module Taxonifi::Lumper::Lumps::ParentChildNameCollection

# File lib/lumper/lumps/parent_child_name_collection.rb, line 72
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 genus to the Model referenced by 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 = 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?
  last_id
end

# File lib/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)
  external_index = {} # identifier => Taxonifi::Name

  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

    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[rank][name]
        exists = false
        # TODO: this hasn't been hit yet
        nc.by_name_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.external_id = external_id
        n.row_number = i
  
        if parent = external_index[parent_id] 
          n.parent = parent
        end

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

    if !row['synonyms'].nil? && row['synonyms'].size > 0 
      other_names = row['synonyms'].split("|")
      other_names.each do |n|
        add_species_names_from_string(nc, n, external_index[parent_id], valid_species_id) 
      end
    end

  end # end row
  nc 
end