sequenceserver 2.2.0 → 3.0

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Files changed (40) hide show
  1. checksums.yaml +4 -4
  2. data/COPYRIGHT.txt +1 -1
  3. data/bin/sequenceserver +4 -2
  4. data/lib/sequenceserver/blast/error.rb +53 -0
  5. data/lib/sequenceserver/blast/job.rb +2 -43
  6. data/lib/sequenceserver/job.rb +21 -11
  7. data/lib/sequenceserver/makeblastdb-modified-with-cache.rb +345 -0
  8. data/lib/sequenceserver/makeblastdb.rb +26 -12
  9. data/lib/sequenceserver/routes.rb +29 -3
  10. data/lib/sequenceserver/server.rb +1 -1
  11. data/lib/sequenceserver/version.rb +1 -1
  12. data/lib/sequenceserver.rb +3 -0
  13. data/public/404.html +27 -0
  14. data/public/config.js +0 -6
  15. data/public/css/grapher.css +1 -1
  16. data/public/css/sequenceserver.css +22 -11
  17. data/public/css/sequenceserver.min.css +2 -2
  18. data/public/js/circos.js +7 -3
  19. data/public/js/dnd.js +3 -3
  20. data/public/js/fastq_to_fasta.js +35 -0
  21. data/public/js/form.js +30 -11
  22. data/public/js/grapher.js +123 -113
  23. data/public/js/hit.js +8 -2
  24. data/public/js/hits_overview.js +4 -1
  25. data/public/js/jquery_world.js +0 -1
  26. data/public/js/kablammo.js +4 -0
  27. data/public/js/length_distribution.js +5 -1
  28. data/public/js/null_plugins/download_links.js +7 -0
  29. data/public/js/null_plugins/hit_buttons.js +11 -0
  30. data/public/js/null_plugins/report_plugins.js +18 -0
  31. data/public/js/query.js +26 -6
  32. data/public/js/report.js +33 -17
  33. data/public/js/search.js +0 -8
  34. data/public/js/sidebar.js +11 -1
  35. data/public/js/tests/mock_data/sequences.js +18 -1
  36. data/public/js/tests/search_query.spec.js +12 -3
  37. data/public/sequenceserver-report.min.js +76 -42
  38. data/public/sequenceserver-search.min.js +34 -33
  39. data/views/layout.erb +9 -12
  40. metadata +32 -23
data/lib/sequenceserver/routes.rb CHANGED
@@ -28,6 +28,10 @@ module SequenceServer
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  # We don't want Sinatra do setup any loggers for us. We will use our own.
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  set :logging, nil
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+
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+ # Override in config.ru if the instance is served under a subpath
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+ # e.g. for example.org/our-sequenceserver set to '/our-sequenceserver'
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+ set :root_path_prefix, ''
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35
  end
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36
 
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  # See
@@ -51,7 +55,9 @@ module SequenceServer
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  frame_options = SequenceServer.config[:frame_options]
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  frame_options && { frame_options: frame_options }
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  }
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+ end
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+ unless ENV['SEQUENCE_SERVER_COMPRESS_RESPONSES'] == 'false'
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  # Serve compressed responses.
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  use Rack::Deflater
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  end
@@ -105,6 +111,7 @@ module SequenceServer
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  # an empty body if the job hasn't finished yet.
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  get '/:jid.json' do |jid|
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  job = Job.fetch(jid)
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+ halt 404, { error: 'Job not found' }.to_json if job.nil?
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  halt 202 unless job.done?
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  report = Report.generate(job)
@@ -132,10 +139,12 @@ module SequenceServer
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  # Returns base HTML. Rest happens client-side: polling for and rendering
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  # the results.
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- get '/:jid' do
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+ get '/:jid' do |jid|
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+ job = Job.fetch(jid)
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+ halt 404, File.read(File.join(settings.root, 'public/404.html')) if job.nil?
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+
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  erb :report, layout: true
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  end
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-
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  # @params sequence_ids: whitespace separated list of sequence ids to
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  # retrieve
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  # @params database_ids: whitespace separated list of database ids to
@@ -165,7 +174,9 @@ module SequenceServer
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  # Download BLAST report in various formats.
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  get '/download/:jid.:type' do |jid, type|
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  job = Job.fetch(jid)
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+ halt 404, { error: 'Job not found' }.to_json if job.nil?
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  out = BLAST::Formatter.new(job, type)
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+ halt 404, { error: 'File not found"' }.to_json unless File.exist?(out.filepath)
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  send_file out.filepath, filename: out.filename, type: out.mime
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  end
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@@ -173,6 +184,7 @@ module SequenceServer
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  content_type :json
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  request_params = JSON.parse(request.body.read)
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  job = Job.fetch(request_params['job_id'])
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+ halt 404, { error: 'Job not found' }.to_json if job.nil?
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  unless job.done?
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  status 422
@@ -266,6 +278,7 @@ module SequenceServer
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  end
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  if request.env['HTTP_ACCEPT'].to_s.include?('application/json')
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+ status 422
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  content_type :json
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  error_data.to_json
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  else
@@ -276,7 +289,8 @@ module SequenceServer
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  # Get the query sequences, selected databases, and advanced params used.
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  def update_searchdata_from_job(searchdata)
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- job = Job.fetch(params[:job_id])
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+ job = fetch_job(params[:job_id])
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+ return { error: 'Job not found' }.to_json if job.nil?
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  return if job.imported_xml_file
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  # Only read job.qfile if we are not going to use Database.retrieve.
@@ -298,5 +312,17 @@ module SequenceServer
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  searchdata[:options][method]['last search'] = [job.advanced]
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  end
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  end
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+
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+ helpers do
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+ def root_path_prefix
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+ settings.root_path_prefix.to_s
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+ end
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+ end
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+
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+ private
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+
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+ def fetch_job(job_id)
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+ Job.fetch(job_id)
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+ end
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  end
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  end
data/lib/sequenceserver/server.rb CHANGED
@@ -1,4 +1,4 @@
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- require 'rack/handler/webrick'
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+ require 'rackup/handler/webrick'
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2
 
