_group?
  true if @rank == 'genus' || @rank == 'subgenus'
end

#genus_group_parent ⇒ Object

Return a Taxonifi::Model::Name representing the finest genus_group_parent. TODO: ICZN specific(?)



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# File 'lib/taxonifi/model/name.rb', line 196

def genus_group_parent
  [ parent_at_rank('subgenus'), parent_at_rank('genus')].compact.first
end

#index_rank ⇒ Object

Return a string indicating at what level this name is indexed within a NameCollection. TODO: Family group extension; ICZN specific



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# File 'lib/taxonifi/model/name.rb', line 88

def index_rank
  case rank
  when 'species', 'subspecies', 'variety'
    'species_group'
  when 'genus', 'subgenus'
    'genus_group'
  when nil, ""
    'unknown'
  else
    rank.downcase
  end
end

#name_author_year_string ⇒ Object

Returns just the name and author year, no parens, no parents. Like:

foo Smith, 1927
Foo Smith, 1927
Fooidae



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# File 'lib/taxonifi/model/name.rb', line 205

def name_author_year_string
  [name, author_year_string].compact.join(" ")
end

#nomenclator_array ⇒ Object

Return an Array of lenght 4 of Names representing a Species or Genus group name

genus, subgenus, species, subspecies, infrasubspecific


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# File 'lib/taxonifi/model/name.rb', line 178

def nomenclator_array
  case @rank
  when 'variety'
    return [parent_name_at_rank('genus'), (parent_name_at_rank('subgenus') ? "(#{parent_name_at_rank('subgenus')})" : nil), parent_name_at_rank('species'),  parent_name_at_rank('subspecies'), "var. #{@name}"]
  when 'species', 'subspecies'
    return [parent_name_at_rank('genus'), (parent_name_at_rank('subgenus') ? "(#{parent_name_at_rank('subgenus')})" : nil), parent_name_at_rank('species'),  parent_name_at_rank('subspecies'), nil]
  when 'subgenus'
    return [parent_name_at_rank('genus'), "(#{@name})", nil, nil, nil]
  when 'genus'
    return [@name, nil, nil, nil, nil]
  else
    return false
  end
   
end

#nomenclator_name ⇒ Object

Return a String, the human readable version of this name (genus, subgenus, species, subspecies)



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# File 'lib/taxonifi/model/name.rb', line 160

def nomenclator_name 
  case @rank
  # TODO: update for infrasubspecifics if we start tracking those
  when 'species', 'subspecies', 'genus', 'subgenus', 'variety'
    nomenclator_array.compact.join(" ")
  else
    @name
  end
end

#nomenclator_name? ⇒ Boolean

Return a Boolean, True if @rank is one of ‘genus’, ‘subgenus’, ‘species’, ‘subspecies’ TODO: update for infrasubspecifics if we start tracking those

Returns:

  • (Boolean) 


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# File 'lib/taxonifi/model/name.rb', line 172

def nomenclator_name?
  %w{genus subgenus species subspecies variety}.include?(@rank)
end

#parent_at_rank(rank) ⇒ Object

Return the parent at a given rank. TODO: move method to Base?



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# File 'lib/taxonifi/model/name.rb', line 226

def parent_at_rank(rank)
  return self if self.rank == rank
  p = @parent
  i = 0
  while !p.nil?
    return p if p.rank == rank
    p = p.parent
    raise NameError, "Loop detected among parents fo [#{self.display_name}]" if i > 75 
  end
  nil 
end

#parent_ids_sf_style ⇒ Object

0-1-14-29g-45s-99-100.

Postfixed g means "genus", postifed s means "subgenus.  As per SpecieFile usage.
TODO: !! malformed because the valid name is not injected.  Note that this can be generated internally post import.



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# File 'lib/taxonifi/model/name.rb', line 242

def parent_ids_sf_style
  ids = [] 
  (ancestors.push self).each do |a|
    case a.rank
    when 'genus'
      ids.push "#{a.id}g"
    when 'subgenus'
      ids.push "#{a.id}s"
    else
      ids.push a.id.to_s
    end
  end
  ids.join("-")
end

#parent_name_at_rank(rank) ⇒ Object

Return the name of a parent at a given rank. TODO: move method to Base?



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# File 'lib/taxonifi/model/name.rb', line 211

def parent_name_at_rank(rank)
  return self.name if self.rank == rank
  p = @parent
  i = 0
  while !p.nil?
    return p.name if p.rank == rank
    p = p.parent
    i+= 1
    raise NameError, "Loop detected among parents for [#{self.display_name}]." if i > 75 
  end
  nil 
end

#prologify ⇒ Object

Return a String of Prolog rules representing this Name



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# File 'lib/taxonifi/model/name.rb', line 282

def prologify
  "false"
end

#species_group? ⇒ Boolean

TODO: test Returne True of False based on @rank

Returns:

  • (Boolean) 


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# File 'lib/taxonifi/model/name.rb', line 271

def species_group?
  true if @rank == 'species' || @rank == 'subspecies'
end