sequenceserver 3.1.2 → 3.1.3

data/views/layout.erb

@@ -74,9 +74,8 @@
       class="container">
       <p
         class="text-center">
-	Please cite data sources and <a style='vertical-align: baseline' href="https://doi.org/10.1093/molbev/msz185">the paper</a> describing <a href="https://wurmlab.com">our</a> <a href="https://sequenceserver.com">SequenceServer BLAST interface</a>.
-        <a style='vertical-align: baseline'
-          href='https://sequenceserver.com'><em>
+	Please cite data sources and <a href="https://doi.org/10.1093/molbev/msz185">the paper</a> describing <a href="https://wurmlab.com">our</a> <a href="https://sequenceserver.com">SequenceServer BLAST interface</a>.
+        <a href='https://sequenceserver.com'><em>
           <%=
             quote = [
 	      "Visualize BLAST results.",
@@ -108,7 +107,7 @@
     </div> <!-- /container -->
   </div>
 
-  <script>
+  <script nonce="<%= env['csp.nonce'] %>">
     document.addEventListener('DOMContentLoaded', function() {
 
         function suggestNewVersion(element, version) {
@@ -156,9 +155,6 @@
             })
             .catch(() => {});
     });
-
   </script>
-  <!-- twitter -->
-  <script>!function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0];if(!d.getElementById(id)){js=d.createElement(s);js.id=id;js.src="//platform.twitter.com/widgets.js";fjs.parentNode.insertBefore(js,fjs);}}(document,"script","twitter-wjs");</script>
 </body>
 </html>

data/views/search.erb

@@ -38,7 +38,7 @@
       </div>
 
       <div class="bg-gray-50 px-4 py-3 sm:px-6 sm:flex sm:flex-row-reverse border-t">
-        <button type="button" class="w-full inline-flex justify-center rounded-md border border-transparent shadow-sm px-4 py-2 bg-seqblue text-base 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" onclick="document.querySelector('[data-help-modal]').classList.add('hidden')">
+        <button type="button" class="js--close-help w-full inline-flex justify-center rounded-md border border-transparent shadow-sm px-4 py-2 bg-seqblue text-base 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">
           Close
         </button>
       </div>

data/views/search_layout.erb

@@ -65,7 +65,7 @@
   <%= yield %>
 
   <div class="mx-auto px-4">
-    <div class="container">
+    <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'>

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: sequenceserver
 version: !ruby/object:Gem::Version
-  version: 3.1.2
+  version: 3.1.3
 platform: ruby
 authors:
 - Queen Mary University of London
@@ -9,7 +9,7 @@ authors:
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2024-07-04 00:00:00.000000000 Z
+date: 2024-08-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: json_pure
@@ -371,7 +371,6 @@ files:
 - lib/sequenceserver/version.rb
 - lib/sequenceserver/zip_file_generator.rb
 - public/404.html
-- public/config.js
 - public/css/app.css
 - public/css/app.min.css
 - public/css/fonts.css
@@ -408,6 +407,7 @@ files:
 - public/js/form.js
 - public/js/grapher.js
 - public/js/hit.js
+- public/js/hits.js
 - public/js/hits_overview.js
 - public/js/hsp.js
 - public/js/jquery_world.js
@@ -433,6 +433,8 @@ files:
 - public/js/share_url.js
 - public/js/sidebar.js
 - public/js/svgExporter.js
+- public/js/tests/alignment_exporter.spec.js
+- public/js/tests/cloud_share_modal.spec.js
 - public/js/tests/database.spec.js
 - public/js/tests/form.spec.js
 - public/js/tests/mock_data/databases.json
@@ -446,9 +448,13 @@ files:
 - public/js/utils.js
 - public/js/visualisation_helpers.js
 - public/packages/circosJS@1.7.0.js
-- public/packages/jquery-ui@1.11.4.js
+- public/packages/jquery-ui@1.13.3.js
 - public/sequenceserver-report.min.js
+- public/sequenceserver-report.min.js.LICENSE.txt
+- public/sequenceserver-report.min.js.map
 - public/sequenceserver-search.min.js
+- public/sequenceserver-search.min.js.LICENSE.txt
+- public/sequenceserver-search.min.js.map
 - public/sequenceserver_logo.webp
 - public/vendor/github/components/jquery@2.1.4.js
 - public/vendor/github/components/jquery@2.1.4/README.md
@@ -3559,7 +3565,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.5.14
+rubygems_version: 3.5.17
 signing_key:
 specification_version: 4
 summary: BLAST search made easy!

