sequenceserver 3.1.3 → 3.2.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/lib/sequenceserver/api_errors.rb +18 -0
- data/lib/sequenceserver/blast/hit.rb +1 -2
- data/lib/sequenceserver/blast/job.rb +15 -5
- data/lib/sequenceserver/blast/report.rb +5 -1
- data/lib/sequenceserver/database.rb +5 -1
- data/lib/sequenceserver/job.rb +26 -10
- data/lib/sequenceserver/makeblastdb.rb +2 -1
- data/lib/sequenceserver/routes.rb +37 -12
- data/lib/sequenceserver/version.rb +1 -1
- data/lib/sequenceserver/zip_file_generator.rb +1 -1
- data/public/404.html +8 -16
- data/public/css/app.css +794 -111
- data/public/css/app.min.css +1 -1
- data/public/css/sequenceserver.min.css +1 -8
- data/public/js/circos.js +103 -96
- data/public/{packages/circosJS@1.7.0.js → js/circosjs.js} +156 -778
- data/public/js/cloud_share_modal.js +55 -58
- data/public/js/collapse_preferences.js +13 -15
- data/public/js/databases.js +4 -3
- data/public/js/databases_tree.js +51 -30
- data/public/js/error_modal.js +35 -22
- data/public/js/exporter.js +2 -0
- data/public/js/form.js +43 -7
- data/public/js/grapher.js +94 -92
- data/public/js/hit.js +21 -19
- data/public/js/hits.js +45 -38
- data/public/js/hits_overview.js +8 -27
- data/public/js/hsp.js +140 -144
- data/public/js/jquery_world.js +24 -15
- data/public/js/kablammo.js +14 -10
- data/public/js/length_distribution.js +23 -37
- data/public/js/null_plugins/report_plugins.js +3 -5
- data/public/js/options.js +17 -19
- data/public/js/query.js +36 -35
- data/public/js/report/alignment_results.js +18 -0
- data/public/js/report/graphical_overview.js +38 -0
- data/public/js/report/report_header.js +28 -0
- data/public/js/report/run_summary.js +43 -0
- data/public/js/report.js +62 -102
- data/public/js/report_root.js +3 -3
- data/public/js/search.js +5 -2
- data/public/js/search_button.js +85 -78
- data/public/js/sequence.js +11 -22
- data/public/js/sequence_modal.js +38 -37
- data/public/js/share_url.js +5 -5
- data/public/js/sidebar.js +148 -86
- data/public/js/svgExporter.js +8 -3
- data/public/js/tests/form.spec.js +1 -1
- data/public/js/tests/visualisation_helpers.spec.js +28 -0
- data/public/js/visualisation_helpers.js +24 -27
- data/public/sequenceserver-report.min.js +1 -1
- data/public/sequenceserver-report.min.js.LICENSE.txt +1 -88
- data/public/sequenceserver-report.min.js.map +1 -1
- data/public/sequenceserver-search.min.js +1 -1
- data/public/sequenceserver-search.min.js.LICENSE.txt +0 -30
- data/public/sequenceserver-search.min.js.map +1 -1
- data/views/error.erb +1 -1
- data/views/layout.erb +123 -130
- data/views/report.erb +3 -2
- data/views/search.erb +10 -14
- metadata +13 -26
- data/public/css/fonts.css +0 -31
- data/public/css/grapher.css +0 -670
- data/public/css/sequenceserver.css +0 -509
- data/public/vendor/github/mbostock/d3@3.5.6/d3.js +0 -9506
- data/public/vendor/github/mbostock/d3@3.5.6.js +0 -1
- data/views/search_layout.erb +0 -153
data/views/error.erb
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data/views/layout.erb
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<!DOCTYPE html>
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<html lang="en">
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<head>
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<meta http-equiv="X-UA-Compatible" content="IE=edge">
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<meta name="viewport" content="width=device-width, initial-scale=1">
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<head>
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<title>SequenceServer: Custom BLAST Server</title>
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<meta name="author" content="Pragmatic Genomics
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<meta name="author" content="Pragmatic Genomics Limited"/>
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<meta charset="UTF-8">
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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<meta name="description" content="Custom BLAST server provided by SequenceServer (https://sequenceserver.com)"/>
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<%= Rack::Csrf.metatag(env) %>
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<link rel="stylesheet" media="screen,print" type="text/css" href="css/sequenceserver.min.css?ver=<%= SequenceServer::VERSION %>"/>
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<% else %>
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<link rel="stylesheet" media="screen,print" type="text/css" href="css/sequenceserver.css"/>
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<% end %>
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<link rel="stylesheet" media="screen,print" type="text/css" href="<%= css_asset_path %>"/>
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.5.2/css/all.min.css" integrity="sha512-SnH5WK+bZxgPHs44uWIX+LLJAJ9/2PkPKZ5QiAj6Ta86w+fsb2TkcmfRyVX3pBnMFcV7oQPJkl9QevSCWr3W6A==" crossorigin="anonymous" referrerpolicy="no-referrer" />
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</head>
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<body>
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<
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class="
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</small>
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</a>
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<ul class="nav navbar-nav navbar-right hover-reset focus-reset">
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<li>
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<a
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href="https://sequenceserver.com/progress-on-BLAST-interface/"
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class="update-check"
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data-version="<%= SequenceServer::VERSION %>"
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target="_blank">
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</a>
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</li>
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<a
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target="_blank"
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href="https://sequenceserver.com/support">
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<i class="fa fa-comment-o"></i>
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Help & Support
