sequenceserver 1.1.0.beta → 1.1.0.beta2

data/sequenceserver.gemspec

@@ -19,17 +19,17 @@ DESC
   # dependencies
   s.required_ruby_version = '>= 2.3.0'
 
-  s.add_dependency('sinatra',   '~> 1.4',  '>= 1.4.5')
+  s.add_dependency('sinatra',   '~> 2.0',  '>= 2.0.0')
   s.add_dependency('json_pure', '~> 1.8',  '>= 1.8.2')
   s.add_dependency('ox',        '~> 2.1',  '>= 2.1.1')
   s.add_dependency('slop',      '~> 3.6',  '>= 3.6.0')
 
   s.add_development_dependency('rake', '~> 10.3', '>= 10.3.2')
-  s.add_development_dependency('rspec', '~> 2.8',  '>= 2.8.0')
-  s.add_development_dependency('capybara', '~> 2.4',  '>= 2.4.4')
-  s.add_development_dependency('rack-test', '~> 0.6',  '>= 0.6.2')
+  s.add_development_dependency('rspec', '~> 3.7',  '>= 3.7.0')
+  s.add_development_dependency('capybara', '~> 2.18',  '>= 2.18.0')
+  s.add_development_dependency('rack-test', '~> 1.0',  '>= 1.0.0')
   s.add_development_dependency('selenium-webdriver', '~> 3.11', '>= 3.11.0')
-  s.add_development_dependency('codeclimate-test-reporter', '~> 0.4', '>= 0.4.7')
+  s.add_development_dependency('codeclimate-test-reporter', '~> 0.6', '>= 0.6.0')
 
   # gem
   s.files         = `git ls-files`.split("\n") - ['Gemfile', 'Gemfile.lock']

data/spec/capybara_spec.rb

@@ -15,12 +15,12 @@ describe 'a browser', :js => true do
 
   it 'runs a simple blastn search' do
     visit '/'
-    fill_in('sequence', :with => sequence)
+    fill_in('sequence', with: sequence, wait: 5)
     check(sample_nucl_db)
     click_button('method')
     # switch to new window because link opens in new window
     page.driver.browser.switch_to.window(page.driver.browser.window_handles.last)
-    page.should have_content('Query')
+    page.should have_content('Query', wait: 5)
   end
 
   it 'properly controls blast button' do
@@ -37,7 +37,7 @@ describe 'a browser', :js => true do
     visit '/'
     fill_in('sequence', :with => sequence)
     check(sample_nucl_db)
-    page.evaluate_script("$('.protein .checkbox').first().hasClass('disabled')")
+    page.evaluate_script("$('.protein .database').first().hasClass('disabled')")
       .should eq(true)
   end
 

data/spec/sequence_spec.rb

@@ -66,9 +66,9 @@ module SequenceServer
 
       sequences.length.should eq 1
       sequences.first.gi.should be_nil
-      sequences.first.seqid.should eq 'lcl|SI2.2.0_06267'
+      sequences.first.seqid.should eq 'SI2.2.0_06267'
       sequences.first.accession.should eq 'SI2.2.0_06267'
-      sequences.first.id.should eq 'lcl|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 == "\

data/views/layout.erb

@@ -61,8 +61,7 @@
     </noscript>
   </div>
 
-  <input type="hidden" id="input_sequence" value="<%= @input_sequence %>">
-  <div id="view"></div>
+  <%= yield %>
 
   <div
     class="footer" id="footer">
@@ -176,17 +175,6 @@
     </div>
   </div> <!-- advanced options -->
 
-  <!-- JS -->
-  <% if settings.production? %>
-    <script src="sequenceserver.min.js"></script>
-  <% else %>
-    <script src="vendor/system.js"></script>
-    <script src="config.js"></script>
-    <script>
-      System.import('js/sequenceserver.js')
-    </script>
-  <% end %>
-
   <!-- twitter -->
   <script>!function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0];if(!d.getElementById(id)){js=d.createElement(s);js.id=id;js.src="//platform.twitter.com/widgets.js";fjs.parentNode.insertBefore(js,fjs);}}(document,"script","twitter-wjs");</script>
 </body>

data/views/report.erb

@@ -0,0 +1,13 @@
+<!-- We will initialise React on this div -->
+<div id="view"></div>
+
+<!-- JS -->
+<% if settings.production? %>
+  <script src="sequenceserver-report.min.js"></script>
+<% else %>
+  <script src="vendor/system.js"></script>
+  <script src="config.js"></script>
+  <script>
+    System.import('js/report.js')
+  </script>
+<% end %>