data/public/config.js

@@ -1,147 +0,0 @@
-System.config({
-  defaultJSExtensions: true,
-  transpiler: "babel",
-  babelOptions: {
-    "optional": [
-      "runtime",
-      "optimisation.modules.system"
-    ],
-    "blacklist": [
-      "strict"
-    ]
-  },
-  paths: {
-    "github:*": "vendor/github/*",
-    "npm:*": "vendor/npm/*"
-  },
-
-  map: {
-    "babel": "npm:babel-core@5.8.23",
-    "babel-runtime": "npm:babel-runtime@5.8.20",
-    "bootstrap": "github:twbs/bootstrap@3.3.5",
-    "core-js": "npm:core-js@1.1.2",
-    "d3": "github:mbostock/d3@3.5.6",
-    "font-awesome": "npm:font-awesome@4.4.0",
-    "jquery": "github:components/jquery@2.1.4",
-    "jquery-ui": "github:components/jqueryui@1.11.4",
-    "nicgirault/circosJs": "github:nicgirault/circosJs@1.7.0",
-    "react": "npm:react@18.0.0",
-    "react-dom": "npm:react-dom@18.0.0",
-    "underscore": "npm:underscore@1.8.3",
-    "vakata/jstree": "github:vakata/jstree@3.3.8",
-    "github:components/jqueryui@1.11.4": {
-      "jquery": "github:components/jquery@2.1.4"
-    },
-    "github:jspm/nodelibs-assert@0.1.0": {
-      "assert": "npm:assert@1.5.0"
-    },
-    "github:jspm/nodelibs-buffer@0.1.1": {
-      "buffer": "npm:buffer@5.7.1"
-    },
-    "github:jspm/nodelibs-events@0.1.1": {
-      "events": "npm:events@1.0.2"
-    },
-    "github:jspm/nodelibs-path@0.1.0": {
-      "path-browserify": "npm:path-browserify@0.0.0"
-    },
-    "github:jspm/nodelibs-process@0.1.2": {
-      "process": "npm:process@0.11.10"
-    },
-    "github:jspm/nodelibs-stream@0.1.0": {
-      "stream-browserify": "npm:stream-browserify@1.0.0"
-    },
-    "github:jspm/nodelibs-util@0.1.0": {
-      "util": "npm:util@0.10.3"
-    },
-    "github:jspm/nodelibs-vm@0.1.0": {
-      "vm-browserify": "npm:vm-browserify@0.0.4"
-    },
-    "github:twbs/bootstrap@3.3.5": {
-      "jquery": "github:components/jquery@2.1.4"
-    },
-    "npm:assert@1.5.0": {
-      "assert": "github:jspm/nodelibs-assert@0.1.0",
-      "buffer": "github:jspm/nodelibs-buffer@0.1.1",
-      "object-assign": "npm:object-assign@4.1.1",
-      "process": "github:jspm/nodelibs-process@0.1.2",
-      "util": "npm:util@0.10.3"
-    },
-    "npm:babel-runtime@5.8.20": {
-      "process": "github:jspm/nodelibs-process@0.1.2"
-    },
-    "npm:buffer@5.7.1": {
-      "base64-js": "npm:base64-js@1.5.1",
-      "ieee754": "npm:ieee754@1.2.1"
-    },
-    "npm:core-js@1.1.2": {
-      "fs": "github:jspm/nodelibs-fs@0.1.2",
-      "process": "github:jspm/nodelibs-process@0.1.2",
-      "systemjs-json": "github:systemjs/plugin-json@0.1.0"
-    },
-    "npm:core-util-is@1.0.3": {
-      "buffer": "github:jspm/nodelibs-buffer@0.1.1"
-    },
-    "npm:font-awesome@4.4.0": {
-      "css": "github:systemjs/plugin-css@0.1.15"
-    },
-    "npm:inherits@2.0.1": {
-      "util": "github:jspm/nodelibs-util@0.1.0"
-    },
-    "npm:loose-envify@1.4.0": {
-      "fs": "github:jspm/nodelibs-fs@0.1.2",
-      "js-tokens": "npm:js-tokens@4.0.0",
-      "process": "github:jspm/nodelibs-process@0.1.2",
-      "stream": "github:jspm/nodelibs-stream@0.1.0",
-      "util": "github:jspm/nodelibs-util@0.1.0"
-    },
-    "npm:path-browserify@0.0.0": {
-      "process": "github:jspm/nodelibs-process@0.1.2"
-    },
-    "npm:process@0.11.10": {
-      "assert": "github:jspm/nodelibs-assert@0.1.0",
-      "fs": "github:jspm/nodelibs-fs@0.1.2",
-      "vm": "github:jspm/nodelibs-vm@0.1.0"
-    },
-    "npm:react-dom@18.0.0": {
-      "buffer": "github:jspm/nodelibs-buffer@0.1.1",
-      "loose-envify": "npm:loose-envify@1.4.0",
-      "process": "github:jspm/nodelibs-process@0.1.2",
-      "react": "npm:react@18.0.0",
-      "scheduler": "npm:scheduler@0.21.0",
-      "stream": "github:jspm/nodelibs-stream@0.1.0"
-    },
-    "npm:react@18.0.0": {
-      "loose-envify": "npm:loose-envify@1.4.0",
-      "process": "github:jspm/nodelibs-process@0.1.2"
-    },
-    "npm:readable-stream@1.1.14": {
-      "buffer": "github:jspm/nodelibs-buffer@0.1.1",
-      "core-util-is": "npm:core-util-is@1.0.3",
-      "events": "github:jspm/nodelibs-events@0.1.1",
-      "inherits": "npm:inherits@2.0.1",
-      "isarray": "npm:isarray@0.0.1",
-      "process": "github:jspm/nodelibs-process@0.1.2",
-      "stream-browserify": "npm:stream-browserify@1.0.0",
-      "string_decoder": "npm:string_decoder@0.10.31"
-    },
-    "npm:scheduler@0.21.0": {
-      "loose-envify": "npm:loose-envify@1.4.0",
-      "process": "github:jspm/nodelibs-process@0.1.2"
-    },
-    "npm:stream-browserify@1.0.0": {
-      "events": "github:jspm/nodelibs-events@0.1.1",
-      "inherits": "npm:inherits@2.0.1",
-      "readable-stream": "npm:readable-stream@1.1.14"
-    },
-    "npm:string_decoder@0.10.31": {
-      "buffer": "github:jspm/nodelibs-buffer@0.1.1"
-    },
-    "npm:util@0.10.3": {
-      "inherits": "npm:inherits@2.0.1",
-      "process": "github:jspm/nodelibs-process@0.1.2"
-    },
-    "npm:vm-browserify@0.0.4": {
-      "indexof": "npm:indexof@0.0.1"
-    }
-  }
-});