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<body class="text-black relative">
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<header id="header" class="border-b border-seqorange print:hidden">
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<div class="mx-auto max-w-7xl px-4 sm:px-6 lg:px-8">
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<div class="flex flex-none items-center">
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<div class="pr-8 md:pr-0 py-4">
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<a href="https://sequenceserver.com" target="_blank" class="flex items-end">
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<img src="<%= asset_path('sequenceserver_logo.webp') %>" alt="SequenceServer logo" width="1620" height="213" class="h-8 w-auto pr-2">
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<span class="text-sm md:text-base">
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<%= SequenceServer::VERSION %>
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</span>
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</a>
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<div class="flex-grow"></div>
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<ul class="flex space-x-2">
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<li>
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<a
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href="https://sequenceserver.com/progress-on-BLAST-interface/"
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class="underline text-seqblue"
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data-update-check
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data-version="<%= SequenceServer::VERSION %>"
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target="_blank">
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</a>
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</li>
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<li>
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<a
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class="text-seqblue flex items-center text-sm md:text-base hover:text-seqorange"
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target="_blank"
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href="https://sequenceserver.com/support">
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<i class="fa-regular fa-comment w-4 h-4 mr-1 fill-current"></i>
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Help & Support
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</a>
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</li>
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</ul>
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</div>
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class="
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<h3>SequenceServer can't work without JavaScript.</h3>
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<ul>
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<noscript>
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<div class="mx-auto px-4">
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<div class="bg-red-100 border border-red-400 text-red-700 px-4 py-3 rounded relative" role="alert">
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<strong class="font-bold">Our website cannot work without JavaScript.</strong>
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<ul class="mt-2 list-disc list-inside">
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<li>Please see if you can enable JavaScript in your browser's preferences.</li>
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<li>If your browser doesn't support JavaScript, please consider upgrading to the latest version or using Firefox or Chrome.</li>
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</noscript>
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<%= yield %>
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%>
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<p class="text-center text-sm print:hidden">
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Please cite data sources and <a class="text-seqblue" href="https://doi.org/10.1093/molbev/msz185">the paper</a> describing <a class="text-seqblue" href="https://wurmlab.com">our</a> <a class="text-seqblue" href="https://sequenceserver.com">SequenceServer BLAST interface</a>.
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<a class="text-seqblue" href='https://sequenceserver.com'>
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<em>
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<%=
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quote = [
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"Visualize BLAST results.",
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"Run BLAST on local computer.",
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"BLAST on Mac.",
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"BLAST on Windows.",
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"Run blast on mac.",
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"Blast analysis software.",
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"Sequence Search on local computer.",
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"Blast DNA sequence search.",
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"Custom BLAST search.",
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"Install blast on Mac.",
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"Perform BLAST analyses.",
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"Custom BLAST web interface.",
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"SequenceServer: Local BLAST with bespoke html interface.",
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"Set up custom BLAST interface with SequenceServer.",
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"Easy BLASTing with SequenceServer.",
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"BLAST against a custom, local database with SequenceServer.",
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"Cloud BLAST custom genome.",
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"NCBI BLAST alternative.",
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"BLAST private transcriptome assembly in the Cloud.",
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"Cloud server for comparative genomics, oligos, crisp, primers and more."