data/views/search.erb

@@ -0,0 +1,45 @@
+<!-- Optional hidden query sequence sent by the server -->
+<input type="hidden" id="input_sequence" value="<%= @input_sequence %>">
+
+<!-- We will initialise React on this div -->
+<div id="view"></div>
+
+<!-- JS -->
+<% if settings.production? %>
+  <script src="sequenceserver-search.min.js"></script>
+<% else %>
+  <script src="vendor/system.js"></script>
+  <script src="config.js"></script>
+  <script>
+    System.import('js/search.js')
+  </script>
+<% end %>
+
+<!-- Markup for advanced options modal -->
+<div
+  class="modal fade" id="help"
+  tabindex="-1">
+  <div
+    class="modal-dialog modal-lg">
+    <div
+      class="modal-content">
+      <div
+        class="modal-header">
+        <h3>Advanced Options</h3>
+      </div>
+      <div
+        class="modal-body">
+        <%= erb :_options %>
+      </div>
+      <div
+        class="modal-footer">
+        <button
+          type="button"
+          class="btn btn-default btn-primary"
+          data-dismiss="modal">
+          Got it!
+        </button>
+      </div>
+    </div>
+  </div>
+</div>

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: sequenceserver
 version: !ruby/object:Gem::Version
-  version: 1.1.0.beta
+  version: 1.1.0.beta2
 platform: ruby
 authors:
 - Anurag Priyam
@@ -11,7 +11,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-03-21 00:00:00.000000000 Z
+date: 2018-03-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: sinatra
@@ -19,20 +19,20 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.4'
+        version: '2.0'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.4.5
+        version: 2.0.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.4'
+        version: '2.0'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.4.5
+        version: 2.0.0
 - !ruby/object:Gem::Dependency
   name: json_pure
   requirement: !ruby/object:Gem::Requirement
@@ -119,60 +119,60 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.8'
+        version: '3.7'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 2.8.0
+        version: 3.7.0
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.8'
+        version: '3.7'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 2.8.0
+        version: 3.7.0
 - !ruby/object:Gem::Dependency
   name: capybara
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.4'
+        version: '2.18'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 2.4.4
+        version: 2.18.0
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.4'
+        version: '2.18'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 2.4.4
+        version: 2.18.0
 - !ruby/object:Gem::Dependency
   name: rack-test
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.6'
+        version: '1.0'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.6.2
+        version: 1.0.0
   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: 0.6.2
+        version: 1.0.0
 - !ruby/object:Gem::Dependency
   name: selenium-webdriver
   requirement: !ruby/object:Gem::Requirement
@@ -199,20 +199,20 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.4'
+        version: '0.6'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.4.7
+        version: 0.6.0
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.4'
+        version: '0.6'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.4.7
+        version: 0.6.0
 description: |
   SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user
   interface for use locally or over the web.
@@ -273,7 +273,6 @@ files:
 - public/css/grapher.css
 - public/css/sequenceserver.css
 - public/css/sequenceserver.min.css
-- public/css/sequenceserver.min.css.gz
 - public/fonts/FontAwesome.otf
 - public/fonts/Source_Sans_Pro_400.eot
 - public/fonts/Source_Sans_Pro_400.svg
@@ -304,8 +303,8 @@ files:
 - public/js/sequenceserver.js
 - public/js/svgExporter.js
 - public/js/visualisation_helpers.js
-- public/sequenceserver.min.js
-- public/sequenceserver.min.js.gz
+- public/sequenceserver-report.min.js
+- public/sequenceserver-search.min.js
 - public/shims
 - public/vendor/.dependencies.json
 - public/vendor/.loaderversions
@@ -2651,11 +2650,6 @@ files:
 - public/vendor/npm/jstransform@10.1.0/visitors/reserved-words-helper.js
 - public/vendor/npm/jstransform@10.1.0/visitors/reserved-words-visitors.js
 - public/vendor/npm/jstransform@10.1.0/visitors/type-syntax.js
-- public/vendor/npm/object-assign@2.1.1.js
