path: root/service-tests/service-tests.rb

# Make updates and copy to container
# docker cp service-tests.rb service-tests:/home/ist/service-tests/service-tests.rb
# even if container is stopped !

require 'minitest/autorun'
require 'rest-client'
require 'nokogiri'
require 'csv'

class WebServiceTests < Minitest::Test

  def get_models
    require '../lazar/lib/lazar.rb'
    $models = OpenTox::Model::Validation.all
    $r_model = $models.select{|m| m if m.model.name == "LOAEL (training_log10)"}[0].id.to_s
    $c_model = $models.select{|m| m if m.model.name == "Mutagenicity (kazius)"}[0].id.to_s
  end

  def test_virtuoso
    puts "\nhttps://virtuoso.in-silico.ch"
    assert_raises RestClient::NotFound do
      response = RestClient.get "https://virtuoso.in-silico.ch"
    end
  end
  
  def test_insilico_website
    puts "\nhttps://in-silico.ch"
    response = RestClient.get "https://in-silico.ch"
    assert_equal response.code, 200
    xml = Nokogiri::HTML.parse(response.body)
    value = xml.at('li.active').text.strip
    assert_equal "Software and services", value
  end
  
  def test_predictive_toxicology
    puts "\nhttps://predictive-toxicology.org/"
    response = RestClient.get "https://predictive-toxicology.org/"
    assert_equal response.code, 200
    xml = Nokogiri::HTML.parse(response.body)
    value = xml.at('title').text
    assert_equal "Predictive Toxicology", value
  end
  
  def test_lazar_batch
    puts "\nhttps://lazar-batch.in-silico.ch"
    require '../batch-login.rb'
    assert_raises RestClient::Unauthorized do
      response = RestClient.get "https://lazar-batch.in-silico.ch"
    end
    assert_raises RestClient::Unauthorized do
      response = RestClient::Request.execute method: :get, url: "https://lazar-batch.in-silico.ch", user: $user+"f", password: $passwd
    end
    assert_raises RestClient::Unauthorized do
      response = RestClient::Request.execute method: :get, url: "https://lazar-batch.in-silico.ch", user: $user, password: $passwd+"f"
    end
    response = RestClient::Request.execute method: :get, url: "https://lazar-batch.in-silico.ch", user: $user, password: $passwd
    xml = Nokogiri::HTML.parse(response.body)
    assert_match xml.at('h1').text.gsub(/\n/,"").strip, "lazar toxicity predictions"
    # batch
    get_models
    response = RestClient::Request.execute method: :post, 
      url:  "https://lazar-batch.in-silico.ch/predict", 
      user: $user,
      password: $passwd,
      payload: {
        multipart: true,
        fileselect: File.new('./test.csv', 'rb'),
        selection: {$r_model => ""}
      }
    assert_equal response.code, 200
    xml = Nokogiri::HTML.parse(response.body)
    value = xml.css('h5').text
    assert_equal "Lowest observed adverse effect level (LOAEL) (Rat)", value
    value = xml.at_css('a#detailsbutton_0').text.strip
    assert_equal "Details", value
  end
  
  def test_dump
    puts "\nhttps://dump.in-silico.ch"
    response = RestClient.get "https://dump.in-silico.ch"
    assert_equal response.code, 200
    xml = Nokogiri::HTML.parse(response.body)
    dumpsize = xml.at('pre').text.split.last.to_i 
    response = RestClient.get "https://dump.in-silico.ch/dump.tar.gz"
    assert_equal response.body.size.to_i, dumpsize
  end
  
