class MiGA::Cli::Action::TaxTest

def closest_relative_tax(cr)
  cli.puts "Closest relative: #{cr[0]} with AAI: #{cr[1]}."
  p = cli.load_project
  if cli[:ref_project]
    if (ref = p.option(:ref_project)).nil?
      raise '--ref-project requested but no reference project has been set'
    end
    if (q = MiGA::Project.load(ref)).nil?
      raise '--ref-project requested but reference project doesn\'t exist'
    end
    cr_d = q.dataset(cr[0])
  else
    cr_d = p.dataset(cr[0])
  end
  tax = cr_d.metadata[:tax] unless cr_d.nil?
  tax ||= {}
  tax
end

def parse_cli
  cli.defaults = { test: 'both', ref_project: false }
  cli.parse do |opt|
    cli.opt_object(opt, [:project, :dataset])
    opt.on(
      '--ref-project',
      'Use the taxonomy from the reference project, not the current project'
    ) { |v| cli[:ref_project] = v }
    opt.on(
      '-t', '--test STRING',
      'Test to perform. Supported values: intax, novel, both'
    ) { |v| cli[:test] = v.downcase }
  end
end

def perform
  d = cli.load_dataset
  cli.say 'Finding closest relative'
  cr = d.closest_relatives(1, cli[:ref_project])
  if cr.nil? or cr.empty?
    raise 'Action not supported for the project or dataset' if cr.nil?
    raise 'No close relatives found'
  else
    query_probability_distributions(d, cr[0])
  end
end

def query_probability_distributions(d, cr)
  cli.say 'Querying probability distributions'
  tax = closest_relative_tax(cr)
  if %w[intax both].include? cli[:test]
    r = test_closest_relative(cr, tax, :intax)
    cli.puts ''
    cli.puts 'Taxonomic classification'
    cli.puts MiGA.tabulate(%w[Rank Taxonomy P-value Signif.], r)
  end
  if %w[novel both].include? cli[:test]
    r = test_closest_relative(cr, tax, :novel)
    r.map! { |i| i.tap { |j| j.delete_at(1) } }
    cli.puts ''
    cli.puts 'Taxonomic novelty'
    cli.puts MiGA.tabulate(%w[Rank P-value Signif.], r)
  end
  cli.puts ''
  cli.puts 'Significance at p-value below: *0.5, **0.1, ***0.05, ****0.01.'
end

def test_closest_relative(cr, tax, test)
  TaxDist.aai_pvalues(cr[1], test).map do |k, v|
    sig = ''
    [0.5, 0.1, 0.05, 0.01].each { |i| sig << '*' if v < i }
    [Taxonomy.LONG_RANKS[k], (tax[k] || '?'), v, sig]
  end
end