sequenceserver 3.0.1 → 3.1.1

data/lib/sequenceserver/routes.rb

@@ -5,9 +5,11 @@ require 'rest-client'
 
 require 'sequenceserver/job'
 require 'sequenceserver/blast'
+require 'sequenceserver/blast/tasks'
 require 'sequenceserver/report'
 require 'sequenceserver/database'
 require 'sequenceserver/sequence'
+require 'rack/csrf'
 
 module SequenceServer
   # Controller.
@@ -32,6 +34,8 @@ module SequenceServer
       # Override in config.ru if the instance is served under a subpath
       # e.g. for example.org/our-sequenceserver set to '/our-sequenceserver'
       set :root_path_prefix, ''
+
+      set :search_layout, :'search_layout'
     end
 
     # See
@@ -55,6 +59,14 @@ module SequenceServer
         frame_options = SequenceServer.config[:frame_options]
         frame_options && { frame_options: frame_options }
       }
+
+      use(
+        Rack::Session::Cookie,
+        key: 'rack.session.sequenceserver',
+        secret: ENV.fetch('SESSION_SECRET') { SecureRandom.alphanumeric(64) }
+      )
+
+      use Rack::Csrf, raise: true, skip: ['POST:/cloud_share']
     end
 
     unless ENV['SEQUENCE_SERVER_COMPRESS_RESPONSES'] == 'false'
@@ -74,7 +86,7 @@ module SequenceServer
 
     # Returns base HTML. Rest happens client-side: rendering the search form.
     get '/' do
-      erb :search, layout: true
+      erb :search, layout: settings.search_layout
     end
 
     # Returns data that is used to render the search form client side. These
@@ -83,7 +95,8 @@ module SequenceServer
       searchdata = {
         query: Database.retrieve(params[:query]),
         database: Database.all,
-        options: SequenceServer.config[:options]
+        options: SequenceServer.config[:options],
+        blastTaskMap: SequenceServer::BLAST::Tasks.to_h
       }
 
       searchdata.update(tree: Database.tree) if SequenceServer.config[:databases_widget] == 'tree'
@@ -100,7 +113,7 @@ module SequenceServer
     post '/' do
       if params[:input_sequence]
         @input_sequence = params[:input_sequence]
-        erb :search, layout: true
+        erb :search, layout: settings.search_layout
       else
         job = Job.create(params)
         redirect to("/#{job.id}")
@@ -114,24 +127,11 @@ module SequenceServer
       halt 404, { error: 'Job not found' }.to_json if job.nil?
       halt 202 unless job.done?
 
-      report = Report.generate(job)
+      report = BLAST::Report.new(job)
       halt 202 unless report.done?
 
-      display_large_result_warning =
-        SequenceServer.config[:large_result_warning_threshold].to_i.positive? &&
-        params[:bypass_file_size_warning] != 'true' &&
-        report.xml_file_size > SequenceServer.config[:large_result_warning_threshold]
-
-      if display_large_result_warning
-        halt 200,
-             {
-               user_warning: 'LARGE_RESULT',
-               download_links: [
-                 { name: 'Standard Tabular Report', url: "download/#{jid}.std_tsv" },
-                 { name: 'Full Tabular Report', url: "/download/#{jid}.full_tsv" },
-                 { name: 'Results in XML', url: "/download/#{jid}.xml" }
-               ]
-             }.to_json
+      if display_large_result_warning?(report.xml_file_size)
+        halt 200, large_result_warning_payload(jid).to_json
       end
 
