sequenceserver 1.0.0.pre.5 → 1.0.0

data/spec/sequence_spec.rb

@@ -0,0 +1,100 @@
+require 'spec_helper'
+require 'sequenceserver/sequence'
+require 'digest/md5'
+
+# Test Sequence class.
+module SequenceServer
+  describe 'Sequence type detection' do
+    it 'should be able to detect nucleotide sequences' do
+      sequences = [
+        'AAAAAAAAAAAAAAAAAAAAAT',
+        '           CAGATGCRRCAAAGCAAACGGCAA 34523453 652352',
+        'ACCNNNNNNXXXXCAUUUUUU',
+        "ACGT\n\t\t\nACCACGGACCACGAAAGCG"
+      ]
+      sequences.each do |sequence|
+        Sequence.guess_type(sequence).should == :nucleotide
+      end
+    end
+
+    it 'should be able to detect protein sequences' do
+      sequences = [
+        'ADSACGHKSJLFCVMGTL',
+        '  345   KSSYPHYSPPPPHS      345 23453 652352',
+        'GEYSNLNNNNNNXXXXSSSSSSSSSSSSSSSSSSSSSSS',
+        "EE\n\t\t\n         \t\t\EEQRRQQSARTSRRQR"
+      ]
+      sequences.each do |sequence|
+        Sequence.guess_type(sequence).should == :protein
+      end
+    end
+
+    it 'should be able to say sequence type detection impossible' do
+      Sequence.guess_type('ACSFGT').should be_nil
+    end
+
+    it 'should be able to tell composition of a sequence string' do
+      Sequence.composition('asdfasdfffffAsdf').should == { 'a' => 2, 'd' => 3,
+                                                           'f' => 7, 's' => 3,
+                                                           'A' => 1 }
+    end
+  end
+
+  describe 'Sequence retrieval' do
+    root = SequenceServer.root
+    database_dir = File.join(root, 'spec', 'database')
+
+    let 'a_normal_database_id' do
+      Digest::MD5.hexdigest File.join(database_dir, 'sample', 'proteins',
+                                      'Solenopsis_invicta',
+                                      'Sinvicta2-2-3.prot.subset.fasta')
+    end
+
+    let 'funky_ids_database_id' do
+      Digest::MD5.hexdigest File.join(database_dir, 'funky_ids',
+                                      'funky_ids.fa')
+    end
+
+    before :all do
+      SequenceServer.config[:database_dir] = database_dir
+      Database.scan_databases_dir
+    end
+
+    it 'should be able to retrieve sequences from database' do
+      sequences = Sequence::Retriever.new('SI2.2.0_06267',
+                                          a_normal_database_id).sequences
+
+      sequences.length.should eq 1
+      sequences.first.gi.should be_nil
+      sequences.first.seqid.should eq 'SI2.2.0_06267'
+      sequences.first.id.should eq 'SI2.2.0_06267'
+      sequences.first.title.should eq 'locus=Si_gnF.scaffold02592'\
+                                      '[1282609..1284114].pep_2 quality=100.00'
+      sequences.first.value.should == "\
+MNTLWLSLWDYPGKLPLNFMVFDTKDDLQAAYWRDPYSIPLAVIFEDPQPISQRLIYEIRTNPSYTLPPPPTKLYSAPI\
+SCRKNKTGHWMDDILSIKTGESCPVNNYLHSGFLALQMITDITKIKLENSDVTIPDIKLIMFPKEPYTADWMLAFRVVI\
+PLYMVLALSQFITYLLILIVGEKENKIKEGMKMMGLNDSVF"
+    end
+
+    it 'should be able to retrieve more than one sequence from a database' do
+      sequences = Sequence::Retriever.new(['SI2.2.0_06267', 'SI2.2.0_13722'],
+                                          a_normal_database_id).sequences
+      sequences.length.should == 2
+    end
+
+    # it 'should be able to retrieve sequences from database even if accession'\
+    #    'contains only numbers' do
+    #   Database.scan_databases_dir
+    #   sequences = Sequence.from_blastdb(123456, funky_ids_database_id)
+    #   sequences.length.should == 1
+    # end
+
+    it 'should be able to retrieve sequences from database for all kinds of'\
+       'funky accessions' do
+      funky_accessions = ['abcdef#', 'abc#def', '123#456'] # , '123456#']
+      sequences = Sequence::Retriever.new(funky_accessions,
+                                          funky_ids_database_id).sequences
+      sequences.length.should == 3
+    end
+  end
+end

