require 'test/unit'
require File.dirname(File.expand_path(__FILE__)) + '/load_bin_path'
require 'fileutils'

tmp = $VERBOSE
$VERBOSE = 5

$XML_SANITY_LINES = ['<sample_enzyme name="trypsin">', '<specificity cut="KR" no_cut="P" sense="C"/>', '<parameter name="diff_search_options" value="0.000000 S 0.000000 C 0.000000 M 0.000000 X 0.000000 T 0.000000 Y"/>']

$XML_SANITY_MATCHES = [/<spectrum_query spectrum="0\d0.\d+.\d+.[123]" start_scan="\d+" end_scan="\d+" precursor_neutral_mass="[\d\.]+" assumed_charge="[123]" index="\d+">/,
  /	<search_hit hit_rank="\d" peptide="[\w\-\.]+" peptide_prev_aa="." peptide_next_aa="." protein=".*" num_tot_proteins="\d+" num_matched_ions="\d+" tot_num_ions="\d+" calc_neutral_pep_mass="[\d\.]+" massdiff="[\+\-][\d\.]+" num_tol_term="\d" num_missed_cleavages="\d" is_rejected="[01]">/, 
  /<search_score name="xcorr" value="[\d\.]+"\/>/,
  /<search_score name="deltacn" value="[\d\.]+"\/>/, 
  /<search_score name="deltacnstar" value="[01]"\/>/, 
  /<search_score name="spscore" value="[\d\.]+"\/>/, 
  /<search_score name="sprank" value="\d+"\/>/,
]




class BioworksToPepXMLTest < Test::Unit::TestCase

  def initialize(arg)
    super(arg)
    @tfiles = File.dirname(__FILE__) + '/tfiles/'
    @tfiles_l = File.dirname(__FILE__) + '/tfiles_large/'
    @tf_mzxml_path = @tfiles_l + "yeast_gly_mzXML"
    @tf_bioworks_xml = @tfiles + "bioworks_small.xml"
    @tf_params = @tfiles + "bioworks32.params"
    @no_delete = true
    @out_path = @tfiles + 'pepxml/'
    @cmd = "ruby -I#{File.join(File.dirname(__FILE__), "..", "lib")} -S bioworks_to_pepxml.rb "
  end

  def test_usage
    assert_match(/usage:/, `#{@cmd}`)
  end

  def _basic(cmd, prc)
    puts "Performing: #{cmd}" if $VERBOSE
    reply = `#{cmd}`
    puts reply if $VERBOSE
    %w(000 020).each do |file|
      ffile = @out_path + file + ".xml"
      prc.call(ffile)
    end
  end

  def test_basic
    if File.exist? @tfiles_l
      cmd = "#{@cmd} -p #{@tf_params} -o #{@out_path} #{@tf_bioworks_xml} -m #{@tf_mzxml_path} -d /work/special/path --copy_mzxml"
      ## FILES EXIST:
      prc = proc {|file| 
        assert(File.exist?(file), "#{file} exists")
        beginning = IO.readlines(file)[0,50].join("\n")
        $XML_SANITY_LINES.each do |line|
          assert(beginning.include?(line), "xml includes line: #{line}")
        end
        $XML_SANITY_MATCHES.each do |match|
          assert_match(match, beginning, "matches")
        end
      }
      _basic(cmd, prc)
      ## COPY MZXML:
      %w(000 020).each do |file|
        mzxml_file = File.join(@out_path, "#{file}.mzXML")
        assert(File.exist?( mzxml_file ), "file: #{mzxml_file} exists")
      end
      ## CLEANUP:
      unless @no_delete then FileUtils.rm_rf(@out_path) end
    else
      assert_nil( puts("--SKIPPING TEST-- (missing dir: #{@tfiles_l})") )
    end
  end

  def test_database
    if File.exist? @tfiles_l
      cmd = "#{@cmd} -p #{@tf_params} -o #{@out_path} #{@tf_bioworks_xml} -m #{@tf_mzxml_path}" 
      db_re = /C:\\Xcalibur\\database\\ecoli_K12_ncbi_20060321.fasta/
      assert_match(db_re, IO.read(@tf_params))
      prc = proc {|file|
        assert(File.exist?(file))
        assert_no_match(db_re, IO.read(file))
      }
      _basic(cmd, prc)
      unless @no_delete then FileUtils.rm_rf(@out_path) end
    else
      assert_nil( puts("--SKIPPING TEST-- (missing dir: #{@tfiles_l})") )
    end
  end
end

$VERBOSE = tmp