       report.to_json
@@ -156,15 +156,35 @@ module SequenceServer
     # in identifiers) and retreival_databases (we don't allow whitespace in a
     # database's name, so it's safe).
     get '/get_sequence/' do
-      sequence_ids = params[:sequence_ids].split(',')
-      database_ids = params[:database_ids].split(',')
+      sequence_ids = params[:sequence_ids].to_s.split(',')
+      database_ids = params[:database_ids].to_s.split(',')
+      if sequence_ids.empty?
+        status 422
+        return { error: 'No sequence ids provided' }.to_json
+      end
+
+      if database_ids.empty?
+        status 422
+        return { error: 'No database ids provided' }.to_json
+      end
       sequences = Sequence::Retriever.new(sequence_ids, database_ids)
       sequences.to_json
     end
 
     post '/get_sequence' do
-      sequence_ids = params['sequence_ids'].split(',')
-      database_ids = params['database_ids'].split(',')
+      sequence_ids = params['sequence_ids'].to_s.split(',')
+      database_ids = params['database_ids'].to_s.split(',')
+
+      if sequence_ids.empty?
+        status 422
+        return 'No sequence ids provided'
+      end
+
+      if database_ids.empty?
+        status 422
+        return 'No database ids provided'
+      end
+
       sequences = Sequence::Retriever.new(sequence_ids, database_ids, true)
       send_file(sequences.file.path,
                 type: sequences.mime,
@@ -307,12 +327,33 @@ module SequenceServer
       # the user hits the back button. Thus we do not test for empty string.
       method = job.method.to_sym
       if job.advanced && job.advanced !=
-                         searchdata[:options][method][:default].join(' ')
+                         searchdata.dig(:options, method, :default, :attributes).to_a.join(' ')
         searchdata[:options] = searchdata[:options].deep_copy
-        searchdata[:options][method]['last search'] = [job.advanced]
+        searchdata[:options][method]['last search'] = { attributes: [job.advanced] }
       end
     end
 
+    def display_large_result_warning?(xml_file_size)
+      threshold = SequenceServer.config[:large_result_warning_threshold].to_i
+      return false unless threshold.positive?
+
+      return false if params[:bypass_file_size_warning] == 'true'
+
+      xml_file_size > threshold
+    end
+
+    def large_result_warning_payload(jid)
+      {
+        user_warning: 'LARGE_RESULT',
+        download_links: [
+          { name: 'Standard Tabular Report', url: "download/#{jid}.std_tsv" },
+          { name: 'Full Tabular Report', url: "/download/#{jid}.full_tsv" },
+          { name: 'Results in XML', url: "/download/#{jid}.xml" },
+          { name: 'Pairwise', url: "/download/#{jid}.pairwise" },
+        ]
+      }
+    end
+
     helpers do
       def root_path_prefix
         settings.root_path_prefix.to_s

data/lib/sequenceserver/sequence.rb

@@ -180,7 +180,7 @@ module SequenceServer
         @database_ids = Array database_ids
         @in_file = in_file
 
-        validate && run
+        validate && create_entry_batch_file && run
       end
 
       attr_reader :sequence_ids, :database_ids, :in_file, :sequences
@@ -197,10 +197,9 @@ module SequenceServer
       def run
         command = "blastdbcmd -outfmt '%g	%i	%a	%t	%s'" \
                   " -db '#{database_names.join(' ')}'" \
-                  " -entry '#{sequence_ids.join(',')}'"
+                  " -entry_batch '#{@batch_file.path}'"
 
         out, = sys(command, path: config[:bin])
-
         @sequences = out.each_line.map do |line|
           # Stop codons in amino acid sequence databases show up as invalid
           # UTF-8 characters in the output and cause the subsequent call to
@@ -208,6 +207,8 @@ module SequenceServer
           line = line.encode('UTF-8', invalid: :replace, replace: 'X')
           Sequence.new(*line.chomp.split('	'))
         end
+
+        @batch_file.unlink
         extend(IO) && write if in_file
       end
 
