Merge pull request #267 from ncbo/bootstrap-5

Upgrade to Bootstrap 5

Gemfile

@@ -6,12 +6,12 @@ source 'https://rubygems.org'
 gem 'rails', '6.1.7.3'
 
 gem 'sass-rails', '~> 5.0'
-gem 'uglifier', '>= 1.0.3'
+gem 'terser'
 # See https://github.com/rails/execjs#readme for more supported runtimes
 # gem 'therubyracer', platforms: :ruby
 # gem 'duktape'
 
-gem 'bootstrap', '~> 4.1.0'
+gem 'bootstrap', '~> 5.2.3'
 gem 'chart-js-rails'
 gem 'jquery-rails'
 gem 'jquery-ui-rails'
@@ -26,9 +26,12 @@ gem 'select2-rails'
 # To use debugger
 # gem 'debugger'
 
+gem 'base64', '0.1.0'
 gem 'cube-ruby', require: 'cube'
 gem 'dalli'
 gem 'flamegraph'
+# Version 2.1 breaks graphql-client. See: https://github.com/github/graphql-client/issues/310.
+gem 'graphql', '~> 2.0.27'
 gem 'graphql-client'
 gem 'haml', '~> 5.1'
 gem 'i18n'

Gemfile.lock

@@ -82,14 +82,14 @@ GEM
     airbrussh (1.4.2)
       sshkit (>= 1.6.1, != 1.7.0)
     ast (2.4.2)
-    autoprefixer-rails (10.4.13.0)
+    autoprefixer-rails (10.4.15.0)
       execjs (~> 2)
-    base64 (0.1.1)
+    base64 (0.1.0)
     bcrypt_pbkdf (1.1.0)
-    bootstrap (4.1.3)
-      autoprefixer-rails (>= 6.0.3)
-      popper_js (>= 1.12.9, < 2)
-      sass (>= 3.5.2)
+    bootstrap (5.2.3)
+      autoprefixer-rails (>= 9.1.0)
+      popper_js (>= 2.11.6, < 3)
+      sassc-rails (>= 2.0.0)
     brakeman (6.0.1)
     builder (3.2.4)
     capistrano (3.17.3)
@@ -136,9 +136,10 @@ GEM
     erubi (1.12.0)
     erubis (2.7.0)
     eventmachine (1.2.7)
-    excon (0.102.0)
-    execjs (2.8.1)
-    faraday (2.7.10)
+    excon (0.103.0)
+    execjs (2.9.0)
+    faraday (2.7.11)
+      base64
       faraday-net_http (>= 2.0, < 3.1)
       ruby2_keywords (>= 0.0.4)
     faraday-excon (2.1.0)
@@ -149,9 +150,9 @@ GEM
     faraday-net_http (3.0.2)
     ffi (1.15.5)
     flamegraph (0.9.5)
-    globalid (1.1.0)
-      activesupport (>= 5.0)
-    graphql (2.0.26)
+    globalid (1.2.1)
+      activesupport (>= 6.1)
+    graphql (2.0.27)
     graphql-client (0.18.0)
       activesupport (>= 3.0)
       graphql
@@ -196,7 +197,7 @@ GEM
       mime-types-data (~> 3.2015)
     mime-types-data (3.2023.0808)
     mini_mime (1.1.5)
-    minitest (5.19.0)
+    minitest (5.20.0)
     multi_json (1.15.0)
     multipart-post (2.3.0)
     mysql2 (0.5.5)
@@ -213,21 +214,21 @@ GEM
       net-protocol
     net-ssh (7.2.0)
     netrc (0.11.0)
-    newrelic_rpm (9.4.2)
+    newrelic_rpm (9.5.0)
     nio4r (2.5.9)
     nokogiri (1.15.4-arm64-darwin)
       racc (~> 1.4)
     nokogiri (1.15.4-x86_64-darwin)
       racc (~> 1.4)
     nokogiri (1.15.4-x86_64-linux)
       racc (~> 1.4)
-    oj (3.16.0)
+    oj (3.16.1)
     open_uri_redirections (0.2.1)
     parallel (1.23.0)
-    parser (3.2.2.3)
+    parser (3.2.2.4)
       ast (~> 2.4.1)
       racc
-    popper_js (1.16.1)
+    popper_js (2.11.8)
     pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
@@ -303,12 +304,11 @@ GEM
       rspec-mocks (~> 3.12)
       rspec-support (~> 3.12)
     rspec-support (3.12.1)
-    rubocop (1.56.2)
-      base64 (~> 0.1.1)
+    rubocop (1.57.2)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
-      parser (>= 3.2.2.3)
+      parser (>= 3.2.2.4)
       rainbow (>= 2.2.2, < 4.0)
       regexp_parser (>= 1.8, < 3.0)
       rexml (>= 3.2.5, < 4.0)
@@ -332,6 +332,14 @@ GEM
       sprockets (>= 2.8, < 4.0)
       sprockets-rails (>= 2.0, < 4.0)
       tilt (>= 1.1, < 3)
+    sassc (2.4.0)
+      ffi (~> 1.9)
+    sassc-rails (2.1.2)
+      railties (>= 4.0.0)
+      sassc (>= 2.0)
+      sprockets (> 3.0)
+      sprockets-rails
+      tilt
     select2-rails (4.0.13)
     sexp_processor (4.17.0)
     spawnling (2.1.5)
@@ -347,17 +355,17 @@ GEM
       net-ssh (>= 2.8.0)
     stackprof (0.2.25)
     temple (0.10.2)
+    terser (1.1.19)
+      execjs (>= 0.3.0, < 3)
     thin (1.8.2)
       daemons (~> 1.0, >= 1.0.9)
       eventmachine (~> 1.0, >= 1.0.4)
       rack (>= 1, < 3)
     thor (1.2.2)
-    tilt (2.2.0)
+    tilt (2.3.0)
     timeout (0.4.0)
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
-    uglifier (4.2.0)
-      execjs (>= 0.3.0, < 3)
     unf (0.1.4)
       unf_ext
     unf_ext (0.0.8.2)
@@ -376,8 +384,9 @@ PLATFORMS
   x86_64-linux
 
