sequenceserver 0.8.9 → 1.0.0.pre.1

data/tests/run

@@ -1,26 +0,0 @@
-#!/usr/bin/env ruby
-# Usage:
-#
-# run all test suites
-#
-#     $ tests/run
-#
-# run a particular test suite
-#
-#     $ tests/run tests/test_sequencehelpers.rb
-#
-
-# script dir
-dir = File.dirname(__FILE__)
-
-# setup load path
-require 'rubygems'
-$LOAD_PATH.unshift(File.join(dir, '..', 'lib'))
-
-# user specified or glob all?
-files = ARGV.empty? ? Dir[File.join(dir, 'test_*.rb')] : ARGV
-
-# run!
-files.each do |file|
-  require File.expand_path(file)
-end

data/tests/test_sequencehelpers.rb

@@ -1,77 +0,0 @@
-require 'sequenceserver'
-require 'sequenceserver/sequencehelpers'
-require 'test/unit'
-
-class Tester < Test::Unit::TestCase
-  include SequenceServer::SequenceHelpers
-  def test_guess_sequence_type_nucleotide
-  #must 'correctly detect nucleotide sequence, even when it includes crap' do   
-    ['AAAAAAAAAAAAAAAAAAAAAT',
-     '           CAGATGCRRCAAAGCAAACGGCAA 34523453 652352',
-     'ACCNNNNNNXXXXCAUUUUUU',
-     "ACGT\n\t\t\nACCACGGACCACGAAAGCG"               ].each do |seq|
-      assert_equal(:nucleotide, guess_sequence_type(seq), message="for #{seq}")
-    end
-  end
-
-  def test_guess_sequence_type_aminoacid
-  #must 'correctly detect aminoacid sequence, even when it includes a lot of crap' do
-  ['ADSACGHKSJLFCVMGTL',
-   '  345   KSSYPHYSPPPPHS      345 23453 652352',
-   'GEYSNLNNNNNNXXXXSSSSSSSSSSSSSSSSSSSSSSS',
-   "EE\n\t\t\n         \t\t\EEQRRQQSARTSRRQR"     ].each do |seq|
-      assert_equal(:protein, guess_sequence_type(seq) , message="for #{seq}")
-    end
-  end
-
-  def test_guess_sequence_type_impossible
-    assert_equal(nil, guess_sequence_type('ACSFGT'), message='too little sequence')
-  end
-
-  ## Tests for type_of_sequences  (multi-fasta  kind of thing the user would enter)
-  def test_type_of_sequences
-    aa_multifasta = ">SDFDSF\nACGTGSDLKJGNLDKSJFLSDKJFLSDKOIU\n>asdfas\nasfasdfffffffffffffffffffff\n>alksjflkasdj slakdjf\nasdfasdfasdfljaslkdjf"
-    aa_multifasta_including_short_seq_missing_lead = "ACGTGSDLKJGNLDKSJFLSDKJFLSDKOIU\n>asdfas\nasf\n>alksjflkasdj slakdjf\nasdfasdfasdfljaslkdjf"
-    aa_singlesequence =  "ACGTGSDLKJGNLDKSJFLSDKJFLSDKOIU\n"
-    nt_multifasta = ">asdf\nAAAAAAAAAAAAAAAAAAAAT\n>sfaslkj\nCAGATGCRRCAAAGCAAACGGCAA\n>asssssjlkj\nACCCANNNNNNXXXXCAUUUUUU"
-    aa_nt_mix = ">alksjflkasdj slakdjf\nasdfasdfasdfljaslkdjf\n>ffffffassdf\nACGCNAGTGCCCCCCCCGANATGGGTGGTTXXXXXGGTG"
-
-    assert_equal(:protein, type_of_sequences(aa_multifasta), 'aa_multifasta')
-    assert_equal(:protein, type_of_sequences(aa_multifasta_including_short_seq_missing_lead ), 'aa_multifasta_short_seq_and_no_>')
-    assert_equal(:protein, type_of_sequences(aa_singlesequence), 'single AA sequence')
-    assert_equal(:nucleotide, type_of_sequences(nt_multifasta), 'nt_multifasta')
-    assert_raise(ArgumentError, 'mixed aa and nt should raise') { type_of_sequences(aa_nt_mix) }
-  end
-
-  def test_composition
-    expected_comp = {"a"=>2, "d"=>3, "f"=>7, "s"=>3, "A"=>1}
-    assert_equal(expected_comp, composition('asdfasdfffffAsdf'))
-  end
-  
-  def test_construct_standard_sequence_hyperlink
-    assert_equal "/get_sequence/?id=one&db=abc def", construct_standard_sequence_hyperlink({:sequence_id => 'one', :databases => %w(abc def)})
-    assert_equal nil, construct_standard_sequence_hyperlink({:sequence_id => ' one', :databases =>  %w(abc def)})
-    assert_equal "/get_sequence/?id=MAL13P1.218&db=abc def", construct_standard_sequence_hyperlink({:sequence_id => 'lcl|MAL13P1.218', :databases =>  %w(abc def)})
-  end
-end
-
-class AppTester < Test::Unit::TestCase
-  def test_process_advanced_blast_options
-    app = SequenceServer::App.new!
-
-    assert_nothing_raised {app.validate_advanced_parameters('')}
-    assert_nothing_raised {app.validate_advanced_parameters('-word_size 5')}
-    assert_raise(ArgumentError, 'security advanced option parser'){app.validate_advanced_parameters('-word_size 5; rm -rf /')}
-    assert_raise(ArgumentError, 'conflicting advanced option'){app.validate_advanced_parameters('-db roar')}
-  end
-end
-
-class SystemHelpersTester < Test::Unit::TestCase
-  include SequenceServer::Helpers::SystemHelpers
-
-  def test_multipart_database_name?
-    assert_equal true, multipart_database_name?('/home/ben/pd.ben/sequenceserver/db/nr.00')
-    assert_equal false, multipart_database_name?('/home/ben/pd.ben/sequenceserver/db/nr')
-    assert_equal true, multipart_database_name?('/home/ben/pd.ben/sequenceserver/db/img3.5.finished.faa.01')
-  end
-end