data/spec/sequenceserver_spec.rb

@@ -0,0 +1,108 @@
+require 'spec_helper'
+
+# Test the main module, startup process, etc.
+module SequenceServer
+  # NOTE:
+  #   Testing SequenceServer's initialization can be a bit tricky. For
+  #   instance, to test num_threads, correct database_dir must be set.
+  describe 'SequenceServer' do
+    let 'root' do
+      SequenceServer.root
+    end
+
+    let 'empty_config' do
+      File.join(root, 'spec', 'empty_config.yml')
+    end
+
+    let 'database_dir' do
+      File.join(root, 'spec', 'database')
+    end
+
+    let 'database_dir_no_db' do
+      File.join(root, 'spec', 'database', 'unformatted',
+                'Cardiocondyla_obscurior')
+    end
+
+    let 'config' do
+      { :config_file  => empty_config }
+    end
+
+    # bin, if set, should be a _directory_ that exists
+    it 'raises appropriate error if bin incorrectly set' do
+      # Raise if bin dir does not exist.
+      expect do
+        SequenceServer.init(config.update :bin => '/foo/bar')
+      end.to raise_error(BIN_DIR_NOT_FOUND)
+
+      # Raise if bin dir is not a directory.
+      expect do
+        SequenceServer.init(config.update :bin => __FILE__)
+      end.to raise_error(BIN_DIR_NOT_FOUND)
+    end
+
+    # database_dir is compulsory
+    it 'raises appropriate error if database_dir not set' do
+      expect do
+        SequenceServer.init(config.update :config_file => empty_config)
+      end.to raise_error(DATABASE_DIR_NOT_SET)
+    end
+
+    # database_dir, when set, should be a _directory_ that exists.
+    it 'raises appropriate error if database_dir incorrectly set' do
+      # Raise if database_dir does not exist.
+      expect do
+        SequenceServer.init(config.update :database_dir => '/foo/bar')
+      end.to raise_error(DATABASE_DIR_NOT_FOUND)
+
+      # Raise if database_dir is not a directory.
+      expect do
+        SequenceServer.init(config.update :database_dir => __FILE__)
+      end.to raise_error(DATABASE_DIR_NOT_FOUND)
+    end
+
+    # database_dir, when correctly set, should contain at least one BLAST+
+    # database.
+    it "raises appropriate error if database_dir doesn't contain any BLAST+"\
+       'database' do
+      expect do
+        SequenceServer.init(config.update :database_dir => database_dir_no_db)
+      end.to raise_error(NO_BLAST_DATABASE_FOUND)
+    end
+
+    # num_threads, if set, should a number not less than 1.
+    it 'raises appropriate error if num_threads incorrectly set' do
+      # Raise if not a number.
+      expect do
+        SequenceServer.init(config.update :database_dir => database_dir,
+                                          :num_threads  => 'foo')
+      end.to raise_error(NUM_THREADS_INCORRECT)
+
+      # Raise if less than 1.
+      expect do
+        SequenceServer.init(config.update :database_dir => database_dir,
+                                          :num_threads  => 0)
+      end.to raise_error(NUM_THREADS_INCORRECT)
+    end
+
+    # extension file, if set, should be a _file_ that exists.
+    it 'raises appropriate error if require incorrectly set' do
+      # Raise if not found.
+      expect do
+        SequenceServer.init(config.update :database_dir => database_dir,
+                                          :require      => 'foo/bar')
+      end.to raise_error(EXTENSION_FILE_NOT_FOUND)
+
+      # Raise if directory.
+      expect do
+        SequenceServer.init(config.update :database_dir => database_dir,
+                                          :require => File.dirname(__FILE__))
+      end.to raise_error(EXTENSION_FILE_NOT_FOUND)
+    end
+
+    it 'has a list of databases after startup' do
+      SequenceServer.init(config.update :database_dir => database_dir)
+      Database.all.should_not be_empty
+      Database.all.length.should == 4
+    end
+  end
+end