@@ -221,11 +222,38 @@ module SequenceServer
 
       def validate
         ids = Database.ids
-        return true if database_ids.is_a?(Array) && !database_ids.empty? &&
-                       (ids & database_ids).length == database_ids.length
+        unless database_ids.is_a?(Array) &&
+               !database_ids.empty? &&
+               (ids & database_ids).length == database_ids.length
+
+          fail(
+            DatabaseUnreachableError,
+            "Database id should be one of: #{ids.join("\n")}"
+          )
+        end
+
+        valid_id_regex = /\A[a-zA-Z0-9-_.:*#|\[\]]+\z/
+        invalid_sequence_ids = sequence_ids.reject do |id|
+          id =~ valid_id_regex
+        end
 
-        fail DatabaseUnreachableError, 'Database id should be one of:' \
-                            " #{ids.join("\n")}"
+        unless invalid_sequence_ids.empty?
+          fail(
+            InvalidSequenceIdError,
+            "Invalid sequence id(s): #{invalid_sequence_ids.join(', ')}"
+          )
+        end
+
+        true
+      end
+
+      ##
+      # Create a temporary file containing sequence ids to fetch.
+      def create_entry_batch_file
+        @batch_file = Tempfile.new("#{Time.now}_batch").tap do |f|
+          f.write(sequence_ids.join("\n"))
+          f.flush
+        end
       end
 
       # rubocop:disable Metrics/MethodLength

data/lib/sequenceserver/server.rb

@@ -22,7 +22,7 @@ module SequenceServer
     def start
       setup_signal_handlers
       @server = WEBrick::HTTPServer.new(options)
-      @server.mount '/', Rack::Handler::WEBrick, app
+      @server.mount '/', Rackup::Handler::WEBrick, app
       @server.start
     end
 

data/lib/sequenceserver/version.rb

@@ -1,4 +1,4 @@
 # Define version number.
 module SequenceServer
-  VERSION = '3.0.1'.freeze
+  VERSION = '3.1.1'.freeze
 end

data/lib/sequenceserver.rb

@@ -8,7 +8,7 @@ Encoding.default_internal = 'UTF-8'
 # Top level module / namespace.
 module SequenceServer
   # The default version of BLAST that will be downloaded and configured for use.
-  BLAST_VERSION = '2.12.0+'.freeze
+  BLAST_VERSION = '2.15.0+'.freeze
 
   # Default location of configuration file.
   DEFAULT_CONFIG_FILE = '~/.sequenceserver.conf'.freeze

data/public/404.html

@@ -14,7 +14,7 @@
 
 <body class="bg-light text-dark text-center">
 
-  <img src="SequenceServer_logo.png" alt="SequenceServer Logo" class="mt-5 mb-3" style="max-width: 200px;">
+  <img src="/sequenceserver_logo.webp" alt="SequenceServer Logo" class="mt-5 mb-3" style="max-width: 200px;">
 
   <div class="container" style="margin-top: 10%;">
     <h1 class="display-4">404 Not Found</h1>

