Merge branch 'master' into feat/GPE-1202

qa-brh.planx-pla.net/manifest.json

@@ -13,7 +13,7 @@
     "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2023.12",
     "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2023.12",
     "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0",
-    "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:fix_gpu-support",
+    "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:feat_whitelist-username",
     "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2023.12",
     "kayako-wrapper": "quay.io/cdis/kayako-wrapper-service:0.2.0",
     "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2023.12",

qa-brh.planx-pla.net/manifests/hatchery/hatchery.json

@@ -71,7 +71,7 @@
       "cpu-limit": "2.0",
       "memory-limit": "16Gi",
       "name": "(Tutorials) Example Analysis Jupyter Lab Notebooks",
-      "image": "quay.io/cdis/brh-notebooks:combined_demos__8f562190843559054baaa7a5604d13455f467c4d",
+      "image": "quay.io/cdis/brh-notebooks:combined_demos__97e141f998c1d96e79fad3bfbc0c9c81726bd582",
       "env": {
         "FRAME_ANCESTORS": "https://qa-brh.planx-pla.net"
       },
@@ -144,7 +144,7 @@
       "nextflow": {
         "enabled": true,
         "job-image-whitelist": [
-          "*"
+          "143731057154.dkr.ecr.us-east-1.amazonaws.com/nextflow-approved/{{username}}:*"
         ],
         "s3-bucket-whitelist": [
           "ngi-igenomes"

qa-mickey.planx-pla.net/dashboard/Public/documentation/_static/alabaster.css

@@ -419,9 +419,7 @@ table.footnote td {
 }
 
 dl {
-    margin-left: 0;
-    margin-right: 0;
-    margin-top: 0;
+    margin: 0;
     padding: 0;
 }
 

qa-mickey.planx-pla.net/dashboard/Public/documentation/_static/basic.css

@@ -237,6 +237,10 @@ a.headerlink {
     visibility: hidden;
 }
 
+a:visited {
+    color: #551A8B;
+}
+
 h1:hover > a.headerlink,
 h2:hover > a.headerlink,
 h3:hover > a.headerlink,

qa-mickey.planx-pla.net/dashboard/Public/documentation/_static/documentation_options.js

@@ -1,5 +1,4 @@
-var DOCUMENTATION_OPTIONS = {
-    URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
+const DOCUMENTATION_OPTIONS = {
     VERSION: '2.1.0',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,

qa-mickey.planx-pla.net/dashboard/Public/documentation/_static/pygments.css

@@ -22,7 +22,6 @@ span.linenos.special { color: #000000; background-color: #ffffc0; padding-left:
 .highlight .cs { color: #8f5902; font-style: italic } /* Comment.Special */
 .highlight .gd { color: #a40000 } /* Generic.Deleted */
 .highlight .ge { color: #000000; font-style: italic } /* Generic.Emph */
-.highlight .ges { color: #000000 } /* Generic.EmphStrong */
 .highlight .gr { color: #ef2929 } /* Generic.Error */
 .highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */
 .highlight .gi { color: #00A000 } /* Generic.Inserted */

qa-mickey.planx-pla.net/dashboard/Public/documentation/_static/searchtools.js

@@ -57,12 +57,12 @@ const _removeChildren = (element) => {
 const _escapeRegExp = (string) =>
   string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string
 
-const _displayItem = (item, searchTerms) => {
+const _displayItem = (item, searchTerms, highlightTerms) => {
   const docBuilder = DOCUMENTATION_OPTIONS.BUILDER;
-  const docUrlRoot = DOCUMENTATION_OPTIONS.URL_ROOT;
   const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX;
   const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX;
   const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY;
+  const contentRoot = document.documentElement.dataset.content_root;
 
   const [docName, title, anchor, descr, score, _filename] = item;
 
