sequenceserver 1.1.0.beta2 → 1.1.0.beta3

data/spec/database/sample/proteins/uniprot/URL

@@ -0,0 +1 @@
+http://www.uniprot.org/uniprot/?query=taxonomy%3Ainsecta+reviewed%3Ayes&sort=score

data/spec/nucleotide_query.fa

@@ -0,0 +1,21 @@
+ATGAATACCCTCTGGCTCTCTTTATGGGATTATCCCGGTAAGCTTCCCTTAAACTTCATG
+GTGTTTGACACGAAGGATGATCTGCAAGCAGCGTATTGGAGAGATCCTTACAGCATACCT
+CTGGCAGTTATCTTCGAGGACCCCCAACCGATATCACAGCGACTTATATATGAAATTAGG
+ACGAATCCTTCATACACTTTGCCGCCACCGCCAACCAAATTGTATTCTGCTCCGATCAGT
+TGTCGAAAGAATAAAACTGGTCACTGGATGGACGACATTTTATCGATAAAAACCGGTGAA
+TCTTGTCCCGTTAACAATTACTTGCATTCTGGCTTCTTGGCTCTGCAAATGATAACGGAT
+ATCACAAAGATAAAATTGGAAAATTCTGACGTGACAATACCGGATATTAAACTCATAATG
+TTTCCTAAAGAGCCGTATACCGCTGACTGGATGCTGGCCTTCAGAGTTGTTATTCCGCTT
+TACATGGTCTTGGCTCTCTCGCAATTTATCACTTATCTTCTGATCCTAATAGTTGGCGAG
+AAGGAAAATAAGATTAAAGAGGGAATGAAGATGATGGGCTTAAATGATTCTGTGTTT
+>SI2.2.0_13722 Si_gnF.scaffold06207[1925625..1928536].pep_1
+ATGTCCGCGAATCGATTGAACGTGCTGGTGACCCTGATGCTCGCCGTCGCGCTTCTTGTG
+ACGGAATCAGGAAATGCACAGGTGGATGGCTATCTCCAATTCAACCCAAAGCGATCCGCC
+GTGAGCTCGCCGCAGAAGTATTGCGGCAAAAAGCTTTCTAATGCTCTACAGATAATCTGT
+GATGGCGTGTACAATTCCATGTTTAAGAAGAGTGGTCAAGATTTTCCCCCGCAAAATAAG
+AGACACATAGCACACAGAATAAATGGGAATGAGGAAGAGAGCTTTACTACGTTAAAGTCG
+AATTTTTTAAACTGGTGTGTTGAAGTTTATCATCGTCACTACAGATTCGTTTTTGTTTCA
+GAGATGGAAATGGCCGATTACCCGCTCGCCTATGATATTTCCCCGTATCTTCCGCCGTTC
+CTGTCGCGAGCGAGGGCACGGGGAATGTTAGACGGTCGCTTCGCCGGCAGACGCTACCGA
+AGGGAGTCGCGGGGCATTCACGAGGAGTGTTGCATCAACGGATGTACGATAAACGAATTG
+ACCAGCTACTGCGGCCCC

