require_relative 'test_helper'
require 'minitest/autorun'
require 'yaml'
require 'fileutils'
require 'genevalidator'
require 'genevalidator/blast'
require 'genevalidator/validation_length_cluster'
require 'genevalidator/validation_length_rank'
require 'genevalidator/validation_blast_reading_frame'
require 'genevalidator/validation_gene_merge'
require 'genevalidator/validation_duplication'
require 'genevalidator/validation_open_reading_frame'
require 'genevalidator/validation_alignment'

module GeneValidator
  class ValidateOutput < Minitest::Test

    prot_input_fasta_file  = "test/test_files/all_validations_prot/all_validations_prot.fasta"
    prot_blast_xml_file    = "#{prot_input_fasta_file}.blast_xml"
    prot_blast_xml_raw_seq = "#{prot_input_fasta_file}.blast_xml.raw_seq"

    prot_blast_tab_file    = "#{prot_input_fasta_file}.blast_tab"
    prot_blast_tab_raw_seq = "#{prot_input_fasta_file}.blast_tab.raw_seq"

    mrna_input_fasta_file  = "test/test_files/all_validations_mrna/all_validations_mrna.fasta"
    mrna_blast_xml_file    = "#{mrna_input_fasta_file}.blast_xml"
    mrna_blast_xml_raw_seq = "#{mrna_input_fasta_file}.blast_xml.raw_seq"

    mrna_blast_tab_file    = "#{mrna_input_fasta_file}.blast_tab"
    mrna_blast_tab_raw_seq = "#{mrna_input_fasta_file}.blast_tab.raw_seq"

    tab_options            = "qseqid sseqid sacc slen qstart qend sstart send length qframe pident evalue"

    database               = 'swissprot -remote'
    threads                = '1'

    # Unwanted Output Files 
    prot_xml_out           = "#{prot_blast_xml_file}.out"
    prot_tab_out           = "#{mrna_blast_tab_file}.out"
    mrna_xml_out           = "#{mrna_blast_xml_file}.out"
    mrna_tab_out           = "#{mrna_blast_tab_file}.out"
    prot_output_dir        = "#{prot_input_fasta_file}.html"
    mrna_output_dir        = "#{mrna_input_fasta_file}.html"
    prot_yaml              = "#{prot_input_fasta_file}.yaml"
    mrna_yaml              = "#{mrna_input_fasta_file}.yaml"

    describe 'Protein dataset' do
      it 'xml and tabular inputs give the same output' do

        original_stdout = $stdout.clone
        $stdout.reopen(prot_xml_out, 'w')

        FileUtils.rm_rf(prot_output_dir) rescue Error

        opts = {
          validations: %w(lenc lenr frame merge dup orf),
          db: database,
          num_threads: threads,
          fast: false,
          input_fasta_file: prot_input_fasta_file,
          blast_xml_file: prot_blast_xml_file,
          raw_sequences: prot_blast_xml_raw_seq,
          test: true
        }

        (GeneValidator::Validation.new(opts, 1, false)).run
        $stdout.reopen original_stdout
        $stdout.reopen(prot_tab_out, 'w')

        FileUtils.rm_rf(prot_output_dir) rescue Error

        opts1 = {
          validations: %w(lenc lenr frame merge dup orf),
          db: database,
          num_threads: threads,
          fast: false,
          input_fasta_file: prot_input_fasta_file,
          blast_tabular_file: prot_blast_tab_file,
          blast_tabular_options: tab_options,
          raw_sequences: prot_blast_tab_raw_seq,
          test: true
        }

        (GeneValidator::Validation.new(opts1, 1, false)).run
        $stdout.reopen original_stdout

        diff = FileUtils.compare_file(prot_xml_out, prot_tab_out)

        File.delete(prot_xml_out)
        File.delete(prot_tab_out)
        File.delete(prot_yaml)

        FileUtils.rm_rf(prot_output_dir)

        assert_equal(true, diff)
      end
    end

    describe 'mRNA dataset' do
      it 'xml and tabular inputs give the same output' do

        original_stdout = $stdout.clone
        $stdout.reopen(mrna_xml_out, 'w')

        FileUtils.rm_rf(mrna_output_dir) rescue Error

        opts = {
          validations: %w(lenc lenr frame merge dup orf align),
          db: database,
          num_threads: threads,
          fast: false,
          input_fasta_file: mrna_input_fasta_file,
          blast_xml_file: mrna_blast_xml_file ,
          raw_sequences: mrna_blast_xml_raw_seq,
          test: true
        }

        (GeneValidator::Validation.new(opts, 1, false)).run
        $stdout.reopen original_stdout
        $stdout.reopen(mrna_tab_out, 'w')

        FileUtils.rm_rf(mrna_output_dir) rescue Error

        opts1 = {
          validations: %w(lenc lenr frame merge dup orf align),
          db: database,
          num_threads: threads,
          fast: false,
          input_fasta_file: mrna_input_fasta_file,
          blast_tabular_file: mrna_blast_tab_file,
          blast_tabular_options: tab_options,
          raw_sequences: mrna_blast_tab_raw_seq,
          test: true
        }

        (GeneValidator::Validation.new(opts1, 1, false)).run
        $stdout.reopen original_stdout

        diff = FileUtils.compare_file(mrna_xml_out, mrna_tab_out)

        File.delete(mrna_xml_out)
        File.delete(mrna_tab_out)
        File.delete(mrna_yaml)

        FileUtils.rm_rf(mrna_output_dir)

        assert_equal(true, diff)
      end
    end
  end
end