require_relative '../../../lib/commands'

module Unipept
  class UnipeptPept2taxaTestCase < Unipept::TestCase
    def test_default_batch_size
      command = Cri::Command.define { name 'pept2taxa' }
      pept2taxa = Commands::Pept2taxa.new({ host: 'http://api.unipept.ugent.be' }, [], command)
      assert_equal(5, pept2taxa.default_batch_size)
    end

    def test_required_fields
      command = Cri::Command.define { name 'pept2taxa' }
      pept2taxa = Commands::Pept2taxa.new({ host: 'http://api.unipept.ugent.be' }, [], command)
      assert_equal(['peptide'], pept2taxa.required_fields)
    end

    def test_help
      out, _err = capture_io_while do
        assert_raises SystemExit do
          Commands::Unipept.run(%w[pept2taxa -h])
        end
      end
      assert(out.include?('show help for this command'))

      out, _err = capture_io_while do
        assert_raises SystemExit do
          Commands::Unipept.run(%w[pept2taxa --help])
        end
      end
      assert(out.include?('show help for this command'))
    end

    def test_run
      out, err = capture_io_while do
        Commands::Unipept.run(%w[pept2taxa --host http://api.unipept.ugent.be ENFVYIAK])
      end
      lines = out.each_line
      assert_equal('', err)
      assert(lines.next.start_with?('peptide,taxon_id,taxon_name,taxon_rank'))
      assert(lines.next.start_with?('ENFVYIAK,'))
    end

    def test_run_with_fasta_multiple_batches
      out, err = capture_io_while do
        Commands::Unipept.run(%w[pept2taxa --host http://api.unipept.ugent.be --batch 2 >test EGGAGSSTGQR ENFVYIAK >tost EGGAGSSTGQR])
      end
      lines = out.each_line
      assert_equal('', err)
      assert(lines.next.start_with?('fasta_header,peptide,taxon_id,taxon_name,taxon_rank'))
      assert(lines.count { |line| line.start_with? '>test,EGGAGSSTGQR,' } >= 1)
      assert(lines.count { |line| line.start_with? '>test,ENFVYIAK,' } >= 1)
      assert(lines.count { |line| line.start_with? '>tost,EGGAGSSTGQR,' } >= 1)
    end

    def test_run_with_fasta_multiple_batches_and_select
      out, err = capture_io_while do
        Commands::Unipept.run(%w[pept2taxa --host http://api.unipept.ugent.be --batch 2 --select taxon_id >test EGGAGSSTGQR ENFVYIAK >tost EGGAGSSTGQR])
      end
      lines = out.each_line
      assert_equal('', err)
      assert(lines.next.start_with?('fasta_header,peptide,taxon_id'))
      assert(lines.count { |line| line.start_with? '>test,EGGAGSSTGQR,' } >= 1)
      assert(lines.count { |line| line.start_with? '>test,ENFVYIAK,' } >= 1)
      assert(lines.count { |line| line.start_with? '>tost,EGGAGSSTGQR,' } >= 1)
    end

    def test_run_with_fasta_multiple_batches_json
      out, err = capture_io_while do
        Commands::Unipept.run(%w[pept2taxa --host http://api.unipept.ugent.be --batch 2 --format json >test EGGAGSSTGQR ENFVYIAK >tost EGGAGSSTGQR])
      end
      lines = out.each_line
      assert_equal('', err)
      output = lines.to_a.join('').chomp
      assert(output.start_with?('['))
      assert(output.end_with?(']'))
      assert(!output.include?('}{'))
      assert(output.include?('fasta_header'))
    end

    def test_run_with_fasta_multiple_batches_xml
      out, err = capture_io_while do
        Commands::Unipept.run(%w[pept2taxa --host http://api.unipept.ugent.be --batch 2 --format xml >test EGGAGSSTGQR ENFVYIAK >tost EGGAGSSTGQR])
      end
      lines = out.each_line
      assert_equal('', err)
      output = lines.to_a.join('').chomp
      assert(output.start_with?('<results>'))
      assert(output.end_with?('</results>'))
      assert(output.include?('<fasta_header>'))
    end
  end
end