data/public/css/app.css

@@ -0,0 +1,121 @@
+@tailwind base;
+@tailwind components;
+@tailwind utilities;
+
+
+/* Backported bootstrap tooltip styles */
+
+.tooltip {
+  position: absolute;
+  z-index: 1070;
+  display: block;
+  font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;
+  font-style: normal;
+  font-weight: 400;
+  line-height: 1.42857143;
+  line-break: auto;
+  text-align: left;
+  text-align: start;
+  text-decoration: none;
+  text-shadow: none;
+  text-transform: none;
+  letter-spacing: normal;
+  word-break: normal;
+  word-spacing: normal;
+  word-wrap: normal;
+  white-space: normal;
+  font-size: 12px;
+  filter: alpha(opacity=0);
+  opacity: 0;
+}
+.tooltip.in {
+  filter: alpha(opacity=90);
+  opacity: 0.9;
+}
+.tooltip.top {
+  padding: 5px 0;
+  margin-top: -3px;
+}
+.tooltip.right {
+  padding: 0 5px;
+  margin-left: 3px;
+}
+.tooltip.bottom {
+  padding: 5px 0;
+  margin-top: 3px;
+}
+.tooltip.left {
+  padding: 0 5px;
+  margin-left: -3px;
+}
+.tooltip.top .tooltip-arrow {
+  bottom: 0;
+  left: 50%;
+  margin-left: -5px;
+  border-width: 5px 5px 0;
+  border-top-color: #000;
+}
+.tooltip.top-left .tooltip-arrow {
+  right: 5px;
+  bottom: 0;
+  margin-bottom: -5px;
+  border-width: 5px 5px 0;
+  border-top-color: #000;
+}
+.tooltip.top-right .tooltip-arrow {
+  bottom: 0;
+  left: 5px;
+  margin-bottom: -5px;
+  border-width: 5px 5px 0;
+  border-top-color: #000;
+}
+.tooltip.right .tooltip-arrow {
+  top: 50%;
+  left: 0;
+  margin-top: -5px;
+  border-width: 5px 5px 5px 0;
+  border-right-color: #000;
+}
+.tooltip.left .tooltip-arrow {
+  top: 50%;
+  right: 0;
+  margin-top: -5px;
+  border-width: 5px 0 5px 5px;
+  border-left-color: #000;
+}
+.tooltip.bottom .tooltip-arrow {
+  top: 0;
+  left: 50%;
+  margin-left: -5px;
+  border-width: 0 5px 5px;
+  border-bottom-color: #000;
+}
+.tooltip.bottom-left .tooltip-arrow {
+  top: 0;
+  right: 5px;
+  margin-top: -5px;
+  border-width: 0 5px 5px;
+  border-bottom-color: #000;
+}
+.tooltip.bottom-right .tooltip-arrow {
+  top: 0;
+  left: 5px;
+  margin-top: -5px;
+  border-width: 0 5px 5px;
+  border-bottom-color: #000;
+}
+.tooltip-inner {
+  max-width: 200px;
+  padding: 3px 8px;
+  color: #fff;
+  text-align: center;
+  background-color: #000;
+  border-radius: 4px;
+}
+.tooltip-arrow {
+  position: absolute;
+  width: 0;
+  height: 0;
+  border-color: transparent;
+  border-style: solid;
+}