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].sample
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%>
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</em>
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</a>
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</div> <!-- /container -->
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<script>
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function suggestNewVersion(element, version) {
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element.textContent = `New version v${version} is available`;
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console.log(`New SequenceServer version available ${version}. Please consider updating.`)
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}
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}
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return;
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const element = document.querySelector('[data-update-check]');
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const currentVersion = element.getAttribute('data-version');
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const cachedVersion = document.cookie.split(';').find((item) => item.trim().startsWith('newVersion='));
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const upToDate = document.cookie.split(';').find((item) => item.trim().startsWith('versionIsLatest='));
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if (upToDate) {
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console.log('SequenceServer is up to date');
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return;
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}
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if (cachedVersion) {
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const newVersion = cachedVersion.split('=')[1];
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if (newVersion !== currentVersion) {
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suggestNewVersion(element, newVersion);
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}
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console.log('Checking for new SequenceServer version...')
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fetch(`https://updates.sequenceserver.com/?version=${currentVersion}`)
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.then(response => {
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if (response.ok) {
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} else {
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console.error('Failed to check for new SequenceServer version')
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}
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})
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.then(data => {
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const date = new Date();
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date.setTime(date.getTime() + (24 * 60 * 60 * 1000));
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const expires = "; expires=" + date.toUTCString();
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if (data.update_available) {
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const newVersion = data.new_version;
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document.cookie = `newVersion=${newVersion}${expires}; path=/`;
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suggestNewVersion(element, newVersion);
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} else {
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console.log('SequenceServer is up to date');
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document.cookie = `versionIsLatest=true${expires}; path=/`;
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}
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})
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.catch(() => {});
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</script>
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</body>
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<!-- We will initialise React on this div -->
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<div id="view" class="mb-6 pt-2 container mx-auto max-w-7xl px-4 sm:px-6 lg:px-8"></div>
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<script src="sequenceserver-report.min.js?ver=<%= SequenceServer::VERSION %>"></script>
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<link rel="stylesheet" href="https://code.jquery.com/ui/1.13.3/themes/base/jquery-ui.css">
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CHANGED
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@@ -8,17 +8,14 @@
|
|
|
8
8
|
<script src="sequenceserver-search.min.js?ver=<%= SequenceServer::VERSION %>"></script>
|
|
9
9
|
|
|
10
10
|
<!-- Markup for advanced options modal -->
|
|
11
|
-
<div class="
|
|
12
|
-
<
|
|
13
|
-
<div class="
|
|
14
|
-
|
|
15
|
-
|
|
16
|
-
|
|
17
|
-
|
|
18
|
-
<div class="bg-white px-4 pt-5 pb-4 sm:p-6 sm:pb-4 border-b">
|
|
19
|
-
<h3 class="text-xl leading-6 font-medium text-gray-900">Advanced Options</h3>
|
|
11
|
+
<div class="relative">
|
|
12
|
+
<dialog class="advanced-modal fixed p-4 w-full max-w-7xl bg-transparent focus:outline-none overflow-visible">
|
|
13
|
+
<div class="relative flex flex-col rounded-lg bg-white shadow">
|
|
14
|
+
<div class="flex items-start justify-between rounded-t border-b p-5">
|
|
15
|
+
<h3 class="text-xl font-medium text-gray-900">
|
|
16
|
+
Options
|
|
17
|
+
</h3>
|
|
20
18
|
</div>
|
|
21
|
-
|
|
22
19
|
<div class="overflow-y-scroll max-h-96 bg-white px-4 pt-5 pb-4 sm:p-6 sm:pb-4">
|
|
23
20
|
<div id="tblastn">
|
|
24
21
|
<%= erb :tblastn_options %>
|
|
@@ -36,12 +33,11 @@
|
|
|
36
33
|
<%= erb :blastp_options %>
|
|
37
34
|
</div>
|
|
38
35
|
</div>
|
|
39
|
-
|
|
40
36
|
<div class="bg-gray-50 px-4 py-3 sm:px-6 sm:flex sm:flex-row-reverse border-t">
|
|
41
|
-
<button type="button" class="
|
|
37
|
+
<button type="button" class="advanced-modal-close w-full inline-flex justify-center rounded-md border border-transparent shadow-sm px-4 py-2 bg-seqblue text-xl font-medium text-white hover:bg-seqorange focus:outline-none focus:ring-2 focus:ring-offset-2 focus:ring-seqorange sm:ml-3 sm:w-auto sm:text-sm">
|
|
42
38
|
Close
|
|
43
39
|
</button>
|
|
44
40
|
</div>
|
|
45
41
|
</div>
|
|
46
|
-
</
|
|
47
|
-
</div>
|
|
42
|
+
</dialog>
|
|
43
|
+
</div>
|
metadata
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: sequenceserver
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 3.