data/tests/test_sequenceserver_blast.rb

@@ -1,60 +0,0 @@
-require 'sequenceserver'
-require 'minitest/spec'
-require 'minitest/autorun'
-require 'rack/test'
-
-ENV['RACK_ENV'] = 'test'
-
-module SequenceServer
-  describe "App" do
-    include Rack::Test::Methods
-
-    def app
-      App
-    end
-
-    def setup
-      @params = {'method' => 'blastn', 'sequence' => 'AGCTAGCTAGCT', 'databases' => ['123']}
-    end
-
-    it 'returns Bad Request (400) if no blast method is provided' do
-      @params.delete('method')
-      post '/', @params
-      last_response.status.must_equal 400
-    end
-
-    it 'returns Bad Request (400) if no input sequence is provided' do
-      @params.delete('sequence')
-      post '/', @params
-      last_response.status.must_equal 400
-    end
-
-    it 'returns Bad Request (400) if no database id is provided' do
-      @params.delete('databases')
-      post '/', @params
-      last_response.status.must_equal 400
-    end
-
-    it 'returns Bad Request (400) if an empty database list is provided' do
-      @params['databases'].pop
-
-      # ensure the list of databases is empty
-      @params['databases'].length.must_equal 0
-
-      post '/', @params
-      last_response.status.must_equal 400
-    end
-
-    it 'returns Bad Request (400) if an incorrect blast method is supplied' do
-      @params['method'] = 'foo'
-      post '/', @params
-      last_response.status.must_equal 400
-    end
-
-    it 'returns Bad Request (400) if incorrect advanced params are supplied' do
-      @params['advanced'] = '-word_size 5; rm -rf /'
-      post '/', @params
-      last_response.status.must_equal 400
-    end
-  end
-end