data/public/css/app.min.css

@@ -0,0 +1 @@
+/*! tailwindcss v3.4.3 | MIT License | https://tailwindcss.com*/*,:after,:before{box-sizing:border-box;border:0 solid #e5e7eb}:after,:before{--tw-content:""}:host,html{line-height:1.5;-webkit-text-size-adjust:100%;-moz-tab-size:4;-o-tab-size:4;tab-size:4;font-family:ui-sans-serif,system-ui,sans-serif,Apple Color Emoji,Segoe UI Emoji,Segoe UI Symbol,Noto Color Emoji;font-feature-settings:normal;font-variation-settings:normal;-webkit-tap-highlight-color:transparent}body{margin:0;line-height:inherit}hr{height:0;color:inherit;border-top-width:1px}abbr:where([title]){-webkit-text-decoration:underline dotted;text-decoration:underline dotted}h1,h2,h3,h4,h5,h6{font-size:inherit;font-weight:inherit}a{color:inherit;text-decoration:inherit}b,strong{font-weight:bolder}code,kbd,pre,samp{font-family:ui-monospace,SFMono-Regular,Menlo,Monaco,Consolas,Liberation Mono,Courier 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0;border-right-color:#000}.tooltip.left .tooltip-arrow{top:50%;right:0;margin-top:-5px;border-width:5px 0 5px 5px;border-left-color:#000}.tooltip.bottom .tooltip-arrow{top:0;left:50%;margin-left:-5px;border-width:0 5px 5px;border-bottom-color:#000}.tooltip.bottom-left .tooltip-arrow{top:0;right:5px;margin-top:-5px;border-width:0 5px 5px;border-bottom-color:#000}.tooltip.bottom-right .tooltip-arrow{top:0;left:5px;margin-top:-5px;border-width:0 5px 5px;border-bottom-color:#000}.tooltip-inner{max-width:200px;padding:3px 8px;color:#fff;text-align:center;background-color:#000;border-radius:4px}.tooltip-arrow{position:absolute;width:0;height:0;border-color:#0000;border-style:solid}.hover\:bg-blue-400:hover{--tw-bg-opacity:1;background-color:rgb(96 165 250/var(--tw-bg-opacity))}.hover\:bg-gray-200:hover{--tw-bg-opacity:1;background-color:rgb(229 231 235/var(--tw-bg-opacity))}.hover\:bg-gray-300:hover{--tw-bg-opacity:1;background-color:rgb(209 213 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(min-width:640px){.sm\:my-8{margin-top:2rem;margin-bottom:2rem}.sm\:ml-3{margin-left:.75rem}.sm\:mt-0{margin-top:0}.sm\:block{display:block}.sm\:inline-block{display:inline-block}.sm\:flex{display:flex}.sm\:h-screen{height:100vh}.sm\:w-auto{width:auto}.sm\:w-full{width:100%}.sm\:max-w-screen-md{max-width:768px}.sm\:grid-cols-3{grid-template-columns:repeat(3,minmax(0,1fr))}.sm\:flex-row-reverse{flex-direction:row-reverse}.sm\:items-center{align-items:center}.sm\:p-0{padding:0}.sm\:p-6{padding:1.5rem}.sm\:px-6{padding-left:1.5rem;padding-right:1.5rem}.sm\:pb-4{padding-bottom:1rem}.sm\:align-middle{vertical-align:middle}.sm\:text-sm{font-size:.875rem;line-height:1.25rem}}@media (min-width:768px){.md\:my-2{margin-top:.5rem;margin-bottom:.5rem}.md\:flex{display:flex}.md\:w-auto{width:auto}.md\:grid-cols-2{grid-template-columns:repeat(2,minmax(0,1fr))}.md\:grid-cols-3{grid-template-columns:repeat(3,minmax(0,1fr))}.md\:space-x-4>:not([hidden])~:not([hidden]){--tw-space-x-reverse:0;margin-right:calc(1rem*var(--tw-space-x-reverse));margin-left:calc(1rem*(1 - var(--tw-space-x-reverse)))}.md\:divide-x>:not([hidden])~:not([hidden]){--tw-divide-x-reverse:0;border-right-width:calc(1px*var(--tw-divide-x-reverse));border-left-width:calc(1px*(1 - var(--tw-divide-x-reverse)))}.md\:divide-y-0>:not([hidden])~:not([hidden]){--tw-divide-y-reverse:0;border-top-width:calc(0px*(1 - var(--tw-divide-y-reverse)));border-bottom-width:calc(0px*var(--tw-divide-y-reverse))}.md\:pl-2{padding-left:.5rem}.md\:pt-0{padding-top:0}}@media (min-width:1024px){.lg\:px-8{padding-left:2rem;padding-right:2rem}}

data/public/css/sequenceserver.css

@@ -5,7 +5,6 @@
 @import url('../vendor/github/nicgirault/circosJs@1.7.0/dist/colorBrewer.css');
 @import url('../vendor/github/twbs/bootstrap@3.3.5/css/bootstrap.min.css');
 @import url('../vendor/npm/font-awesome@4.4.0/css/font-awesome.min.css');
-@import url('../vendor/github/vakata/jstree@3.3.8/dist/themes/default/style.min.css');
 @import url('grapher.css');
 @import url('fonts.css');
 