|
|
4
|
+
version: 3.2.0
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- Queen Mary University of London
|
|
@@ -9,7 +9,7 @@ authors:
|
|
|
9
9
|
autorequire:
|
|
10
10
|
bindir: bin
|
|
11
11
|
cert_chain: []
|
|
12
|
-
date:
|
|
12
|
+
date: 2026-10-27 00:00:00.000000000 Z
|
|
13
13
|
dependencies:
|
|
14
14
|
- !ruby/object:Gem::Dependency
|
|
15
15
|
name: json_pure
|
|
@@ -111,20 +111,14 @@ dependencies:
|
|
|
111
111
|
requirements:
|
|
112
112
|
- - "~>"
|
|
113
113
|
- !ruby/object:Gem::Version
|
|
114
|
-
version: '
|
|
115
|
-
- - ">="
|
|
116
|
-
- !ruby/object:Gem::Version
|
|
117
|
-
version: 2.3.2
|
|
114
|
+
version: '3.4'
|
|
118
115
|
type: :runtime
|
|
119
116
|
prerelease: false
|
|
120
117
|
version_requirements: !ruby/object:Gem::Requirement
|
|
121
118
|
requirements:
|
|
122
119
|
- - "~>"
|
|
123
120
|
- !ruby/object:Gem::Version
|
|
124
|
-
version: '
|
|
125
|
-
- - ">="
|
|
126
|
-
- !ruby/object:Gem::Version
|
|
127
|
-
version: 2.3.2
|
|
121
|
+
version: '3.4'
|
|
128
122
|
- !ruby/object:Gem::Dependency
|
|
129
123
|
name: sinatra
|
|
130
124
|
requirement: !ruby/object:Gem::Requirement
|
|
@@ -293,20 +287,14 @@ dependencies:
|
|
|
293
287
|
requirements:
|
|
294
288
|
- - "~>"
|
|
295
289
|
- !ruby/object:Gem::Version
|
|
296
|
-
version: 4.
|
|
297
|
-
- - ">="
|
|
298
|
-
- !ruby/object:Gem::Version
|
|
299
|
-
version: 4.18.1
|
|
290
|
+
version: 4.35.0
|
|
300
291
|
type: :development
|
|
301
292
|
prerelease: false
|
|
302
293
|
version_requirements: !ruby/object:Gem::Requirement
|
|
303
294
|
requirements:
|
|
304
295
|
- - "~>"
|
|
305
296
|
- !ruby/object:Gem::Version
|
|
306
|
-
version: 4.
|
|
307
|
-
- - ">="
|
|
308
|
-
- !ruby/object:Gem::Version
|
|
309
|
-
version: 4.18.1
|
|
297
|
+
version: 4.35.0
|
|
310
298
|
- !ruby/object:Gem::Dependency
|
|
311
299
|
name: simplecov
|
|
312
300
|
requirement: !ruby/object:Gem::Requirement
|
|
@@ -373,9 +361,6 @@ files:
|
|
|
373
361
|
- public/404.html
|
|
374
362
|
- public/css/app.css
|
|
375
363
|
- public/css/app.min.css
|
|
376
|
-
- public/css/fonts.css
|
|
377
|
-
- public/css/grapher.css
|
|
378
|
-
- public/css/sequenceserver.css
|
|
379
364
|
- public/css/sequenceserver.min.css
|
|
380
365
|
- public/fonts/FontAwesome.otf
|
|
381
366
|
- public/fonts/Source_Sans_Pro_400.eot
|
|
@@ -395,6 +380,7 @@ files:
|
|
|
395
380
|
- public/fonts/fontawesome-webfont.woff2
|
|
396
381
|
- public/js/alignment_exporter.js
|
|
397
382
|
- public/js/circos.js
|
|
383
|
+
- public/js/circosjs.js
|
|
398
384
|
- public/js/cloud_share_modal.js
|
|
399
385
|
- public/js/collapse_preferences.js
|
|
400
386
|
- public/js/databases.js
|
|
@@ -425,6 +411,10 @@ files:
|
|
|
425
411
|
- public/js/options.js
|
|
426
412
|
- public/js/query.js
|
|
427
413
|
- public/js/report.js
|
|
414
|
+
- public/js/report/alignment_results.js
|
|
415
|
+
- public/js/report/graphical_overview.js
|
|
416
|
+
- public/js/report/report_header.js
|
|
417
|
+
- public/js/report/run_summary.js
|
|
428
418
|
- public/js/report_root.js
|
|
429
419
|
- public/js/search.js
|
|
430
420
|
- public/js/search_button.js
|
|
@@ -445,9 +435,9 @@ files:
|
|
|
445
435
|