data/spec/spec_helper.rb

@@ -0,0 +1,11 @@
+require 'codeclimate-test-reporter'
+CodeClimate::TestReporter.start
+
+require 'sequenceserver'
+require 'rack/test'
+require 'rspec'
+require 'capybara/rspec'
+
+RSpec.configure do |config|
+  config.include Capybara::DSL
+end

data/views/result.erb

@@ -82,42 +82,64 @@
                 <div
                   class="page-content collapse in"
                   id="<%="Query_#{query.number}_hit_#{hit.number}_alignment"%>">
-                  <p>
-                    Hit length: <%= hit.length %>, Number of HSP(s): <%= hit.hsps.length %>
-                  </p>
-                  <% hit.hsps.each do |hsp| %>
+                  <div
+                    class="row">
                     <div
-                      class="hsps" id="<%="Query_#{query.number}_hit_#{hit.number}_#{hsp.number}"%>"
-                      data-hsp-evalue="<%= hsp.evalue %>" data-hsp-start="<%= hsp.qstart %>"
-                      data-hsp-end="<%= hsp.qend %>" data-hsp-frame="<%= hsp.sframe %>">
-                      <table
-                        class="table table-condensed hsp-stats">
-                        <thead>
-                          <% hsp.stats.keys.each do |key| %>
-                            <th> <%= key %> </th>
-                          <% end %>
-                        </thead>
-                        <tbody>
-                          <tr>
-                            <% hsp.stats.values.each do |value| %>
-                              <td> <%= prettify value %> </th>
-                            <% end %>
-                          </tr>
-                        </tbody>
-                      </table>
-                      <div class="alignment"><%= hsp.pp %></div>
+                      class="col-md-4">
+                      Hit length: <%= hit.length %>
+                    </div>
+                    <div
+                      class="hit-links text-right col-md-8">
+                      <label>
+                        <input
+                        type="checkbox" value="<%= hit.accession %>" data-target="<%= "#Query_#{query.number}_hit_#{hit.number}" %>">
+                        Select
+                      </label>
+                      <% hit.links.each do |link| %>
+                        | <%= a link %>
+                      <% end %>
                     </div>
-                  <% end %>
-                  <div class="hit-links text-right">
-                    <label>
-                      <input
-                      type="checkbox" value="<%= hit.accession %>" data-target="<%= "#Query_#{query.number}_hit_#{hit.number}" %>">
-                      Select
-                    </label>
-                    <% hit.links.each do |link| %>
-                      | <%= a link %>
-                    <% end %>
                   </div>
+                  <table
+                    class="table hsps">
+                    <tbody>
+                      <% hit.hsps.each do |hsp| %>
+                        <tr>
+                          <td>
+                            <%= hsp.number %>.
+                          </td>
+                          <td
+                            style="width: 100%;">
+                            <div
+                              class="hsp" id="<%="Query_#{query.number}_hit_#{hit.number}_#{hsp.number}"%>"
+                              data-hsp-evalue="<%= hsp.evalue %>" data-hsp-start="<%= hsp.qstart %>"
+                              data-hsp-end="<%= hsp.qend %>" data-hsp-frame="<%= hsp.sframe %>">
+                              <table
+                                class="table table-condensed hsp-stats">
+                                <thead>
+                                  <% hsp.stats.keys.each do |key| %>
+                                    <th>
+                                      <%= key %>
+                                    </th>
+                                  <% end %>
+                                </thead>
+                                <tbody>
+                                  <tr>
+                                    <% hsp.stats.values.each do |value| %>
+                                      <td>
+                                        <%= prettify value %>
+                                      </th>
+                                    <% end %>
+                                  </tr>
+                                </tbody>
+                              </table>
+                              <div class="alignment"><%= hsp.pp %></div>
+                            </div>
+                          </td>
+                        </tr>
+                      <% end %>
+                    </tbody>
+                  </table>
                 </div>
               </div>
             <% end %>

