require File.expand_path(File.dirname(__FILE__) + '/../../test_helper')
require 'rbbt-util'
require 'rbbt/association'
require 'rbbt/association'
require 'rbbt/association/database'

class TestAssociationDatabase < Test::Unit::TestCase
   
  EFFECT =<<-END
#: :sep=" "#:type=:double
#SG TG Effect directed?
MDM2 TP53 inhibition false
TP53 NFKB1|GLI1 activation|activation true|true
  END

  EFFECT_OPTIONS = {
    :source => "SG=~Associated Gene Name",
    :target => "TG=~Associated Gene Name=>Ensembl Gene ID",
    :persist => false,
    :identifiers => datafile_test('identifiers'),
  }

  EFFECT_TSV = TSV.open EFFECT, EFFECT_OPTIONS.dup
  def test_tsv
    assert_equal %w(NFKB1 GLI1), EFFECT_TSV["TP53"]["TG"]
  end

  EFFECT_DATABASE = Association.database(EFFECT_TSV, EFFECT_OPTIONS.dup)
  
  def test_open_new_tsv
    tsv = Association.database EFFECT_TSV, :fields => ["Effect"], :target => "TG=~Associated Gene Name=>Ensembl Gene ID"
    assert_equal ["Ensembl Gene ID", "Effect"], tsv.fields
    assert_equal "SG", tsv.key_field
    assert tsv.include? "MDM2"
  end

  def test_open_new_tsv_reverse
    tsv = Association.database EFFECT_TSV, :fields => ["Effect"], :target => "SG=~Associated Gene Name=>Ensembl Gene ID", :zipped => true
    assert_equal ["Ensembl Gene ID", "Effect"], tsv.fields
    assert_equal "TG", tsv.key_field
    assert tsv.include? "NFKB1"
  end

  def test_database_translate
    database = Association.database(EFFECT_TSV, EFFECT_OPTIONS.merge({:source => "SG=~Associated Gene Name=>Ensembl Gene ID", :target => "TG"}))
    assert_equal %w(inhibition), database["ENSG00000135679"]["Effect"]
    assert_equal %w(activation activation), database["ENSG00000141510"]["Effect"]
  end

  def test_database
    assert_equal %w(inhibition), EFFECT_DATABASE["MDM2"]["Effect"]
    assert_equal %w(activation activation), EFFECT_DATABASE["TP53"]["Effect"]
  end

  def test_index_list
    file = datafile_test('gene_ages')
    tsv = Association.database(file)
    assert_equal [["Bilateria"], ["Euteleostomi"], ["Duplicate"]], tsv["ENSG00000000003"]
  end

end