data/spec/protein_query.fa

@@ -0,0 +1,21 @@
+ATGAATACCCTCTGGCTCTCTTTATGGGATTATCCCGGTAAGCTTCCCTTAAACTTCATG
+GTGTTTGACACGAAGGATGATCTGCAAGCAGCGTATTGGAGAGATCCTTACAGCATACCT
+CTGGCAGTTATCTTCGAGGACCCCCAACCGATATCACAGCGACTTATATATGAAATTAGG
+ACGAATCCTTCATACACTTTGCCGCCACCGCCAACCAAATTGTATTCTGCTCCGATCAGT
+TGTCGAAAGAATAAAACTGGTCACTGGATGGACGACATTTTATCGATAAAAACCGGTGAA
+TCTTGTCCCGTTAACAATTACTTGCATTCTGGCTTCTTGGCTCTGCAAATGATAACGGAT
+ATCACAAAGATAAAATTGGAAAATTCTGACGTGACAATACCGGATATTAAACTCATAATG
+TTTCCTAAAGAGCCGTATACCGCTGACTGGATGCTGGCCTTCAGAGTTGTTATTCCGCTT
+TACATGGTCTTGGCTCTCTCGCAATTTATCACTTATCTTCTGATCCTAATAGTTGGCGAG
+AAGGAAAATAAGATTAAAGAGGGAATGAAGATGATGGGCTTAAATGATTCTGTGTTT
+>SI2.2.0_13722 Si_gnF.scaffold06207[1925625..1928536].pep_1
+ATGTCCGCGAATCGATTGAACGTGCTGGTGACCCTGATGCTCGCCGTCGCGCTTCTTGTG
+ACGGAATCAGGAAATGCACAGGTGGATGGCTATCTCCAATTCAACCCAAAGCGATCCGCC
+GTGAGCTCGCCGCAGAAGTATTGCGGCAAAAAGCTTTCTAATGCTCTACAGATAATCTGT
+GATGGCGTGTACAATTCCATGTTTAAGAAGAGTGGTCAAGATTTTCCCCCGCAAAATAAG
+AGACACATAGCACACAGAATAAATGGGAATGAGGAAGAGAGCTTTACTACGTTAAAGTCG
+AATTTTTTAAACTGGTGTGTTGAAGTTTATCATCGTCACTACAGATTCGTTTTTGTTTCA
+GAGATGGAAATGGCCGATTACCCGCTCGCCTATGATATTTCCCCGTATCTTCCGCCGTTC
+CTGTCGCGAGCGAGGGCACGGGGAATGTTAGACGGTCGCTTCGCCGGCAGACGCTACCGA
+AGGGAGTCGCGGGGCATTCACGAGGAGTGTTGCATCAACGGATGTACGATAAACGAATTG
+ACCAGCTACTGCGGCCCC

data/spec/routes_spec.rb

@@ -1,5 +1,7 @@
 require 'spec_helper'
 
+require 'rack/test'
+
 # Basic unit tests for HTTP / Rack interface.
 module SequenceServer
   describe 'Routes' do

data/spec/sample_reports/blastn_sample/job.yaml

@@ -2,6 +2,7 @@
 id: blastn_sample
 method: blastn
 advanced_params: {}
+exitstatus: 0
 
 databases:
 - !ruby/struct:SequenceServer::Database

data/spec/sample_reports/blastp_sample/job.yaml

@@ -2,6 +2,7 @@
 id: blastp_sample
 method: blastp
 advanced_params: {}
+exitstatus: 0
 
 databases:
 - !ruby/struct:SequenceServer::Database

data/spec/sample_reports/blastx_sample/job.yaml

@@ -2,6 +2,7 @@
 id: blastx_sample
 method: blastx
 advanced_params: {}
+exitstatus: 0
 
 databases:
 - !ruby/struct:SequenceServer::Database

data/spec/sample_reports/no_hits_sample/job.yaml

@@ -2,6 +2,7 @@
 id: no_hits_sample
 method: blastn
 advanced_params: {}
+exitstatus: 0
 
 databases:
 - !ruby/struct:SequenceServer::Database

data/spec/sample_reports/tblastn_sample/job.yaml

@@ -2,6 +2,7 @@
 id: tblastn_sample
 method: tblastn
 advanced_params: {}
+exitstatus: 0
 
 databases:
 - !ruby/struct:SequenceServer::Database

data/spec/sample_reports/tblastx_sample/job.yaml

@@ -2,6 +2,7 @@
 id: tblastx_sample
 method: tblastx
 advanced_params: {}
+exitstatus: 0
 
 databases:
 - !ruby/struct:SequenceServer::Database

data/spec/sample_reports/with_hits_sample/job.yaml

@@ -2,6 +2,7 @@
 id: with_hits_sample
 method: blastn
 advanced_params: {}
+exitstatus: 0
 
 databases:
 - !ruby/struct:SequenceServer::Database

data/spec/sequenceserver_spec.rb

@@ -83,7 +83,7 @@ module SequenceServer
     it 'has a list of databases after startup' do
       SequenceServer.init()
       # assuming database_dir is set to spec/database/sample
-      Database.all.length.should == 2
+      Database.all.length.should == 4
       Database.all.should_not be_empty
     end
   end

data/spec/spec_helper.rb

@@ -1,18 +1,4 @@
-require 'codeclimate-test-reporter'
-CodeClimate::TestReporter.start
+require 'simplecov'
+SimpleCov.start
 
