Class: Taxonifi::Model::NameCollection

Inherits:
Collection
  • Object
show all
Defined in:
lib/taxonifi/model/name_collection.rb

Overview

A collection of taxonomic names.

Instance Attribute Summary collapse

Attributes inherited from Collection

#by_id_index, #collection, #current_free_id

Instance Method Summary collapse

Methods inherited from Collection

#children_of_object, #object_by_id, #objects_without_parents, #parent_id_vector, subclass_prefixes

Methods included from SharedClassMethods

included

Constructor Details

#initialize(options = {}) ⇒ NameCollection

Returns a new instance of NameCollection.



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# File 'lib/taxonifi/model/name_collection.rb', line 47

def initialize(options = {})
  super 
  @by_name_index = {'genus_group' => {}, 'species_group' => {}, 'unknown' => {}}     # Lumping species and genus group names, unranked named are in 'unknown'
  Taxonifi::RANKS[0..-5].inject(@by_name_index){|hsh, v| hsh.merge!(v => {})}        # TODO: Still needed?! 
  @ref_collection = options[:ref_collection]
  @citations = {} 
  @combinations = []
  @nomenclators = {} 
  @nomenclator_index = options[:initial_nomenclator_index] 
  @nomenclator_index ||= 1
  @duplicate_entry_buffer = {} # Move to Collection?!
  true
end

Instance Attribute Details

#by_name_index ⇒ Object

A Hash. Keys are the name (String), values are ids of Names in the collection. { rank => { name => [ids] }} There are two special ranks “genus_group” and “species_group”. E.g.: => {‘bar’ => [1,2,93]})



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

def by_name_index
  @by_name_index
end

#citations ⇒ Object

TaxonNameID => [[ nomenclator_index, Ref ], … []]



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# File 'lib/taxonifi/model/name_collection.rb', line 45

def citations
  @citations
end

#combinations ⇒ Object

An optional collection of existing combinations of species names, as represented by individual arrays of Taxonifi::Model::Names. Note you can not use a Taxonifi::Model::SpeciesName for this purpose because getting/setting names therin will affect other combinations TODO: DEPRECATE? !?!



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

def combinations
  @combinations
end

#duplicate_entry_buffer ⇒ Object

A Hash. Contains metadata when non-unique names are found in input parsing row identifier => { redundant row identifier => {properties hash}} TODO: reconsider, move to superclass or down to record base TODO: Test



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# File 'lib/taxonifi/model/name_collection.rb', line 29

def duplicate_entry_buffer
  @duplicate_entry_buffer
end

#nomenclator_index ⇒ Object

An Integer used for indexing nomenclator records in @nomenclators. Contains the next available index value.



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# File 'lib/taxonifi/model/name_collection.rb', line 42

def nomenclator_index
  @nomenclator_index
end

#nomenclators ⇒ Object

A Hash. Index (keys) created by the collection, values are an Array of Strings representing the genus, subgenus, species, and subspecies name. Automatically populated when .add_object is used. Alternately populated with .add_nomenclator(Name) Nomenclator values are not repeated.

Index is used in @citations. { @nomenclator_index => [genus_string, subgenus_string, species_string, subspecies_string, infrasubspecific_string (e.g. variety)], … } !! The names represented in the Array of strings does NOT have to be represented in the NameCollection.



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# File 'lib/taxonifi/model/name_collection.rb', line 39

def nomenclators
  @nomenclators
end

#ref_collection ⇒ Object

A Taxonifi::Model::RefCollection, optionally generated from Author/Year strings



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

def ref_collection
  @ref_collection
end

Instance Method Details

#add_citation(name, ref, nomenclator_index, properties) ⇒ Object

Add a Citation Returns the index of the Nomenclator added. TODO: Test/Validate



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# File 'lib/taxonifi/model/name_collection.rb', line 165

def add_citation(name, ref, nomenclator_index, properties)
  if @citations[name.id]
    return false if @citations[name.id].collect{|i| [i[0],i[1]] }.include?([ref.id, nomenclator_index])
    @citations[name.id].push([ref.id, nomenclator_index, properties])
  else
    @citations[name.id] = [[ref.id, nomenclator_index, properties]]
  end
  true
end