@@ -162,29 +161,6 @@ a.disabled:hover,
   padding: 0 0 0 1px;
 }
 
-/**
- * Take out border, cut down margin and padding, and remove background color
- * from panel.
- */
-.panel {
-  border: none;
-  -webkit-box-shadow: none;
-  -moz-box-shadow: none;
-  box-shadow: none;
-}
-
-.panel .panel-heading {
-  padding: 0;
-  background-color: inherit;
-  border-bottom: 1px solid #c74f14;
-}
-
-.panel .panel-heading h4 {
-  margin: 0;
-  font-size: 16px;
-  font-weight: bold;
-}
-
 /**
  * Take padding-right out of .control-label and keep padding of .input-group.
  * Works better when browser is resized to smaller width.
@@ -350,11 +326,6 @@ td.nowrap-ellipsis {
   background-color: red;
 }
 
-.dnd-errors {
-  color: red;
-  font-size: 18px;
-}
-
 .modal-error {
   color: red;
   font-size: 18px;
@@ -372,89 +343,6 @@ td.nowrap-ellipsis {
   background-color: inherit;
 }
 
-.query-container {
-  margin-top: 35px;
-  margin-bottom: 35px;
-  position: relative;
-}
-
-.notifications {
-  position: fixed;
-  top: 0;
-  left: 0;
-  width: 100%;
-  height: 32px;
-  padding-right: 35px;
-  padding-left: 35px;
-}
-
-.notification {
-  margin-top: 6px;
-}
-
-.notification .alert-info,
-.notification .alert-danger {
-  -webkit-border-radius: 6px;
-  -moz-border-radius: 6px;
-  border-radius: 6px;
-  -webkit-box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3);
-  -moz-box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3);
-  box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3);
-  font-weight: bold;
-  text-shadow: 0 1px 0 rgba(255, 255, 255, 0.5);
-  text-align: center;
-  padding: 6px 12px 6px 12px;
-}
-
-.databases .list-group-item {
-  border: none;
-  padding: 1px 0 0;
-}
-
-#help pre:hover {
-  background-color: #ffc;
-}
-
-label[for="advanced"] {
-  font-size: 16px;
-  display: table-cell;
-  width: 1%;
-  white-space: nowrap;
-  vertical-align: middle;
-  padding: 5px 12px 5px 0;
-  cursor: default;
-  pointer-events: none;
-}
-
-input[name="advanced"] {
-  border-top-left-radius: 4px !important;
-  border-bottom-left-radius: 4px !important;
-}
-
-input[type=checkbox] {
-  vertical-align: top;
-}
-
-#method {
-  letter-spacing: 1px;
-}
-
-#methods li {
-  cursor: pointer;
-  text-align: center;
-  padding-top: 4px;
-  padding-bottom: 4px;
-  letter-spacing: 1px;
-}
-
-.dropdown-menu li {
-  border-bottom: 1px solid #ccc;
-}
-
-.dropdown-menu li:last-child {
-  border-bottom: 0;
-}
-
 /**********************
         Sidebar
  **********************/
@@ -575,28 +463,6 @@ input[type=checkbox] {
   vertical-align: super;
 }
 
-.dnd-overlay {
-  position: absolute;
-  top: 51px;
-  left: 0;
-  right: 0;
-  bottom: 0;
-  z-index: 1000;
-  background-color: rgba(255, 255, 255, 0.75);
-}
-
-.dnd-overlay * {
-  pointer-events: none;
-}
-
-.dnd-overlay-container {
-  padding-top: 72px;
-}
-
-.dnd-overlay-container p {
-  font-size: 48px;
-}
-
 /* higlight when hit is selected */
 .glow {
   border-left: 2px solid #c74f14;
@@ -649,20 +515,6 @@ input[type=checkbox] {
   display: table-cell;
 }
 
-
-/** For advanced params dropdown **/
-.input-group-btn {
-  vertical-align: top;
-}
-#advanced-params-dropdown {
-  padding: 0;
-}
-#advanced-params-dropdown li {
-  padding: 10px;
-  cursor: pointer;
-  letter-spacing: 1px;
-}
-
 .share-url-component input[type="text"] {
   width: 100%;
 }