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  module SequenceServer
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  # Simple wrapper around WEBrick and Rack::Handler::WEBrick to host
data/lib/sequenceserver/version.rb CHANGED
@@ -1,4 +1,4 @@
1
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  # Define version number.
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  module SequenceServer
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- VERSION = '2.2.0'.freeze
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+ VERSION = '3.0'.freeze
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  end
data/lib/sequenceserver.rb CHANGED
@@ -2,6 +2,9 @@ require 'English'
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  require 'socket'
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  require 'resolv'
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+ Encoding.default_external = 'UTF-8'
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+ Encoding.default_internal = 'UTF-8'
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+
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  # Top level module / namespace.
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  module SequenceServer
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  # The default version of BLAST that will be downloaded and configured for use.
data/public/404.html ADDED
@@ -0,0 +1,27 @@
1
+ <!DOCTYPE html>
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+ <html lang="en">
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+
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+ <head>
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+ <meta charset="utf-8">
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+ <meta name="viewport" content="width=device-width, initial-scale=1">
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+
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+ <title>SequenceServer: Not Found</title>
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+
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+ <!-- Bootstrap CSS -->
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+ <link href="https://cdn.jsdelivr.net/npm/bootstrap@5.0.2/dist/css/bootstrap.min.css" rel="stylesheet"
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+ integrity="sha384-EVSTQN3/azprG1Anm3QDgpJLIm9Nao0Yz1ztcQTwFspd3yD65VohhpuuCOmLASjC" crossorigin="anonymous">
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+ </head>
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+
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+ <body class="bg-light text-dark text-center">
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+
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+ <img src="SequenceServer_logo.png" alt="SequenceServer Logo" class="mt-5 mb-3" style="max-width: 200px;">
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+
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+ <div class="container" style="margin-top: 10%;">
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+ <h1 class="display-4">404 Not Found</h1>
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+ <p class="lead">Sorry, the page you are looking for could not be found.</p>
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+ <a href="/" class="btn btn-primary mt-3">Start over</a>
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+ </div>
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+
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+ </body>
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+
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+ </html>
data/public/config.js CHANGED
@@ -29,7 +29,6 @@ System.config({
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  "react-dom": "npm:react-dom@18.0.0",
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  "underscore": "npm:underscore@1.8.3",
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  "vakata/jstree": "github:vakata/jstree@3.3.8",
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- "webshim": "npm:webshim@1.15.8",
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  "github:components/jqueryui@1.11.4": {
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  "jquery": "github:components/jquery@2.1.4"
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  },
@@ -143,11 +142,6 @@ System.config({
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  },
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  "npm:vm-browserify@0.0.4": {
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  "indexof": "npm:indexof@0.0.1"
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- },
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- "npm:webshim@1.15.8": {
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- "fs": "github:jspm/nodelibs-fs@0.1.2",
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- "path": "github:jspm/nodelibs-path@0.1.0",
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- "process": "github:jspm/nodelibs-process@0.1.2"
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  }
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  }
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  });
data/public/css/grapher.css CHANGED
@@ -44,7 +44,7 @@ svg .axis path,
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  font-weight: bold;
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  }
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- /* Graphical overview of hits */
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+ /* Graphical overview of aligning hit sequences to the query */
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  .alignment-overview.svg-container {
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  text-align: center;
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  }
data/public/css/sequenceserver.css CHANGED
@@ -84,6 +84,8 @@ h4 > .fa {
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  */
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  .disabled {
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  color: #ccc !important;
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+ cursor: not-allowed;
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+ pointer-events: none; /* This prevents the click from happening */
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  }
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  a.disabled:hover,
@@ -219,6 +221,15 @@ a.disabled:hover,
219
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  color: #5f5f5f;
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  }
221
223
 
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+ .clamped-paragraph {
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+ -webkit-line-clamp: 2;
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+ -webkit-box-orient: vertical;
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+ display: -webkit-box;
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+ overflow: hidden;
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+ text-overflow: ellipsis;
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+ overflow-wrap: break-word;
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+ }
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+
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  /**
223
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  * Set max-width and font-family on tooltips.
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  */
@@ -363,24 +374,22 @@ td.nowrap-ellipsis {
363
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364
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  .query-container {
365
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  margin-top: 35px;
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- margin-bottom: 0;
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+ margin-bottom: 35px;
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+ position: relative;
367
379
  }
368
380
 
369
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  .notifications {
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- position: relative;
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+ position: fixed;
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+ top: 0;
384
+ left: 0;
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+ width: 100%;
371
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  height: 32px;
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-
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- /**
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- * Notifications should appear over the bottom border of the textarea, high
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- * enough that they do not interfere with the database listing below and
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- * narrow enough not to cover the textarea resize handle on the right. */
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- top: -16px;
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- margin-right: 35px;
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- margin-left: 35px;
387
+ padding-right: 35px;
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+ padding-left: 35px;
380
389
  }
381
390
 
382
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  .notification {
383
- height: 32px !important;
392
+ margin-top: 6px;
384
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  }
385
394
 
386
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  .notification .alert-info,
@@ -413,6 +422,8 @@ label[for="advanced"] {
413
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  white-space: nowrap;
414
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  vertical-align: middle;
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  padding: 5px 12px 5px 0;
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+ cursor: default;
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+ pointer-events: none;
416
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  }
417
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418
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  input[name="advanced"] {