sequenceserver-beta 0.8.7.beta1

data/tests/run

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+#!/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

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+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

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+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

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+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/test_ui.rb~

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+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 => 'e205221dd32dc53ebfc9fb48cbdecd9e').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 => '6669b1c88665158621afc06407ce88ea').set
+    b.checkbox(:value => '6669b1c88665158621afc06407ce88ea').checked?.should eq(true)
+
+    # nuc dbs now disabled
+    b.checkbox(:value => 'e205221dd32dc53ebfc9fb48cbdecd9e').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?('Sequences producing significant alignments: ').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

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+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

data/views/500.erb

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+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+    "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xml:lang="en" lang="en" xmlns="http://www.w3.org/1999/xhtml">
+<head>
+    <title>SequenceServer</title>
+    <meta name="author" content="Anurag Priyam" />
+    <meta name="author" content="Yannick Wurm" />
+    <meta name="author" content="Cedric Wurm" />
+    <meta content="text/html; charset=UTF-8" http-equiv="Content-Type"/>
+
+    <%# without a space after erb's closing tag, a / gets appended to css' path %>
+    <link rel="stylesheet" media="screen" type="text/css" href=<%= uri('/css/beige.css') %> />
+</head>
+
+<body>
+  <div class="container">
+    <h1>Oops! Something went wonky!</h1>
+	<p>Apologies, there was an error with your request: 
+	  <strong><%=request.env['sinatra.error'].message %> </strong></p>
+    <p>If the error persists please contact the administrator</p>
+  </div>
+</body>

data/views/_options.erb

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+<%#
+
+  NOTE: The markup below is displayed in a modal window.  Use less than 70
+        characters per line to preserve formatting.
+%>
+
+<h6>General Search Options</h6>
+
+<br/>
+
+<ul class="unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-evalue <Real>
+  Expectation value (E) threshold for saving hits
+  Default = '10'| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-word_size <Integer, >=2>
+  Word size for wordfinder algorithm| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-gapopen <Integer>
+  Cost to open a gap| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-gapextend <Integer>
+  Cost to extend a gap| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-matrix <String>
+  Scoring matrix name (normally BLOSUM62)| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-threshold <Real, >=0>
+  Minimum word score such that the word is added to the BLAST lookup
+  table| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-comp_based_stats <String>
+  Use composition-based statistics for blastp / tblastn:
+      D or d: default (equivalent to 2)
+      0 or F or f: no composition-based statistics
+      1: Composition-based statistics as in NAR 29:2994-3005, 2001
+      2 or T or t : Composition-based score adjustment as in
+      Bioinformatics 21:902-911, 2005, conditioned on sequence
+      properties
+      3: Composition-based score adjustment as in Bioinformatics
+      21:902-911, 2005, unconditionally
+  For programs other than tblastn, must either be absent or be D, F
+  or 0
+  Default = `2'| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-num_descriptions <Integer, >=0>
+  Number of database sequences to show one-line descriptions for
+  Default = `500'| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q| -num_alignments <Integer, >=0>
+  Number of database sequences to show alignments for
+  Default = `250'| %></pre>
+  </li>
+</ul>
+
+<br/>
+
+<h6>Query filtering options</h6>
+
+<br/>
+
+<ul class="unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-seg <String>
+  Filter query sequence with SEG (Format: 'yes', 'window locut hicut',
+  or 'no' to disable)
+  Default = `no'| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-soft_masking <Boolean>
+  Apply filtering locations as soft masks
+  Default = `false'| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-lcase_masking
+  Use lower case filtering in query and subject sequence(s)?| %></pre>
+  </li>
+</ul>
+
+<br/>
+
+<h6>Restrict search or results</h6>
+
+<br/>
+
+<ul class="unstyled">
+  <li>
+<pre><%= ERB::Util.h %q|-gilist <String>
+  Restrict search of database to list of GI's
+    * Incompatible with:  negative_gilist, seqidlist, remote, subject,
+  subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-seqidlist <String>
+  Restrict search of database to list of SeqId's
+    * Incompatible with:  gilist, negative_gilist, remote, subject,
+  subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-negative_gilist <String>
+  Restrict search of database to everything except the listed GIs
+    * Incompatible with:  gilist, seqidlist, remote, subject,
+      subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-entrez_query <String>
+  Restrict search with the given Entrez query
+    * Requires:  remote| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-db_soft_mask <String>
+  Filtering algorithm ID to apply to the BLAST database as soft masking
+    * Incompatible with:  subject, subject_loc| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-culling_limit <Integer, >=0>
+  If the query range of a hit is enveloped by that of at least this
+  many higher-scoring hits, delete the hit
+    * Incompatible with:  best_hit_overhang, best_hit_score_edge| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-best_hit_overhang <Real, (>0 and <0.5)>
+  Best Hit algorithm overhang value (recommended value: 0.1)
+    * Incompatible with:  culling_limit| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-best_hit_score_edge <Real, (>0 and <0.5)>
+  Best Hit algorithm score edge value (recommended value: 0.1)
+    * Incompatible with:  culling_limit| %></pre>
+  </li>
+  <li>
+<pre><%= ERB::Util.h %q|-max_target_seqs <Integer, >=1>
+  Maximum number of aligned sequences to keep| %></pre>
+  </li>
+</ul>