  def test_lazar
    puts "\nhttps://lazar.in-silico.ch"
    get_models
    response = RestClient.get "https://lazar.in-silico.ch"
    assert_equal response.code, 200
    xml = Nokogiri::HTML.parse(response.body)
    assert_match xml.at('h1').text.gsub(/\n/,"").strip, "lazar toxicity predictions"
    puts "\npredict regression: https://lazar.in-silico.ch/predict"
    # regression
    response = RestClient.post "https://lazar.in-silico.ch/predict", {identifier: "O=[N+]([O-])c1ccccc1", selection: {$r_model=>""}}
    xml = Nokogiri::HTML.parse(response.body)
    value = xml.css('td')[1].css('p')[2].text.split[1].to_f
    assert value.between?(0.06,0.09)
    puts "\npredict classification: https://lazar.in-silico.ch/predict"
    # classification
    response = RestClient.post "https://lazar.in-silico.ch/predict", {identifier: "O=[N+]([O-])c1ccccc1", selection: {$c_model=>""}}
    xml = Nokogiri::HTML.parse(response.body)
    value = xml.css('td')[1].css('p')[4].text.split.last
    assert_equal "mutagenic", value
    # regression
    puts "\nmodel details regression: https://lazar.in-silico.ch/predict/modeldetails/#{$r_model}"
    response = RestClient.get "https://lazar.in-silico.ch/predict/modeldetails/#{$r_model}"
    xml = Nokogiri::HTML.parse(response.body)
    puts "check metadata\n"
    links = xml.css('a')
    assert_equal "https://github.com/opentox/loael-paper/blob/revision/data/training_log10.csv", links[0].children.text.strip
    assert_equal "training_log10", links[1].children.text.strip
    assert_equal "Algorithm::Similarity.tanimoto", links[2].children.text.strip
    assert_equal "Algorithm::Caret.rf", links[3].children.text.strip
    text = xml.css('div.panel-body')[0]
    a,b = text.children[4].text.strip.split("\n")
    assert_equal "Type:", a.strip
    assert_equal "Regression", b.strip
    a,b = text.children[6].text.strip.split("\n")
    assert_equal "Training compounds:", a.strip
    assert_equal "671", b.strip
    text = xml.css('div.panel-body')[1]
    a,b,c = text.children[8].text.strip.split
    assert_equal "Descriptors:", a.strip
    assert_equal "fingerprint,", b.strip
    assert_equal "MP2D", c.strip
    # classification
    puts "\nmodel details classification: https://lazar.in-silico.ch/predict/modeldetails/#{$c_model}"
    response = RestClient.get "https://lazar.in-silico.ch/predict/modeldetails/#{$c_model}"
    xml = Nokogiri::HTML.parse(response.body)
    puts "check metadata\n"
    links = xml.css('a')
    assert_equal "http://cheminformatics.org/datasets/", links[0].children.text.strip
    assert_equal "kazius", links[1].children.text.strip
    assert_equal "Algorithm::Similarity.tanimoto", links[2].children.text.strip
    assert_equal "Algorithm::Classification.weighted_majority_vote", links[3].children.text.strip
    text = xml.css('div.panel-body')[0]
    a,b = text.children[4].text.strip.split("\n")
    assert_equal "Type:", a.strip
    assert_equal "Classification", b.strip
    a,b = text.children[6].text.strip.split("\n")
    assert_equal "Training compounds:", a.strip
    assert_equal "4069", b.strip
    text = xml.css('div.panel-body')[1]
    a,b,c = text.children[8].text.strip.split
    assert_equal "Descriptors:", a.strip
    assert_equal "fingerprint,", b.strip
    assert_equal "MP2D", c.strip
  end

  def test_nano_lazar
    puts "\nhttps://nano-lazar.in-silico.ch"
    response = RestClient.get "https://nano-lazar.in-silico.ch"
    assert_equal response.code, 200
    xml = Nokogiri::HTML.parse(response.body)
    assert_match xml.at('h1').text.gsub(/\n/,"").strip, "nano-lazar toxicity predictions"
    
    params = {example_coating_0: "N-(2-Mercaptopropionyl)glycine",
              example_core:	"Au",
              example_id:	"5878a6097b6c9b003a862710",
              example_pc:	"{}",
              input_coating_0: "N-(2-Mercaptopropionyl)glycine",
              input_core:	"Au",
              prediction_model:	"5878aa1d7b6c9b003a8629b1",
              type:	"fingerprint"
    }
    puts "\npredict example: https://nano-lazar.in-silico.ch/predict"
    response = RestClient.post "https://nano-lazar.in-silico.ch/predict", params
    xml = Nokogiri::HTML.parse(response.body)
    value = xml.css('tbody').css('tr')[1].css('td')[0].css('a').text.gsub(/\n/,"").strip
    assert_equal value, "G15.AC"
  end

  def test_aop
    puts "\nhttps://aop.in-silico.ch"
    response = RestClient.get "https://aop.in-silico.ch"
    assert_equal response.code, 200
    xml = Nokogiri::HTML.parse(response.body)
    assert_match xml.at('h1').text.gsub(/\n/,"").strip, "PubChem read across"
    puts "\nhttps://aop.in-silico.ch/cid/31703"
    response = RestClient.get "https://aop.in-silico.ch/cid/31703"
    assert_equal response.code, 200
    xml = Nokogiri::HTML.parse(response.body)
    value =  xml.at('th').text.split.first.strip
    assert_equal "(7S,9S)-7-[(2R,4S,5S,6S)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy-6,9,11-trihydroxy-9-(2-hydroxyacetyl)-4-methoxy-8,10-dihydro-7H-tetracene-5,12-dione", value
  end