 require 'sequenceserver'
-require 'rack/test'
-require 'rspec'
-
-begin
-  require 'capybara/rspec'
-  require 'selenium-webdriver'
-
-  RSpec.configure do |config|
-    config.include Capybara::DSL
-  end
-
-  $capybara_available = true
-rescue
-end

data/views/layout.erb

@@ -102,51 +102,6 @@
     </div> <!-- /container -->
   </div>
 
-  <div
-    id="error"
-    class="modal fade"
-    tabindex="-1">
-  </div> <!-- error -->
-
-  <div
-    class="modal fade" id="error-no-response">
-    <div
-      class="modal-dialog">
-      <div
-        class="modal-content">
-        <div
-          class="modal-header">
-          <h3>Server didn't respond</h3>
-        </div>
-
-        <div
-          class="modal-body">
-          <p>
-            Could be a temporary network issue, or the service might be
-            configured to "time out" long requests.
-          </p>
-
-          <p>
-            Please try again
-            later, or report to the admin or <a
-              href="https://groups.google.com/forum/?fromgroups#!forum/sequenceserver">SequenceServer
-              Google Group</a> (if you are the admin) if problem persists.
-          </p>
-        </div>
-
-        <div
-          class="modal-footer">
-          <button
-            type="button"
-            class="btn btn-danger"
-            data-dismiss="modal">
-            Okay
-          </button>
-        </div>
-      </div>
-    </div>
-  </div> <!-- error-no-response -->
-
   <div
     class="modal fade" id="help"
     tabindex="-1">

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: sequenceserver
 version: !ruby/object:Gem::Version
-  version: 1.1.0.beta2
+  version: 1.1.0.beta3
 platform: ruby
 authors:
 - Anurag Priyam
@@ -11,7 +11,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-03-30 00:00:00.000000000 Z
+date: 2018-04-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: sinatra
@@ -173,6 +173,26 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: 1.0.0
+- !ruby/object:Gem::Dependency
+  name: sauce_whisk
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.0.19
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.0.19
 - !ruby/object:Gem::Dependency
   name: selenium-webdriver
   requirement: !ruby/object:Gem::Requirement
@@ -199,20 +219,20 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.6'
+        version: '1.0'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.6.0
+        version: 1.0.8
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.6'
+        version: '1.0'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.6.0
+        version: 1.0.8
 description: |
   SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user
   interface for use locally or over the web.
@@ -244,9 +264,9 @@ files:
 - config.ru
 - docker/Dockerfile
 - lib/sequenceserver.rb
+- lib/sequenceserver/api_errors.rb
 - lib/sequenceserver/blast.rb
 - lib/sequenceserver/blast/constants.rb
-- lib/sequenceserver/blast/exceptions.rb
 - lib/sequenceserver/blast/formatter.rb
 - lib/sequenceserver/blast/hit.rb
 - lib/sequenceserver/blast/hsp.rb
@@ -292,6 +312,7 @@ files:
 - public/js/alignment_exporter.js
 - public/js/alignmentsoverview.js
 - public/js/circos.js
+- public/js/errormodal.js
 - public/js/exporter.js
 - public/js/grapher.js
 - public/js/kablammo.js
@@ -3674,6 +3695,15 @@ files:
 - spec/database/funky_sequences/funky_na_sequences.fa.nsd
 - spec/database/funky_sequences/funky_na_sequences.fa.nsi
 - spec/database/funky_sequences/funky_na_sequences.fa.nsq
+- spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nhd
+- spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nhi
+- spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nhr
+- spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nin
+- spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nog
+- spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nsd
+- spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nsi
+- spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nsq
+- spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.txt
 - spec/database/sample/links.rb
 - spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta
 - spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.phd
@@ -3684,6 +3714,15 @@ files:
 - spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psd
 - spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psi
 - spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psq
+- spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.phd
+- spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.phi
+- spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.phr
+- spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pin
+- spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pog
+- spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.psd
+- spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.psi
+- spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.psq
+- spec/database/sample/proteins/uniprot/URL
 - spec/database/sample/si_uniprot_idmap.yml
 - spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta
 - spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nhd
@@ -3702,27 +3741,27 @@ files:
 - spec/database_spec.rb
 - spec/doctor_spec.disabled.rb
 - spec/empty_config.yml
+- spec/nucleotide_query.fa
+- spec/protein_query.fa
 - spec/routes_spec.rb
 - spec/sample.conf
 - spec/sample_reports/blastn_sample/job.yaml
-- spec/sample_reports/blastn_sample/rfile
+- spec/sample_reports/blastn_sample/stdout
 - spec/sample_reports/blastp_sample/job.yaml
-- spec/sample_reports/blastp_sample/rfile
+- spec/sample_reports/blastp_sample/stdout
 - spec/sample_reports/blastx_sample/job.yaml
-- spec/sample_reports/blastx_sample/rfile
+- spec/sample_reports/blastx_sample/stdout
 - spec/sample_reports/no_hits_sample/job.yaml
-- spec/sample_reports/no_hits_sample/rfile
+- spec/sample_reports/no_hits_sample/stdout
 - spec/sample_reports/tblastn_sample/job.yaml
-- spec/sample_reports/tblastn_sample/rfile
+- spec/sample_reports/tblastn_sample/stdout
 - spec/sample_reports/tblastx_sample/job.yaml
-- spec/sample_reports/tblastx_sample/rfile
+- spec/sample_reports/tblastx_sample/stdout
 - spec/sample_reports/with_hits_sample/job.yaml
-- spec/sample_reports/with_hits_sample/rfile
+- spec/sample_reports/with_hits_sample/stdout
 - spec/sequence_spec.rb
 - spec/sequenceserver_spec.rb
 - spec/spec_helper.rb
-- views/400.erb
-- views/500.erb
 - views/_options.erb
 - views/layout.erb
 - views/report.erb