 DEPENDENCIES
+  base64 (= 0.1.0)
   bcrypt_pbkdf (>= 1.0, < 2.0)
-  bootstrap (~> 4.1.0)
+  bootstrap (~> 5.2.3)
   brakeman
   capistrano (~> 3.17)
   capistrano-bundler
@@ -392,6 +401,7 @@ DEPENDENCIES
   dalli
   ed25519 (>= 1.2, < 2.0)
   flamegraph
+  graphql (~> 2.0.27)
   graphql-client
   haml (~> 5.1)
   html2haml
@@ -420,9 +430,9 @@ DEPENDENCIES
   sass-rails (~> 5.0)
   select2-rails
   stackprof
+  terser
   thin
-  uglifier (>= 1.0.3)
   will_paginate (~> 3.0)
 
 BUNDLED WITH
-   2.4.18
+   2.4.19

app/assets/javascripts/admin/licenses.js

@@ -1,11 +1,11 @@
 jQuery(".admin.index").ready(function() {
 
-  jQuery('a[data-toggle="tab"]').on('shown.bs.tab', function (e) {
-    var href = jQuery(e.target).data('href');
-    if (typeof href !== 'undefined' && href === '/admin/licenses') {
+  jQuery('button[data-bs-toggle="tab"]').on('shown.bs.tab', function (e) {
+    const target = jQuery(e.target).data('bsTarget');
+    if (typeof target !== 'undefined' && target === '#licensing') {
       jQuery.ajax({
         method: 'GET',
-        url: href,
+        url: 'admin/licenses',
         success: function(data){},
         error: function(data){}
       });

app/assets/javascripts/bioportal.js.erb

@@ -430,7 +430,7 @@ function bpPopWindow(e) {
     newWindow.focus()
   };
 }
-jQuery("div.footer-support, div.dropdown-menu.dropdown-menu-right").on("click", "a.pop_window", { w: "800", h: "600" }, bpPopWindow)
+jQuery("div.footer-support, ul.dropdown-menu.dropdown-menu-end").on("click", "a.pop_window", { w: "800", h: "600" }, bpPopWindow)
 