  def test_dg2_Elena
    puts "\nhttps://dg2.in-silico.ch"
    response = RestClient.get "https://dg2.in-silico.ch"
    assert_equal response.code, 200
    xml = Nokogiri::HTML.parse(response.body)
    batch_file_id = xml.search("label")[4].attributes["for"].value.gsub(/existing|\[|\]/,"")
    batch_file_name = xml.search("label")[4].text.strip
    assert_match xml.at('h1').text.gsub(/\n/,"").strip, "lazar toxicity predictions"
    puts "\nsingle prediction Mazzatorta: https://dg2.in-silico.ch/predict"
    response = RestClient.post "https://dg2.in-silico.ch/predict", {identifier: "O=[N+]([O-])c1ccccc1", selection: {"Mazzatorta"=>""}}
    xml = Nokogiri::HTML.parse(response.body)
    value = xml.css('td')[1].css('p')[0].text.split[1].to_f
    assert value, 0.384
    puts "\nsingle prediction lazar LOAEL: https://dg2.in-silico.ch/predict"
    response = RestClient.post "https://dg2.in-silico.ch/predict", {identifier: "O=[N+]([O-])c1ccccc1", selection: {"5ba4e38b5e110b01688fa0ca"=>""}}
    xml = Nokogiri::HTML.parse(response.body)
    value = xml.css('td')[1].css('p')[2].text.split[1].to_f
    assert value, 0.0807
    
    puts "\nbatch prediction with first dataset in existing list\n"
    response = RestClient.post "https://dg2.in-silico.ch/predict", {existing: {batch_file_id=>""}, selection: {"5ba4e38b5e110b01688fa0ca"=>""}}
    assert_equal response.code, 200
    xml = Nokogiri::HTML.parse(response.body)
    title = xml.search("h3").text
    assert_equal title, "Batch Prediction Results:RHC_input"
    sleep 3
    href = xml.search("a#downbutton_0")[0]["href"]
    puts "\ndownload csv batch results\n"
    response = RestClient.get href
    csv = CSV.new(response.body)
    header = csv.first
    ["ID", "Original ID", "Input", "Endpoint"].each do |h|
      assert_includes header, h
    end
    
    puts "\nmodel details lazar LOAEL: https://dg2.in-silico.ch/predict/modeldetails/5ba4e38b5e110b01688fa0ca"
    response = RestClient.get "https://dg2.in-silico.ch/predict/modeldetails/5ba4e38b5e110b01688fa0ca"
    xml = Nokogiri::HTML.parse(response.body)
    puts "check metadata\n"
    links = xml.css('a')
    assert_equal "https://github.com/opentox/loael-paper/blob/revision/data/training_log10.csv", links[0].children.text.strip
    assert_equal "training_log10", links[1].children.text.strip
    assert_equal "Algorithm::Similarity.tanimoto", links[2].children.text.strip
    assert_equal "Algorithm::Caret.rf", links[3].children.text.strip
    text = xml.css('div.panel-body')[0]
    a,b = text.children[4].text.strip.split("\n")
    assert_equal "Type:", a.strip
    assert_equal "Regression", b.strip
    a,b = text.children[6].text.strip.split("\n")
    assert_equal "Training compounds:", a.strip
    assert_equal "671", b.strip
    text = xml.css('div.panel-body')[1]
    a,b,c = text.children[8].text.strip.split
    assert_equal "Descriptors:", a.strip
    assert_equal "fingerprint,", b.strip
    assert_equal "MP2D", c.strip
  end

  def test_dg3_Elena
    puts "\nhttps://dg3.in-silico.ch"
    response = RestClient.get "https://dg3.in-silico.ch"
    assert_equal response.code, 200
    xml = Nokogiri::HTML.parse(response.body)
    assert_match xml.at('h1').text.gsub(/\n/,"").strip, "lazar toxicity predictions"
  end

  def test_test1_Elena
    puts "\nhttps://test1.in-silico.ch"
    response = RestClient.get "https://test1.in-silico.ch"
    assert_equal response.code, 200
    xml = Nokogiri::HTML.parse(response.body)
    assert_match xml.at('h1').text.gsub(/\n/,"").strip, "Nestec Toxicity Predictions"
  end

  #def test_git_server
  #TODO Net::HTTPBadResponse: wrong status line: "SSH-2.0-OpenSSH_7.8"
  #  response = RestClient.get "https://git.in-silico.ch"
  #end

  def test_server_invalid_cert
    puts "\ninvalid cert test4"
    assert_raises RestClient::SSLCertificateNotVerified do
      response = RestClient.get "https://test4.in-silico.ch"
    end
  end

end