Module: Taxonifi::Lumper::Lumps::ParentChildNameCollection

Defined in:
lib/taxonifi/lumper/lumps/parent_child_name_collection.rb

Overview

Handles DwC-esque files (e.g. as dumped by EoL), i.e. a file with columns like: 

[identifier parent child rank synonyms]

Instantiates individual names for all names (including synonym lists) into a NameCollection. See ‘test/test_lumper_parent_child_name_collection’ for example use.

Class Method Summary collapse

Class Method Details

.add_species_names_from_string(nc, string, parent = nil, synonym_id = nil) ⇒ Object

Add the last name in a species epithet string if new, record a new combination otherwise.

Assumes ALL parents have been previously added, including those used in Synonym combinations. For example, given a row with name, synonym fields like:

'Neortholomus scolopax (Say, 1832)', 'Lygaeus scolopax Say, 1832']

The names Neortholomus and Lygaeus must exist.



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# File 'lib/taxonifi/lumper/lumps/parent_child_name_collection.rb', line 97

def self.add_species_names_from_string(nc, string, parent = nil, synonym_id = nil)
  names = Taxonifi::Splitter::Builder.build_species_name(string) # A Taxonifi::Model::SpeciesName instance
  if !parent.nil?                                                # nc.object_by_id(parent_id)
    names.names.last.parent = parent                             # swap out the parent with the id referenced by the parent_id 
  else
    raise Taxonifi::Lumper::LumperError, "Parent of [#{names.names.last.name}] within [#{names.display_name}] not yet instantiated. \n !! To resolve: \n\t 1) If this is not a species name your file may be missing a value in the 'Rank' column (nil values are assumed to be species, all other ranks must be populated). \n\t 2) Parent names must be read before children, check that this is the case."
  end

  last_id = nil
  if !nc.name_exists?(names.names.last)
    last_id = nc.add_object(names.names.last).id
    nc.object_by_id(last_id).related_name = nc.object_by_id(synonym_id) if !synonym_id.nil?
  else

    tmp_genus = names.genus.clone
    # tmp_subgenus = names.subgenus.clone if !names.subgenus.nil?
    tmp_species = names.species.clone
    tmp_subspecies = names.subspecies.clone if !names.subspecies.nil?

    case parent.rank
    when 'genus' 
      tmp_genus.parent = parent.parent # OK
    when 'subgenus'
      tmp_genus.parent = parent.parent # OK
    when 'species'
      tmp_genus.parent = parent.parent.parent
      tmp_species = parent
      tmp_subspecies.parent = tmp_species
    end
    
    # tmp_subgenus.parent = tmp_genus if !tmp_subgenus.nil?
    # real_subgenus = nc.object_by_id(nc.name_exists?(tmp_subgenus)) if !tmp_subgenus.nil? 

    real_genus = nc.object_by_id(nc.name_exists?(tmp_genus)) 
    real_species = nc.object_by_id(nc.name_exists?(tmp_species)) 

    # !! Existing demo data Lygaeoidea have synonyms in which the genus name is not instantiated.  This might be a problem with DwC file 
    # validation in general, something to look at, for now, throw up our hands and move on.
    return last_id if (real_genus.nil? || real_species.nil?)

    real_subgenus = nil # revisit
    real_subspecies = nc.object_by_id(nc.name_exists?(tmp_subspecies))  if !tmp_subspecies.nil?
  
    rc = [real_genus, real_subgenus, real_species, real_subspecies]
    nc.combinations.push rc
  end

  last_id
end

.name_collection(csv) ⇒ Object

Raises:



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# File 'lib/taxonifi/lumper/lumps/parent_child_name_collection.rb', line 7

def self.name_collection(csv)
  raise Taxonifi::Lumper::LumperError, "CSV does not have the required headers (#{Taxonifi::Lumper::LUMPS[:eol_basic].join(", ")})." if  !Taxonifi::Lumper.available_lumps(csv.headers).include?(:eol_basic)

  nc = Taxonifi::Model::NameCollection.new(:initial_id => 1)

  # identifier => Taxonifi::Name
  external_index = {} 

  # Array of Hashes {:synonyms => "Name|Name1|Name2", :external_index => external_index[parent_id], :valid_species_id => valid_species_id}, {} ...
  synonym_list = [] 

  csv.each_with_index do |row,i|
    name = row['child']
    rank = row['rank'].downcase if !row['rank'].nil?
    parent_id = row['parent'].to_i
    external_id = row['identifier'].to_i
    valid_species_id = nil

    # Fix me
    index_rank = 'species_group' if rank == 'species' || rank == 'subspecies'
    index_rank = 'genus_group' if rank == 'subgenus' || rank == 'genus'
    index_rank ||= rank

    case rank
    when 'species', nil
     valid_species_id = add_species_names_from_string(nc, name, external_index[parent_id])
     external_index.merge!(external_id => nc.object_by_id(valid_species_id))
    else  # Just a single string, we don't have to break anything down.
      n = nil

      if nc.by_name_index[index_rank][name]
        exists = false
        # TODO: this hasn't been hit yet
        nc.by_name_index[index_rank][name].each do |id|
          if nc.parent_id_vector(id).pop == nc.parent_id_vector(parent_id)
            exists = true
            break
          end
        end
        if !exists
          n = Taxonifi::Model::Name.new()
        end 
      else 
        n = Taxonifi::Model::Name.new()
      end

      # Build the name
      if !n.nil?
        # TODO: No author, year have yet been observed for genus and higher names
        n.rank = rank
        n.name = name
        n.row_number = i
        n.add_property(:external_id, external_id)

        if parent = external_index[parent_id] 
          n.parent = parent
        end

        if !nc.name_exists?(n)
          nc.add_object(n)
          external_index.merge!(external_id => n) 
        end
      end
    end

    if !row['synonyms'].nil? && row['synonyms'].size > 0 
      #  puts n.name if external_index[parent_id].nil?
      synonym_list.push({:synonyms => row['synonyms'], :valid_species_id => valid_species_id, :external_index => external_index[parent_id]})
    end

  end # end row

  # parse the synonyms last, because names might have been mixed
  synonym_list.each do |s|
    other_names = s[:synonyms].split("|")
    other_names.each do |n|
      # puts ":: #{n} :: #{s[:external_index]} :: #{s[:valid_species_id]}" if s[:external_index].nil?
      add_species_names_from_string(nc, n, s[:external_index], s[:valid_species_id]) 
    end
  end

  nc 
end