data/tests/test_ui.rb

@@ -1,104 +0,0 @@
-require 'rspec'
-require 'watir-webdriver'
-require 'headless'
-
-# These shared examples should work for
-shared_examples_for 'a browser' do
-  let(:seqserv_url){'http://localhost:4567'}
-
-  it 'should simply go the seqserv webpage' do
-    b.goto seqserv_url
-    b.url.gsub(/\/$/,'').should eq(seqserv_url)
-    b.ready_state.should eq('complete')
-  end
-
-  it 'should do a simple blastp' do
-    b.goto seqserv_url
-
-    # Nucleotide database should be available
-    b.checkbox(:value => 'ed4250adc44601256f6bbbd4ab5cc80c').enabled?.should eq(true)
-
-    # First up the blast button should be disabled
-    b.button(:id => 'method').text.should eq('BLAST')
-    b.button(:id => 'method').enabled?.should eq(false)
-
-    # Pick a protein blast database
-    b.checkbox(:value => 'b9a05001b93ca2587b447dacb9906f2a').set
-    b.checkbox(:value => 'b9a05001b93ca2587b447dacb9906f2a').checked?.should eq(true)
-
-    # nuc dbs now disabled
-    b.checkbox(:value => 'ed4250adc44601256f6bbbd4ab5cc80c').enabled?.should eq(false)
-
-    # The blast button should still be disabled
-    b.button(:id => 'method').text.should eq('BLAST')
-    b.button(:id => 'method').enabled?.should eq(false)
-
-    # Give a sequence we know should hit
-    b.textarea(:name => 'sequence').set 'YTLPPPPTKLYSAPISCRKNKTGHWMDDILSIKTGESCPVNNYLHSGFLA'
-
-    #blast butn now active
-    b.button(:id => 'method').text.should eq('BLASTP')
-    b.button(:id => 'method').enabled?.should eq(true)
-
-    # Run the blast
-    b.button(:id => 'method').click
-
-    while b.div(:id => 'result').text.include?('Waiting for BLAST to be run')
-    end
-
-    # blast should have worked
-    b.div(:id => 'result').text.include?('FASTA of 11 retrievable').should eq(true)
-  end
-end
-
-#####################################################################################
-#+++++++++++ Below is admin code, hopefully not necessary to mess around with to test new UI specs
-
-# NOT thread-safe, at least because of the interaction with headless
-class BrowserAdmin
-  def self.setup_browser(type)
-    case type
-    when :firefox then
-      Watir::Browser.new :firefox
-    when :chrome then
-      Watir::Browser.new :chrome
-    when :headless_firefox then
-      @headless = Headless.new
-      @headless.start
-      Watir::Browser.new :firefox
-    when :headless_chrome then
-      @headless = Headless.new
-      @headless.start
-      Watir::Browser.new :chrome
-    else
-      raise "Unknown browser type asked for: #{type.inspect}"
-    end
-  end
-
-  def self.teardown_browser(browser)
-    browser.close
-
-    # Re-head again, but maybe this makes no difference
-    @headless.destroy unless @headless.nil?
-    @headless = nil
-  end
-end
-
-
-describe 'ui' do
-  [:firefox, :chrome, :headless_firefox, :headless_chrome].each do |bro|
-    context bro.to_s do
-      it_behaves_like 'a browser' do
-        browser = nil
-        before do
-          browser = BrowserAdmin.setup_browser bro
-        end
-        after do
-          BrowserAdmin.teardown_browser browser
-        end
-        let(:b){browser}
-      end
-    end
-  end
-end
-

data/tests/ui.specs.todo

@@ -1,10 +0,0 @@
-it "should automatically focus sequence input box" do
-  # when the page loads, check that sequence input box is focussed
-  #
-  # NOTE: unless #75 is resolved, make sure to test this functionality only if
-  # HTML5 autofocus attribute is supported
-end
-
-it "should ensure spell checking is disabled for sequence input box" do
-  # NOTE: only if the browser supports it
-end