#add_duplicate_entry_metadata(name_id, row_identifier, data_hash) ⇒ Object

Add a record to @duplicate_entry_buffer



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# File 'lib/taxonifi/model/name_collection.rb', line 251

def add_duplicate_entry_metadata(name_id, row_identifier, data_hash)
  @duplicate_entry_buffer[name_id] = Hash.new if !@duplicate_entry_buffer[name_id]
  @duplicate_entry_buffer[name_id].merge!(row_identifier => data_hash)
end

#add_nomenclator(nomenclator_array) ⇒ Object

Add a Nomenclator (Array) to the index. Returns the index of the Nomenclator added. TODO: Test



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# File 'lib/taxonifi/model/name_collection.rb', line 146

def add_nomenclator(nomenclator_array)
  raise if (!nomenclator_array.class == Array) || (nomenclator_array.length != 5)
  if @nomenclators.has_value?(nomenclator_array)
    return @nomenclators.key(nomenclator_array) 
  else
    @nomenclators.merge!(@nomenclator_index => nomenclator_array) 
    @nomenclator_index += 1
    return @nomenclator_index - 1
  end
end

#add_object(obj) ⇒ Object

Add an individual Name instance, indexing it.



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# File 'lib/taxonifi/model/name_collection.rb', line 122

def add_object(obj)
  super
  index_by_name(obj)
  derive_nomenclator(obj) if obj.nomenclator_name?
  obj
end

#add_object_pre_indexed(obj) ⇒ Object

Add an individaul Name instance, without indexing it.



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# File 'lib/taxonifi/model/name_collection.rb', line 130

def add_object_pre_indexed(obj)
  super
  index_by_name(obj)
  obj
end

#add_original_genus_id_property ⇒ Object

For all species group names, assigns to property ‘original_genus_id’ the id of the parent genus group name if parens are not set. Returns an Array of ids for those names for which the property has NOT been set.



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# File 'lib/taxonifi/model/name_collection.rb', line 258

def add_original_genus_id_property
  not_added = [] 
  by_name_index['species_group'].values.flatten.uniq.each do |id|
    name = object_by_id(id) 
    if name.parens != true
      name.add_property('original_genus_id', name.genus_group_parent.id)
    else
      not_added.push(name.id)
    end
  end
  not_added
end

#add_species_name(sn) ⇒ Object

Add a Taxonifi::Model::SpeciesName object as individual objects.



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# File 'lib/taxonifi/model/name_collection.rb', line 177

def add_species_name(sn)
  raise "Failed trying to load [#{sn.display_name}]. SpeciesName#genus#parent must be set before using add_species_name." if sn.genus.parent.nil?
  current_parent_id = sn.genus.parent.id 
  sn.names.each do |o|
    o.parent = object_by_id(current_parent_id)
    if id = name_exists?(o)
      cp_id = id 
    else
      add_object(o)
      cp_id = o.id
    end
    current_parent_id = cp_id
  end
  current_parent_id # return the id of the last name created
end

#add_species_name_unindexed(sn) ⇒ Object

As #add_species_name but do not assign ids to the incoming names TODO: deprecate?



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

def add_species_name_unindexed(sn)
  sn.names.each do |o|
    if !name_exists?(o)
      add_object(o)
    end
  end
end

#derive_nomenclator(obj) ⇒ Object

TODO: Test



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# File 'lib/taxonifi/model/name_collection.rb', line 137

def derive_nomenclator(obj)
  if obj.nomenclator_name? && !obj.authors.nil? && !obj.year.nil?
    add_nomenclator(obj.nomenclator_array)
  end
end

#encompassing_rank ⇒ Object

Return the highest RANK for which there is no name in this collection.



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# File 'lib/taxonifi/model/name_collection.rb', line 71

def encompassing_rank
  highest = RANKS.size
  @collection.each do |n|
    h = RANKS.index(n.rank)
    highest = h if h < highest
  end
  RANKS[highest - 1]
end

#generate_ref_collection(initial_id = 0) ⇒ Object

Take the author/years of these names and generate a RefCollection. Start the ids assigned to the references with initial_id.