- public/js/tests/report.spec.js
|
|
446
436
|
- public/js/tests/search_button.spec.js
|
|
447
437
|
- public/js/tests/search_query.spec.js
|
|
438
|
+
- public/js/tests/visualisation_helpers.spec.js
|
|
448
439
|
- public/js/utils.js
|
|
449
440
|
- public/js/visualisation_helpers.js
|
|
450
|
-
- public/packages/circosJS@1.7.0.js
|
|
451
441
|
- public/packages/jquery-ui@1.13.3.js
|
|
452
442
|
- public/sequenceserver-report.min.js
|
|
453
443
|
- public/sequenceserver-report.min.js.LICENSE.txt
|
|
@@ -1204,8 +1194,6 @@ files:
|
|
|
1204
1194
|
- public/vendor/github/jspm/nodelibs-vm@0.1.0.js
|
|
1205
1195
|
- public/vendor/github/jspm/nodelibs-vm@0.1.0/index.js
|
|
1206
1196
|
- public/vendor/github/jspm/nodelibs-vm@0.1.0/package.json
|
|
1207
|
-
- public/vendor/github/mbostock/d3@3.5.6.js
|
|
1208
|
-
- public/vendor/github/mbostock/d3@3.5.6/d3.js
|
|
1209
1197
|
- public/vendor/github/nicgirault/circosJs@1.7.0.js
|
|
1210
1198
|
- public/vendor/github/nicgirault/circosJs@1.7.0/LICENSE.txt
|
|
1211
1199
|
- public/vendor/github/nicgirault/circosJs@1.7.0/bower.json
|
|
@@ -3530,7 +3518,6 @@ files:
|
|
|
3530
3518
|
- views/layout.erb
|
|
3531
3519
|
- views/report.erb
|
|
3532
3520
|
- views/search.erb
|
|
3533
|
-
- views/search_layout.erb
|
|
3534
3521
|
- views/tblastn_options.erb
|
|
3535
3522
|
- views/tblastx_options.erb
|
|
3536
3523
|
homepage: https://sequenceserver.com
|
|
@@ -3565,7 +3552,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
|
3565
3552
|
- !ruby/object:Gem::Version
|
|
3566
3553
|
version: '0'
|
|
3567
3554
|
requirements: []
|
|
3568
|
-
rubygems_version: 3.5.
|
|
3555
|
+
rubygems_version: 3.5.22
|
|
3569
3556
|
signing_key:
|
|
3570
3557
|
specification_version: 4
|
|
3571
3558
|
summary: BLAST search made easy!
|
data/public/css/fonts.css
DELETED
|
@@ -1,31 +0,0 @@
|
|
|
1
|
-
/**
|
|
2
|
-
* See:
|
|
3
|
-
* http://stackoverflow.com/questions/11002820/why-should-we-include-ttf-eot-woff-svg-in-a-font-face
|
|
4
|
-
* */
|
|
5
|
-
@font-face {
|
|
6
|
-
font-family: 'Source Sans Pro';
|
|
7
|
-
font-style: normal;
|
|
8
|
-
font-weight: 400;
|
|
9
|
-
src:
|
|
10
|
-
local('Source Sans Pro'),
|
|
11
|
-
local('SourceSansPro-Regular'),
|
|
12
|
-
url('../fonts/Source_Sans_Pro_400.woff2') format('woff2'),
|
|
13
|
-
url('../fonts/Source_Sans_Pro_400.woff') format('woff'),
|
|
14
|
-
url('../fonts/Source_Sans_Pro_400.ttf') format('truetype'),
|
|
15
|
-
url('../fonts/Source_Sans_Pro_400.svg') format('svg'),
|
|
16
|
-
url('../fonts/Source_Sans_Pro_400.eot') format('embedded-opentype');
|
|
17
|
-
}
|
|
18
|
-
|
|
19
|
-
@font-face {
|
|
20
|
-
font-family: 'Source Sans Pro';
|
|
21
|
-
font-style: normal;
|
|
22
|
-
font-weight: 700;
|
|
23
|
-
src:
|
|
24
|
-
local('Source Sans Pro Bold'),
|
|
25
|
-
local('SourceSansPro-Bold'),
|
|
26
|
-
url('../fonts/Source_Sans_Pro_700.woff2') format('woff2'),
|
|
27
|
-
url('../fonts/Source_Sans_Pro_700.woff') format('woff'),
|
|
28
|
-
url('../fonts/Source_Sans_Pro_700.ttf') format('truetype'),
|
|
29
|
-
url('../fonts/Source_Sans_Pro_700.svg') format('svg'),
|
|
30
|
-
url('../fonts/Source_Sans_Pro_700.eot') format('embedded-opentype');
|
|
31
|
-
}
|