-- public/vendor/npm/object-assign@2.1.1/.jspm-hash
-- public/vendor/npm/object-assign@2.1.1/.jspm.json
-- public/vendor/npm/object-assign@2.1.1/index.js
-- public/vendor/npm/object-assign@2.1.1/package.json
 - public/vendor/npm/path-browserify@0.0.0.js
 - public/vendor/npm/path-browserify@0.0.0/.jspm-hash
 - public/vendor/npm/path-browserify@0.0.0/.jspm.json
@@ -2670,70 +2664,8 @@ files:
 - public/vendor/npm/process@0.10.1/browser.js
 - public/vendor/npm/process@0.10.1/index.js
 - public/vendor/npm/process@0.10.1/package.json
-- public/vendor/npm/qs@2.4.1.js
-- public/vendor/npm/qs@2.4.1/.jshintignore
-- public/vendor/npm/qs@2.4.1/.jshintrc
-- public/vendor/npm/qs@2.4.1/.jspm-hash
-- public/vendor/npm/qs@2.4.1/.jspm.json
-- public/vendor/npm/qs@2.4.1/.npmignore
-- public/vendor/npm/qs@2.4.1/.travis.yml
-- public/vendor/npm/qs@2.4.1/CHANGELOG.md
-- public/vendor/npm/qs@2.4.1/CONTRIBUTING.md
-- public/vendor/npm/qs@2.4.1/LICENSE
-- public/vendor/npm/qs@2.4.1/Makefile
-- public/vendor/npm/qs@2.4.1/README.md
-- public/vendor/npm/qs@2.4.1/index.js
-- public/vendor/npm/qs@2.4.1/lib.js
-- public/vendor/npm/qs@2.4.1/lib/index.js
-- public/vendor/npm/qs@2.4.1/lib/parse.js
-- public/vendor/npm/qs@2.4.1/lib/stringify.js
-- public/vendor/npm/qs@2.4.1/lib/utils.js
-- public/vendor/npm/qs@2.4.1/package.json
-- public/vendor/npm/qs@2.4.1/test/parse.js
 - public/vendor/npm/qs@2.4.1/test/stringify.js
 - public/vendor/npm/react-router@0.13.3.js
-- public/vendor/npm/react-router@0.13.3/.jspm-hash
-- public/vendor/npm/react-router@0.13.3/.jspm.json
-- public/vendor/npm/react-router@0.13.3/README.md
-- public/vendor/npm/react-router@0.13.3/lib.js
-- public/vendor/npm/react-router@0.13.3/lib/Cancellation.js
-- public/vendor/npm/react-router@0.13.3/lib/History.js
-- public/vendor/npm/react-router@0.13.3/lib/Match.js
-- public/vendor/npm/react-router@0.13.3/lib/Navigation.js
-- public/vendor/npm/react-router@0.13.3/lib/PathUtils.js
-- public/vendor/npm/react-router@0.13.3/lib/PropTypes.js
-- public/vendor/npm/react-router@0.13.3/lib/Redirect.js
-- public/vendor/npm/react-router@0.13.3/lib/Route.js
-- public/vendor/npm/react-router@0.13.3/lib/ScrollHistory.js
-- public/vendor/npm/react-router@0.13.3/lib/State.js
-- public/vendor/npm/react-router@0.13.3/lib/TestUtils.js
-- public/vendor/npm/react-router@0.13.3/lib/Transition.js
-- public/vendor/npm/react-router@0.13.3/lib/actions/LocationActions.js
-- public/vendor/npm/react-router@0.13.3/lib/behaviors/ImitateBrowserBehavior.js
-- public/vendor/npm/react-router@0.13.3/lib/behaviors/ScrollToTopBehavior.js
-- public/vendor/npm/react-router@0.13.3/lib/components/ActiveHandler.js
-- public/vendor/npm/react-router@0.13.3/lib/components/ContextWrapper.js
-- public/vendor/npm/react-router@0.13.3/lib/components/DefaultRoute.js
-- public/vendor/npm/react-router@0.13.3/lib/components/Link.js
-- public/vendor/npm/react-router@0.13.3/lib/components/NotFoundRoute.js
-- public/vendor/npm/react-router@0.13.3/lib/components/Redirect.js
-- public/vendor/npm/react-router@0.13.3/lib/components/Route.js
-- public/vendor/npm/react-router@0.13.3/lib/components/RouteHandler.js
-- public/vendor/npm/react-router@0.13.3/lib/createRouter.js
-- public/vendor/npm/react-router@0.13.3/lib/createRoutesFromReactChildren.js
-- public/vendor/npm/react-router@0.13.3/lib/getWindowScrollPosition.js
-- public/vendor/npm/react-router@0.13.3/lib/index.js
-- public/vendor/npm/react-router@0.13.3/lib/isReactChildren.js
-- public/vendor/npm/react-router@0.13.3/lib/locations/HashLocation.js
-- public/vendor/npm/react-router@0.13.3/lib/locations/HistoryLocation.js
-- public/vendor/npm/react-router@0.13.3/lib/locations/RefreshLocation.js
-- public/vendor/npm/react-router@0.13.3/lib/locations/StaticLocation.js
-- public/vendor/npm/react-router@0.13.3/lib/locations/TestLocation.js
-- public/vendor/npm/react-router@0.13.3/lib/runRouter.js
-- public/vendor/npm/react-router@0.13.3/lib/supportsHistory.js
-- public/vendor/npm/react-router@0.13.3/package.json
-- public/vendor/npm/react-router@0.13.3/umd/ReactRouter.js
-- public/vendor/npm/react-router@0.13.3/umd/ReactRouter.min.js
 - public/vendor/npm/react@0.13.3.js
 - public/vendor/npm/react@0.13.3/.jspm-hash
 - public/vendor/npm/react@0.13.3/.jspm.json
@@ -3793,6 +3725,8 @@ files:
 - views/500.erb
 - views/_options.erb
 - views/layout.erb
+- views/report.erb
+- views/search.erb
 homepage: http://sequenceserver.com
 licenses:
 - AGPL-3.0