data/lib/sequenceserver/blast/exceptions.rb

@@ -1,27 +0,0 @@
-module SequenceServer
-  module BLAST
-    # To signal error in query sequence or options.
-    #
-    # ArgumentError is raised when BLAST+'s exit status is 1; see [1].
-    class ArgumentError < ArgumentError
-    end
-
-    # To signal internal errors.
-    #
-    # RuntimeError is raised when BLAST+'s exits status is one of 2, 3, 4, or
-    # 255; see [1].  These are rare, infrastructure errors, used internally,
-    # and of concern only to the admins/developers.
-    class RuntimeError < RuntimeError
-      def initialize(status, message)
-        @status  = status
-        @message = message
-      end
-
-      attr_reader :status, :message
-
-      def to_s
-        "#{status}, #{message}"
-      end
-    end
-  end
-end

data/views/400.erb

@@ -1,29 +0,0 @@
-<div
-  class="modal-dialog">
-  <div
-    class="modal-content">
-    <div
-      class="modal-header">
-      <h3>
-        Oops! Request Failed
-      </h3>
-    </div>
-
-    <div
-      class="modal-body">
-      <p>
-        <%= error.message %>
-      </p>
-    </div>
-
-    <div
-      class="modal-footer">
-      <button
-        type="button"
-        class="btn btn-default btn-danger"
-        data-dismiss="modal">
-        Close
-      </button>
-    </div>
-  </div>
-</div>

data/views/500.erb

@@ -1,41 +0,0 @@
-<div
-  class="modal-dialog modal-lg">
-  <div
-    class="modal-content">
-    <div
-      class="modal-header">
-      <h3>
-        Sorry BLAST failed
-      </h3>
-    </div>
-
-    <div
-      class="modal-body">
-      <p>
-      Sorry BLAST failed - please try again. If this message persists, there is
-      a problem with the server. In this case, please report the bug on our <a
-      href="https://groups.google.com/forum/?fromgroups#!forum/sequenceserver">
-      issue tracker</a>?
-
-<pre class="pre-scrollable">
-  <%=
-    ["#{error.class} - #{error.message}:", *error.backtrace].map do |line|
-      ERB::Util.h line
-    end.join("\n")
-  %>
-</pre>
-
-      </p>
-    </div>
-
-    <div
-      class="modal-footer">
-      <button
-        type="button"
-        class="btn btn-danger"
-        data-dismiss="modal">
-        Done
-      </button>
-    </div>
-  </div>
-</div>