sequenceserver 2.1.0 → 3.0

data/lib/sequenceserver/routes.rb

@@ -28,6 +28,10 @@ module SequenceServer
 
       # We don't want Sinatra do setup any loggers for us. We will use our own.
       set :logging, nil
+
+      # 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, ''
     end
 
     # See
@@ -51,7 +55,9 @@ module SequenceServer
         frame_options = SequenceServer.config[:frame_options]
         frame_options && { frame_options: frame_options }
       }
+    end
 
+    unless ENV['SEQUENCE_SERVER_COMPRESS_RESPONSES'] == 'false'
       # Serve compressed responses.
       use Rack::Deflater
     end
@@ -105,16 +111,40 @@ module SequenceServer
     # an empty body if the job hasn't finished yet.
     get '/:jid.json' do |jid|
       job = Job.fetch(jid)
+      halt 404, { error: 'Job not found' }.to_json if job.nil?
       halt 202 unless job.done?
-      Report.generate(job).to_json
+
+      report = Report.generate(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
+      end
+
+      report.to_json
     end
 
     # Returns base HTML. Rest happens client-side: polling for and rendering
     # the results.
-    get '/:jid' do
+    get '/:jid' do |jid|
+      job = Job.fetch(jid)
+      halt 404, File.read(File.join(settings.root, 'public/404.html')) if job.nil?
+
       erb :report, layout: true
     end
-
     # @params sequence_ids: whitespace separated list of sequence ids to
     # retrieve
     # @params database_ids: whitespace separated list of database ids to
@@ -144,14 +174,17 @@ module SequenceServer
     # Download BLAST report in various formats.
     get '/download/:jid.:type' do |jid, type|
       job = Job.fetch(jid)
+      halt 404, { error: 'Job not found' }.to_json if job.nil?
       out = BLAST::Formatter.new(job, type)
-      send_file out.file, filename: out.filename, type: out.mime
+      halt 404, { error: 'File not found"' }.to_json unless File.exist?(out.filepath)
+      send_file out.filepath, filename: out.filename, type: out.mime
     end
 
     post '/cloud_share' do
       content_type :json
       request_params = JSON.parse(request.body.read)
       job = Job.fetch(request_params['job_id'])
+      halt 404, { error: 'Job not found' }.to_json if job.nil?
 
       unless job.done?
         status 422
@@ -245,6 +278,7 @@ module SequenceServer
       end
 
       if request.env['HTTP_ACCEPT'].to_s.include?('application/json')
+        status 422
         content_type :json
         error_data.to_json
       else
@@ -255,7 +289,8 @@ module SequenceServer
 
     # Get the query sequences, selected databases, and advanced params used.
     def update_searchdata_from_job(searchdata)
-      job = Job.fetch(params[:job_id])
+      job = fetch_job(params[:job_id])
+      return { error: 'Job not found' }.to_json if job.nil?
       return if job.imported_xml_file
 
       # Only read job.qfile if we are not going to use Database.retrieve.
@@ -277,5 +312,17 @@ module SequenceServer
         searchdata[:options][method]['last search'] = [job.advanced]
       end
     end
+
+    helpers do
+      def root_path_prefix
+        settings.root_path_prefix.to_s
+      end
+    end
+
+    private
+
+    def fetch_job(job_id)
+      Job.fetch(job_id)
+    end
   end
 end

data/lib/sequenceserver/server.rb

@@ -1,4 +1,4 @@
-require 'rack/handler/webrick'
+require 'rackup/handler/webrick'
 
 module SequenceServer
   # Simple wrapper around WEBrick and Rack::Handler::WEBrick to host

data/lib/sequenceserver/sys.rb

@@ -67,7 +67,7 @@ module SequenceServer
 
       # Now move the temporary file to the given path.
       # TODO: don't we need to explicitly close the temp file here?
-      FileUtils.mv(temp_files.delete(channel), filename)
+      FileUtils.cp(temp_files[channel], filename)
     end
 
     # Read the remaining temp files into memory. For large outputs,

data/lib/sequenceserver/version.rb

@@ -1,4 +1,4 @@
 # Define version number.
 module SequenceServer
-  VERSION = '2.1.0'.freeze
+  VERSION = '3.0'.freeze
 end

data/lib/sequenceserver.rb

@@ -2,6 +2,9 @@ require 'English'
 require 'socket'
 require 'resolv'
 
+Encoding.default_external = 'UTF-8'
+Encoding.default_internal = 'UTF-8'
+
 # Top level module / namespace.
 module SequenceServer
   # The default version of BLAST that will be downloaded and configured for use.
@@ -62,6 +65,9 @@ module SequenceServer
 
     # SequenceServer initialisation routine.
     def init(config = {})
+      # Reset makeblastdb cache, because configuration may have changed.
+      @makeblastdb = nil
+
       # Use default config file if caller didn't specify one.
       config[:config_file] ||= DEFAULT_CONFIG_FILE
 
@@ -201,10 +207,13 @@ module SequenceServer
 
       logger.debug("Will look for BLAST+ databases in: #{config[:database_dir]}")
 
-      makeblastdb.scan
-      fail NO_BLAST_DATABASE_FOUND, config[:database_dir] if !makeblastdb.any_formatted?
+      fail NO_BLAST_DATABASE_FOUND, config[:database_dir] unless makeblastdb.any_formatted?
 