data/views/search.erb

@@ -79,7 +79,7 @@
           <div
             class="dnd-errors">
             <div
-              class="dnd-error"
+              class="dnd-error row"
               id="dnd-multi-notification"
               style="display: none;">
               <div
@@ -89,7 +89,7 @@
             </div>
 
             <div
-              class="dnd-error"
+              class="dnd-error row"
               id="dnd-large-file-notification"
               style="display: none;">
               <div
@@ -99,7 +99,7 @@
             </div>
 
             <div
-              class="dnd-error"
+              class="dnd-error row"
               id="dnd-format-notification"
               style="display: none;">
               <div
@@ -148,7 +148,7 @@
             <textarea
               class="form-control text-monospace" name="sequence" id="sequence"
               rows="10"
-              autofocus="true"
+              autofocus
               spellcheck="false"
               placeholder="Paste query sequence(s) or drag file containing query sequence(s) in FASTA format here ..." ></textarea>
           </div>
@@ -158,7 +158,7 @@
       <div
         class="notifications">
         <div
-          class="notification"
+          class="notification row"
           id="nucleotide-sequence-notification"
           style="display: none;">
           <div
@@ -168,7 +168,7 @@
         </div>
 
         <div
-          class="notification"
+          class="notification row"
           id="protein-sequence-notification"
           style="display: none;">
           <div
@@ -178,7 +178,7 @@
         </div>
 
         <div
-          class="notification"
+          class="notification row"
           id="mixed-sequence-notification"
           style="display: none;">
           <div
@@ -225,38 +225,43 @@
         <div
           class="col-md-8">
           <div
-            class="form-group advanced">
-            <label
-              class="col-md-3 control-label"
-              for="advanced">
-              Advanced Parameters:
-            </label>
+            class="form-group">
             <div
-              class="col-md-9">
+              class="col-md-12">
               <div
                 class="input-group">
+                <label
+                  class="control-label cursor-pointer"
+                  for="advanced">
+                  Advanced Parameters:
+                </label>
                 <input
                   type="text"
                   class="form-control" name="advanced" id="advanced"
                   title="View, and enter advanced parameters."
                   placeholder="eg: -evalue 1.0e-5 -num_alignments 100"/>
-                  <div class="input-group-addon cursor-pointer" data-toggle="modal" data-toggle="modal" data-target="#help">
+                  <div class="input-group-addon cursor-pointer" data-toggle="modal" data-target="#help">
                     <i class="fa fa-question"></i>
                   </div>
               </div>
             </div>
           </div>
         </div>
-
         <div
           class="col-md-4">
           <div
-            class="btn-group btn-block" id="methods">
-            <button
-              type="submit"
-              id="method" class="btn btn-primary col-md-12">
-              blast
-            </button>
+            class="form-group">
+            <div
+              class="col-md-12">
+              <div
+                id="methods">
+                <button
+                  type="submit"
+                  id="method" class="btn btn-primary form-control">
+                  blast
+                </button>
+              </div>
+            </div>
           </div>
         </div>
       </div>
@@ -295,7 +300,7 @@
       <br>
       Please Cite:
       <a href='http://www.sequenceserver.com'>
-        Priyam, Woodcroft, Rai & Wurm, <strong>SequenceServer</strong> (<em>in prep</em>)</a>
+        Priyam, Woodcroft, Rai & Wurm, <strong>SequenceServer</strong> (<em>in prep</em>)
       </a>
       &amp; relevant data sources.
     </p>