class MiGA::Cli::Action::TaxDist

def cannid(a, b)
  (a > b ? [b, a] : [a, b]).join('-')
end

def get_tab_index(dir)
  if cli[:index].nil?
    ds = cli.load_and_filter_datasets
    ds.keep_if { |d| !d.metadata[:tax].nil? }
    cli.say 'Indexing taxonomy'
    tax_index = TaxIndex.new
    ds.each { |d| tax_index << d }
    tab = File.expand_path('index.tab', dir)
    File.open(tab, 'w') { |fh| fh.print tax_index.to_tab }
  else
    tab = cli[:index]
  end
  tab
end

def parse_cli
  cli.parse do |opt|
    cli.opt_object(opt, [:project])
    cli.opt_filter_datasets(opt)
    opt.on(
      '-i', '--index FILE',
      'Pre-calculated tax-index (in tabular format) to be used',
      'If passed, dataset filtering arguments are ignored'
    ) { |v| cli[:index] = v }
    opt.on(
      '-m', '--metric STR',
      'Distance metric used to evaluate the distribution',
      'By default: AAI for genomes projects, ANI for clade projects'
    ) { |v| cli[:metric] = v.downcase }
  end
end

def perform
  dist = read_distances
  Dir.mktmpdir do |dir|
    tab = get_tab_index(dir)
    dist = traverse_taxonomy(tab, dist)
  end
  cli.say 'Generating report'
  dist.keys.each do |k|
    dist[k][5] = dist[k][4].reverse.join(' ')
    dist[k][4] = dist[k][4].first
    puts (k.split('-') + dist[k]).join("\t")
  end
end

def read_distances
  p = cli.load_project
  cli[:metric] ||= p.clade? ? 'ani' : 'aai'
  res_n = "#{cli[:metric]}_distances"
  cli.say "Reading distances: 1-#{cli[:metric].upcase}"
  res = p.result(res_n)
  raise "#{res_n} not yet calculated" if res.nil?
  matrix = res.file_path(:matrix)
  raise "#{res_n} has no matrix" if matrix.nil?
  dist = {}
  mfh = (matrix =~ /\.gz$/) ?
    Zlib::GzipReader.open(matrix) : File.open(matrix, 'r')
  mfh.each_line do |ln|
    next if mfh.lineno == 1
    row = ln.chomp.split("\t")
    dist[cannid(row[1], row[2])] = [row[3], row[5], row[6], 0, ['root:biota']]
    cli.advance('Lines:', mfh.lineno, nil, false) if (mfh.lineno % 1_000) == 0
  end
  cli.say ''
  mfh.close
  dist
end

def traverse_taxonomy(tab, dist)
  cli.say 'Traversing taxonomy'
  rank_i = 0
  Taxonomy.KNOWN_RANKS.each do |rank|
    next if rank == :ns
    rank_n = 0
    rank_i += 1
    in_rank = nil
    ds_name = []
    File.open(tab, 'r') do |fh|
      fh.each_line do |ln|
        if ln =~ /^ {0,#{(rank_i - 1) * 2}}\S+:\S+:/
          in_rank = nil
          ds_name = []
        elsif ln =~ /^ {#{rank_i * 2}}(#{rank}:(\S+)):/
          in_rank = $2 == '?' ? nil : $1
          ds_name = []
        elsif ln =~ /^ *# (\S+)/ && !in_rank.nil?
          ds_i = $1
          ds_name << ds_i
          ds_name.each do |ds_j|
            k = cannid(ds_i, ds_j)
            next if dist[k].nil?
            rank_n += 1
            dist[k][3] = rank_i
            dist[k][4].unshift in_rank
          end
        end
      end
    end
    cli.say "o #{rank}: #{rank_n} pairs of datasets"
  end
  dist
end