@@ -75,20 +75,24 @@ const _displayItem = (item, searchTerms) => {
     if (dirname.match(/\/index\/$/))
       dirname = dirname.substring(0, dirname.length - 6);
     else if (dirname === "index/") dirname = "";
-    requestUrl = docUrlRoot + dirname;
+    requestUrl = contentRoot + dirname;
     linkUrl = requestUrl;
   } else {
     // normal html builders
-    requestUrl = docUrlRoot + docName + docFileSuffix;
+    requestUrl = contentRoot + docName + docFileSuffix;
     linkUrl = docName + docLinkSuffix;
   }
   let linkEl = listItem.appendChild(document.createElement("a"));
   linkEl.href = linkUrl + anchor;
   linkEl.dataset.score = score;
   linkEl.innerHTML = title;
-  if (descr)
+  if (descr) {
     listItem.appendChild(document.createElement("span")).innerHTML =
       " (" + descr + ")";
+    // highlight search terms in the description
+    if (SPHINX_HIGHLIGHT_ENABLED)  // set in sphinx_highlight.js
+      highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
+  }
   else if (showSearchSummary)
     fetch(requestUrl)
       .then((responseData) => responseData.text())
@@ -97,6 +101,9 @@ const _displayItem = (item, searchTerms) => {
           listItem.appendChild(
             Search.makeSearchSummary(data, searchTerms)
           );
+        // highlight search terms in the summary
+        if (SPHINX_HIGHLIGHT_ENABLED)  // set in sphinx_highlight.js
+          highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
       });
   Search.output.appendChild(listItem);
 };
@@ -115,14 +122,15 @@ const _finishSearch = (resultCount) => {
 const _displayNextItem = (
   results,
   resultCount,
-  searchTerms
+  searchTerms,
+  highlightTerms,
 ) => {
   // results left, load the summary and display it
   // this is intended to be dynamic (don't sub resultsCount)
   if (results.length) {
-    _displayItem(results.pop(), searchTerms);
+    _displayItem(results.pop(), searchTerms, highlightTerms);
     setTimeout(
-      () => _displayNextItem(results, resultCount, searchTerms),
+      () => _displayNextItem(results, resultCount, searchTerms, highlightTerms),
       5
     );
   }
@@ -360,7 +368,7 @@ const Search = {
     // console.info("search results:", Search.lastresults);
 
     // print the results
-    _displayNextItem(results, results.length, searchTerms);
+    _displayNextItem(results, results.length, searchTerms, highlightTerms);
   },
 
   /**

qa-mickey.planx-pla.net/dashboard/Public/documentation/_static/sphinx_highlight.js

@@ -29,14 +29,19 @@ const _highlight = (node, addItems, text, className) => {
       }
 
       span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+      const rest = document.createTextNode(val.substr(pos + text.length));
       parent.insertBefore(
         span,
         parent.insertBefore(
-          document.createTextNode(val.substr(pos + text.length)),
+          rest,
           node.nextSibling
         )
       );
       node.nodeValue = val.substr(0, pos);
+      /* There may be more occurrences of search term in this node. So call this
+       * function recursively on the remaining fragment.
+       */
+      _highlight(rest, addItems, text, className);
 
       if (isInSVG) {
         const rect = document.createElementNS(
@@ -140,5 +145,10 @@ const SphinxHighlight = {
   },
 };
 
-_ready(SphinxHighlight.highlightSearchWords);
-_ready(SphinxHighlight.initEscapeListener);
+_ready(() => {
+  /* Do not call highlightSearchWords() when we are on the search page.
+   * It will highlight words from the *previous* search query.
+   */
+  if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords();
+  SphinxHighlight.initEscapeListener();
+});

qa-mickey.planx-pla.net/dashboard/Public/documentation/genindex.html

@@ -1,15 +1,15 @@
 <!DOCTYPE html>
 
-<html lang="en">
+<html lang="en" data-content_root="./">
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>Index &#8212; va-doc 2.1.0 documentation</title>
-    <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=4f649999" />
-    <link rel="stylesheet" type="text/css" href="_static/alabaster.css?v=039e1c02" />
-    <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js?v=0218eca2"></script>
+    <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=b3523f8e" />
+    <link rel="stylesheet" type="text/css" href="_static/alabaster.css?v=cb25574f" />
+    <script src="_static/documentation_options.js?v=20623aea"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
-    <script src="_static/sphinx_highlight.js?v=4825356b"></script>
+    <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="#" />
     <link rel="search" title="Search" href="search.html" />
 
@@ -86,8 +86,8 @@ <h3 id="searchlabel">Quick search</h3>
       &copy;2021, Center for Translational Data Science at the University of Chicago.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 7.1.2</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.13</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 7.2.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
 
     </div>