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# File 'lib/taxonifi/model/name_collection.rb', line 206

def generate_ref_collection(initial_id = 0)
  rc = Taxonifi::Model::RefCollection.new(:initial_id => initial_id)
  temp_index = {} 
  @collection.each do |n|
    index = n.author_year_index
    if !temp_index[index] && index.size > 0
      temp_index.merge!(index => nil)
      ref = Taxonifi::Model::Ref.new(authors: n.authors, year: n.year) 
      rc.add_object(ref)
    end
  end
  @ref_collection = rc 
end

#genus_group_name_strings ⇒ Object

Return an Array of Strings



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# File 'lib/taxonifi/model/name_collection.rb', line 272

def genus_group_name_strings
  by_name_index['genus_group'].keys
end

#homonyms_at_rank(rank) ⇒ Object

Return an Array of “homonyms” within the rank provided. Useful for finding missmatched upper heirarchies, if nc is a name_collection:

homonyms = nc.homonyms_at_rank('genus')
homonyms.keys.sort.each do |n|
  puts "#{n} (#{homonyms[n].size}) :"
  homonyms[n].each do |p|
    puts "  #{p.ancestors.collect{|i| i.name}.join(",")}"
  end
end



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# File 'lib/taxonifi/model/name_collection.rb', line 239

def homonyms_at_rank(rank) 
  raise if !RANKS.include?(rank)
  uniques = {}
  names_at_rank(rank).each do |n|
    uniques.merge!(n.name => []) if !uniques[n.name]
    uniques[n.name].push n
  end
  uniques.delete_if{|k| uniques[k].size < 2}
  uniques
end

#name_exists?(name = Taxonifi::Model::Name) ⇒ Boolean

Returns id of matching existing name or false if there is no match. !! assumes parent is set Matches against name, year, and all parents (by id).

!! nominotypic names are considered to be the same (species and generic). See

@combinations to instantiate these

TODO: This is likely already overly ICZN flavoured.

Returns:

  • (Boolean) 


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# File 'lib/taxonifi/model/name_collection.rb', line 100

def name_exists?(name = Taxonifi::Model::Name) 
  # species/genus group names are indexed for indexing purposes 
  rank = name.index_rank

  if by_name_index[rank][name.name_author_year_string]
    by_name_index[rank][name.name_author_year_string].each do |id|
      full_parent_vector = parent_id_vector(name.parent.id) 
      return id if full_parent_vector == parent_id_vector(id)  # this hits species/genus group names

      vector = parent_id_vector(id)
      next if vector.last != name.parent.id                    # can stop looking at this possiblity
      vector.pop                                               # compare just parents
      if vector == full_parent_vector 
        exists = true
        return id
      end
    end
  end 
  false 
end

#name_string_array ⇒ Object

Return an array of the names in the collection DEPRECATE for name_strings



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# File 'lib/taxonifi/model/name_collection.rb', line 283

def name_string_array
  collection.collect{|n| n.display_name}
end

#names_at_rank(rank) ⇒ Object

Returns an Array of the names objects in the collection at a rank. TODO: Should index this on add_object



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# File 'lib/taxonifi/model/name_collection.rb', line 82

def names_at_rank(rank)
  raise if !RANKS.include?(rank)
  names = []
  @collection.each do |n|
    names << n if n.rank == rank
  end
  names
end

#nomenclator_id_for_name(name) ⇒ Object

Return the Integer (index) for a name



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# File 'lib/taxonifi/model/name_collection.rb', line 158

def nomenclator_id_for_name(name)
  @nomenclators.key(name.nomenclator_array) 
end

#object_class ⇒ Object 



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# File 'lib/taxonifi/model/name_collection.rb', line 65

def object_class
  Taxonifi::Model::Name
end

#species_group_name_strings ⇒ Object

Return an Array of Strings



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

def species_group_name_strings
  by_name_index['species_group'].keys
end