       Database.collection = makeblastdb.formatted_fastas
+      check_database_compatibility unless config[:optimistic].to_s == 'true'
+    end
+
+    def check_database_compatibility
       Database.each do |database|
         logger.debug "Found #{database.type} database '#{database.title}' at '#{database.path}'"
         if database.non_parse_seqids?

data/public/404.html

@@ -0,0 +1,27 @@
+<!DOCTYPE html>
+<html lang="en">
+
+<head>
+  <meta charset="utf-8">
+  <meta name="viewport" content="width=device-width, initial-scale=1">
+
+  <title>SequenceServer: Not Found</title>
+
+  <!-- Bootstrap CSS -->
+  <link href="https://cdn.jsdelivr.net/npm/bootstrap@5.0.2/dist/css/bootstrap.min.css" rel="stylesheet"
+    integrity="sha384-EVSTQN3/azprG1Anm3QDgpJLIm9Nao0Yz1ztcQTwFspd3yD65VohhpuuCOmLASjC" crossorigin="anonymous">
+</head>
+
+<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;">
+
+  <div class="container" style="margin-top: 10%;">
+    <h1 class="display-4">404 Not Found</h1>
+    <p class="lead">Sorry, the page you are looking for could not be found.</p>
+    <a href="/" class="btn btn-primary mt-3">Start over</a>
+  </div>
+
+</body>
+
+</html>

data/public/config.js

@@ -29,7 +29,6 @@ System.config({
     "react-dom": "npm:react-dom@18.0.0",
     "underscore": "npm:underscore@1.8.3",
     "vakata/jstree": "github:vakata/jstree@3.3.8",
-    "webshim": "npm:webshim@1.15.8",
     "github:components/jqueryui@1.11.4": {
       "jquery": "github:components/jquery@2.1.4"
     },
@@ -143,11 +142,6 @@ System.config({
     },
     "npm:vm-browserify@0.0.4": {
       "indexof": "npm:indexof@0.0.1"
-    },
-    "npm:webshim@1.15.8": {
-      "fs": "github:jspm/nodelibs-fs@0.1.2",
-      "path": "github:jspm/nodelibs-path@0.1.0",
-      "process": "github:jspm/nodelibs-process@0.1.2"
     }
   }
 });

data/public/css/grapher.css

@@ -44,7 +44,7 @@ svg .axis path,
   font-weight: bold;
 }
 
-/* Graphical overview of hits */
+/* Graphical overview of aligning hit sequences to the query */
 .alignment-overview.svg-container {
   text-align: center;
 }

data/public/css/sequenceserver.css

@@ -84,6 +84,8 @@ h4 > .fa {
  */
 .disabled {
   color: #ccc !important;
+  cursor: not-allowed;
+  pointer-events: none; /* This prevents the click from happening */
 }
 
 a.disabled:hover,
@@ -219,6 +221,15 @@ a.disabled:hover,
   color: #5f5f5f;
 }
 
+.clamped-paragraph {
+  -webkit-line-clamp: 2;
+  -webkit-box-orient: vertical;
+  display: -webkit-box;
+  overflow: hidden;
+  text-overflow: ellipsis;
+  overflow-wrap: break-word;
+}
+
 /**
  * Set max-width and font-family on tooltips.
  */
@@ -363,24 +374,22 @@ td.nowrap-ellipsis {
 
 .query-container {
   margin-top: 35px;
-  margin-bottom: 0;
+  margin-bottom: 35px;
+  position: relative;
 }
 
 .notifications {
-  position: relative;
+  position: fixed;
+  top: 0;
+  left: 0;
+  width: 100%;
   height: 32px;
-
-  /**
-   * Notifications should appear over the bottom border of the textarea, high
-   * enough that they do not interfere with the database listing below and
-   * narrow enough not to cover the textarea resize handle on the right. */
-  top: -16px;
-  margin-right: 35px;
-  margin-left: 35px;
+  padding-right: 35px;
+  padding-left: 35px;
 }
 
 .notification {
-  height: 32px !important;
+  margin-top: 6px;
 }
 
 .notification .alert-info,
@@ -413,6 +422,8 @@ label[for="advanced"] {
   white-space: nowrap;
   vertical-align: middle;
   padding: 5px 12px 5px 0;
+  cursor: default;
+  pointer-events: none;
 }
 
 input[name="advanced"] {