bio-miga/miga

# @package MiGA
# @license Artistic-2.0

require 'miga/taxonomy'

##
# Indexing methods based on taxonomy.
class MiGA::TaxIndex < MiGA::MiGA
  # Instance-level

  ##
  # Datasets in the index.
  attr_reader :datasets
  # Taxonomy root.
  attr_reader :root

  ##
  # Initialize an empty MiGA::TaxIndex
  def initialize
    @root = MiGA::TaxIndexTaxon.new(:root, 'biota')
    @datasets = []
  end

  ##
  # Index +dataset+, a MiGA::Dataset object.
  def <<(dataset)
    return nil if dataset.metadata[:tax].nil?

    taxon = @root
    MiGA::Taxonomy.KNOWN_RANKS.each do |rank|
      next if rank == :ns

      taxon = taxon.add_child(rank, dataset.metadata[:tax][rank])
    end
    taxon.add_dataset dataset
    @datasets << dataset
  end

  ##
  # Finds all the taxa in the collection at the +rank+ taxonomic rank
  def taxa_by_rank(rank)
    rank = MiGA::Taxonomy.normalize_rank(rank)
    taxa = [@root]
    select = []
    loop do
      new_taxa = []
      taxa.map(&:children).flatten.each do |ch|
        if ch.rank == rank
          select << ch
        elsif !ch.children.empty?
          new_taxa << ch
        end
      end
      taxa = new_taxa
      break if taxa.empty?
    end
    select
  end

  ##
  # Generate JSON String for the index.
  def to_json
    MiGA::Json.generate(
      root: root.to_hash,
      datasets: datasets.map(&:name)
    )
  end

  ##
  # Generate tabular String for the index.
  def to_tab(unknown = false)
    root.to_tab(unknown)
  end
end

##
# Helper class for MiGA::TaxIndex.
class MiGA::TaxIndexTaxon < MiGA::MiGA
  # Instance-level

  ##
  # Rank of the taxon.
  attr_reader :rank
  # Name of the taxon.
  attr_reader :name
  # Children of the taxon.
  attr_reader :children
  # Datasets directly classified at the taxon (not at children).
  attr_reader :datasets

  ##
  # Initalize taxon at +rank+ with +name+.
  def initialize(rank, name)
    @rank = rank.to_sym
    @name = (name.nil? ? nil : name.miga_name)
    @children = []
    @datasets = []
  end

  ##
  # String representation of the taxon.
  def tax_str; "#{rank}:#{name.nil? ? '?' : name}"; end

  ##
  # Add child at +rank+ with +name+.
  def add_child(rank, name)
    rank = rank.to_sym
    name = name.miga_name unless name.nil?
    child = children.find { |it| it.rank == rank and it.name == name }
    if child.nil?
      child = MiGA::TaxIndexTaxon.new(rank, name)
      @children << child
    end
    child
  end

  ##
  # Add dataset at the current taxon (not children).
  def add_dataset(dataset) @datasets << dataset; end

  ##
  # Get the number of datasets in the taxon (including children).
  def datasets_count
    children.map(&:datasets_count).reduce(datasets.size, :+)
  end

  ##
  # Get all the datasets in the taxon (including children).
  def all_datasets
    children.map(&:datasets).reduce(datasets, :+)
  end

  ##
  # JSON String of the taxon.
  def to_json(*a)
    {
      str: tax_str,
      datasets: datasets.map(&:name),
      children: children
    }.to_json(a)
  end

  ##
  # Hash representation of the taxon.
  def to_hash
    {
      str: tax_str,
      datasets: datasets.map(&:name),
      children: children.map(&:to_hash)
    }
  end

  ##
  # Tabular String of the taxon.
  def to_tab(unknown, indent = 0)
    o = ''
    if unknown or not datasets.empty? or not name.nil?
      o = "#{' ' * indent}#{tax_str}: #{datasets_count}\n"
    end
    indent += 2
    datasets.each { |ds| o << "#{' ' * indent}# #{ds.name}\n" }
    children.each { |it| o << it.to_tab(unknown, indent) }
    o
  end
end