 /**************************************************************
  * Standardized BP modal popups

app/assets/javascripts/bp_annotatorplus.js

@@ -56,7 +56,7 @@ function get_annotations() {
   }
 
   jQuery("#annotations_container").hide();
-  jQuery(".annotator_spinner").show();
+  jQuery(".annotator_spinner").css('display', 'inline-block');
   ajax_process_halt();
 
   var params = {},
@@ -148,12 +148,12 @@ function get_annotations() {
     success: function(data) {
       set_last_params(params);
       display_annotations(data, bp_last_params);
-      jQuery(".annotator_spinner").hide(200);
+      jQuery(".annotator_spinner").hide();
       jQuery("#annotations_container").show(300);
     },
     error: function(data) {
       set_last_params(params);
-      jQuery(".annotator_spinner").hide(200);
+      jQuery(".annotator_spinner").hide();
       jQuery("#annotations_container").hide();
       jQuery("#annotator_error").html(" Problem getting annotations, please try again");
     }

app/assets/javascripts/bp_ontology_viewer.js.erb

@@ -254,7 +254,9 @@ jQuery(document).ready(function() {
   if (typeof jQuery.bioportal.ont_pages[content_section].init === 'function') {
     jQuery.bioportal.ont_pages[content_section].init(jQuery.bioportal.ont_pages[content_section]);
   }
-  jQuery("#ont-" + content_section + "-tab").tab("show");
+  const triggerEl = document.querySelector(`#navbar-ontology a[data-bs-target="#ont_${content_section}_content"]`);
+  const tabTrigger = new bootstrap.Tab(triggerEl);
+  bootstrap.Tab.getInstance(triggerEl).show();
 
   // Retrieve AJAX content if not already displayed
   if ($.QueryString["skip_ajax_tabs"] != 'true') {

app/assets/javascripts/bp_search.js.erb

@@ -370,7 +370,7 @@ function performSearch() {
             // Display error message if no results found
             if (data.collection.length === 0) {
                 result_count.html("");
-                jQuery("#search_results").html("<h2 style='padding-top: 1em;'>No matches found</h2>");
+                jQuery("#search_results").html("<h2>No matches found</h2>");
             } else {
                 if (jQuery("#ontology_ontologyId").val() === null) {
                     resultsOntCount = jQuery("<span>");

app/assets/javascripts/submissions.js.erb

@@ -72,7 +72,7 @@ function addContact(event) {
   var removeButton = newContact.querySelector("button").cloneNode(true);
   removeButton.classList.replace("btn-success", "btn-danger");
   removeButton.classList.replace("add-contact", "remove-contact");
-  removeButton.classList.add("ml-1")
+  removeButton.classList.add("ms-1")
   removeButton.querySelector("i").classList.replace("fa-plus", "fa-minus");
   newContact.appendChild(removeButton);
 

app/assets/stylesheets/admin.scss

@@ -65,6 +65,7 @@ table.dataTable tbody tr.selected {
 .ontologies_list_container .dataTables_filter {
   float: right;
   padding-top: 3px;
+  padding-bottom: 5px;
 }
 
 .ontologies_list_container .dataTables_filter input {

app/assets/stylesheets/annotator.scss

@@ -1,9 +1,5 @@
-div#semanticTypes_chzn.chzn-container input.default {
-  font-style: oblique !important;
-}
-
-div#semanticTypes_chzn.chzn-container-active input.default {
-  font-style: normal !important;
+select#semantic_types + .chosen-container {
+  display: block;
 }
 
 div#annotations_filter, div#annotations_info {

app/assets/stylesheets/bioportal.scss

@@ -912,9 +912,9 @@ button.fg-button-menu, button.fg-button {
 /************************************
  * Top navigation bar
  ************************************/
-.btn-bp-login {
+div#topNavigationToggler a.btn.btn-login {
   color: #C58612;
-  border-color: #C58612 !important;
+  border-color: #C58612;
 
   &:hover {
     color: #234979;
@@ -926,23 +926,6 @@ button.fg-button-menu, button.fg-button {
   background-color: #234979;
 }
 
-.nav_text a {
-  font-family: 'Droid Sans', sans-serif;
-  font-size: 1.1em;
-  padding: 25px 15px;
-  position: relative;
-  text-decoration: none;
-  top: 11px;
-}
-
-.nav_text a:hover {
-  color: lightGray !important;
-}
-
-.nav_text_active a {
-  color: lightGray !important;
-}
-
 /************************************
  * Ontology picker
  ************************************/