sequenceserver 3.1.3 → 3.2.0

data/public/vendor/github/mbostock/d3@3.5.6.js

@@ -1 +0,0 @@
-module.exports = require("github:mbostock/d3@3.5.6/d3");

data/views/search_layout.erb

@@ -1,153 +0,0 @@
-<!DOCTYPE html>
-<html lang="en">
-
-<head>
-  <title>SequenceServer: Custom BLAST Server</title>
-  <meta name="author" content="Pragmatic Genomics Limited"/>
-  <meta charset="UTF-8">
-  <meta name="viewport" content="width=device-width, initial-scale=1.0">
-  <%= Rack::Csrf.metatag(env) %>
-  <link rel="stylesheet" media="screen,print" type="text/css" href="css/app.min.css"/>
-  <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" />
-</head>
-
-<body>
-  <header id="header" class="bg-gray-100 shadow-lg w-full">
-    <div class="mx-auto max-w-7xl px-4 sm:px-6 lg:px-8">
-      <div class="flex flex-none items-center">
-        <div class="py-4">
-          <a href="https://sequenceserver.com" target="_blank" class="flex items-end">
-            <img src="sequenceserver_logo.webp" alt="sequenceserver_logo" width="1620" height="213" class="h-8 w-auto pr-2">
-            <small>
-              <%= SequenceServer::VERSION %>
-            </small>
-          </a>
-        </div>
-
-        <div class="flex-grow"></div>
-        <ul class="flex space-x-2">
-          <li>
-            <a
-              href="https://sequenceserver.com/progress-on-BLAST-interface/"
-              class="underline text-seqblue"
-              data-update-check
-              data-version="<%= SequenceServer::VERSION %>"
-              target="_blank">
-            </a>
-          </li>
-          <li>
-            <a
-              class="text-seqblue flex items-center"
-              target="_blank"
-              href="https://sequenceserver.com/support">
-
-              <i class="fa-solid fa-comment w-4 h-4 mr-1 fill-current"></i>
-              Help &amp; Support
-            </a>
-          </li>
-        </ul>
-      </div>
-    </div>
-  </header>
-
-  <noscript>
-    <div class="mx-auto px-4">
-      <div class="bg-red-100 border border-red-400 text-red-700 px-4 py-3 rounded relative" role="alert">
-        <strong class="font-bold">Our website cannot work without JavaScript.</strong>
-        <ul class="mt-2 list-disc list-inside">
-          <li>Please see if you can enable JavaScript in your browser's preferences.</li>
-          <li>If your browser doesn't support JavaScript, please consider upgrading to the latest version or using Firefox or Chrome.</li>
-        </ul>
-      </div>
-    </div>
-  </noscript>
-
-  <%= yield %>
-
-  <div class="mx-auto px-4">
-    <div class="container mx-auto max-w-screen-xl">
-      <p class="text-center">
-        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>.
-        <a class="text-seqblue" href='https://sequenceserver.com'>
-          <em>
-            <%=
-              quote = [
-                "Visualize BLAST results.",
-                "Run BLAST on local computer.",
-                "BLAST on Mac.",
-                "BLAST on Windows.",
-                "Run blast on mac.",
-                "Blast analysis software.",
-                "Sequence Search on local computer.",
-                "Blast DNA sequence search.",
-                "Custom BLAST search.",
-                "Install blast on Mac.",
-                "Perform BLAST analyses.",
-                "Custom BLAST web interface.",
-                "SequenceServer: Local BLAST with bespoke html interface.",
-                "Set up custom BLAST interface with SequenceServer.",
-                "Easy BLASTing with SequenceServer.",
-                "BLAST against a custom, local database with SequenceServer.",
-                "Cloud BLAST custom genome.",
-                "NCBI BLAST alternative.",
-                "BLAST private transcriptome assembly in the Cloud.",
-                "Cloud server for comparative genomics, oligos, crisp, primers and more."
-              ].sample
-            %>
-          </em>
-        </a>
-      </p>
-  </div>
-
-  <script>
-    document.addEventListener('DOMContentLoaded', function() {
-
-        function suggestNewVersion(element, version) {
-            element.textContent = `New version v${version} is available`;
-            console.log(`New SequenceServer version available ${version}. Please consider updating.`)
-        }
-
-        const element = document.querySelector('[data-update-check]');
-        const currentVersion = element.getAttribute('data-version');
-        const cachedVersion = document.cookie.split(';').find((item) => item.trim().startsWith('newVersion='));
-        const upToDate = document.cookie.split(';').find((item) => item.trim().startsWith('versionIsLatest='));
-        if (upToDate) {
-            console.log('SequenceServer is up to date');
-            return;
-        }
-        if (cachedVersion) {
-            const newVersion = cachedVersion.split('=')[1];
-            if (newVersion !== currentVersion) {
-              suggestNewVersion(element, newVersion);
-            }
-            return;
-        }
-        console.log('Checking for new SequenceServer version...')
-        fetch(`https://updates.sequenceserver.com/?version=${currentVersion}`)
-            .then(response => {
-                if (response.ok) {
-                    return response.json();
-                } else {
-                    console.error('Failed to check for new SequenceServer version')
-                }
-            })
-            .then(data => {
-                const date = new Date();
-                date.setTime(date.getTime() + (24 * 60 * 60 * 1000));
-                const expires = "; expires=" + date.toUTCString();
-
-                if (data.update_available) {
-                    const newVersion = data.new_version;
-                    document.cookie = `newVersion=${newVersion}${expires}; path=/`;
-                    suggestNewVersion(element, newVersion);
-                } else {
-                    console.log('SequenceServer is up to date');
-                    document.cookie = `versionIsLatest=true${expires}; path=/`;
-                }
-            })
-            .catch(() => {});
-    });
-
-  </script>
-</body>
-</html>