Contents

require File.join(File.expand_path(File.dirname(__FILE__)), '../../test_helper.rb')
require 'rbbt/entity'
require 'rbbt/ner/finder'
require 'rbbt/ner/finder'
require 'rbbt/sources/organism'
require 'rbbt/sources/kegg'
require 'rbbt/sources/NCI'

class TestFinder < Test::Unit::TestCase

  def test_namespace_and_format
    f = Finder.new(CMD.cmd("head -n 1000", :in => Open.open(Organism.identifiers(Organism.default_code("Hsa")).produce.find)))
    assert_equal Organism.default_code("Hsa"), f.instances.first.namespace
    assert_equal "Ensembl Gene ID", f.instances.first.format
  end

  def test_find
    f = Finder.new(Organism.lexicon(Organism.default_code("Hsa")), :grep => ["SF3B1"])

    assert_equal "ENSG00000115524", f.find("SF3B1").first
    if defined? Entity
      assert_equal "Ensembl Gene ID", f.find("SF3B1").first.format
    end
  end

  def test_find2
    f = Finder.new(Organism.lexicon(Organism.default_code("Hsa")), :grep => ["RASGRF2"])

    m = f.find("RAS").first

    assert f.find("RAS").include? "ENSG00000113319"
  end

  def test_find_mutation
    f = Finder.new(Organism.lexicon(Organism.default_code("Hsa")), :grep => ["RASGRF2"])
    f.add_instance({"Genomic Mutation" => /\w+:\w+:\w+/})

    m =  f.find("The mutation 1:1234:A is intergenic").first
    assert_equal "1:1234:A", m.info[:code]
  end

end

Version data entries

7 entries across 7 versions & 1 rubygems

Version	Path
rbbt-text-1.2.0	test/rbbt/ner/test_finder.rb
rbbt-text-1.1.9	test/rbbt/ner/test_finder.rb
rbbt-text-1.1.8	test/rbbt/ner/test_finder.rb
rbbt-text-1.1.7	test/rbbt/ner/test_finder.rb
rbbt-text-1.1.6	test/rbbt/ner/test_finder.rb
rbbt-text-1.1.5	test/rbbt/ner/test_finder.rb
rbbt-text-1.1.4	test/rbbt/ner/test_finder.rb