Merge pull request #18 from ncbo/master

A remerge of Sync: bring OntoPortal up-to-date with BioPortal releases 6.13.2 and onward

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

@@ -79,20 +79,20 @@ GEM
       zeitwerk (~> 2.3)
     addressable (2.8.5)
       public_suffix (>= 2.0.2, < 6.0)
-    airbrussh (1.4.2)
+    airbrussh (1.5.0)
       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)
+    capistrano (3.18.0)
       airbrussh (>= 1.0.0)
       i18n
       rake (>= 10.0.0)
@@ -127,18 +127,18 @@ GEM
     crass (1.0.6)
     cube-ruby (0.0.3)
     daemons (1.4.1)
-    dalli (3.2.5)
-    date (3.3.3)
+    dalli (3.2.6)
+    date (3.3.4)
     diff-lcs (1.5.0)
-    domain_name (0.5.20190701)
-      unf (>= 0.0.5, < 1.0.0)
+    domain_name (0.6.20231109)
     ed25519 (1.3.0)
     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 (0.104.0)
+    execjs (2.9.1)
+    faraday (2.7.11)
+      base64
       faraday-net_http (>= 2.0, < 3.1)
       ruby2_keywords (>= 0.0.4)
     faraday-excon (2.1.0)
@@ -147,11 +147,11 @@ GEM
     faraday-multipart (1.0.4)
       multipart-post (~> 2)
     faraday-net_http (3.0.2)
-    ffi (1.15.5)
+    ffi (1.16.3)
     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
@@ -180,7 +180,7 @@ GEM
     listen (3.8.0)
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
-    loofah (2.21.3)
+    loofah (2.22.0)
       crass (~> 1.0.2)
       nokogiri (>= 1.12.0)
     lz4-ruby (0.3.3)
@@ -194,46 +194,43 @@ GEM
     method_source (1.0.0)
     mime-types (3.5.1)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2023.0808)
+    mime-types-data (3.2023.1003)
     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)
-    net-imap (0.3.7)
+    net-imap (0.4.5)
       date
       net-protocol
     net-pop (0.1.2)
       net-protocol
-    net-protocol (0.2.1)
+    net-protocol (0.2.2)
       timeout
     net-scp (4.0.0)
       net-ssh (>= 2.6.5, < 8.0.0)
-    net-smtp (0.3.3)
+    net-smtp (0.4.0)
       net-protocol
     net-ssh (7.2.0)
     netrc (0.11.0)
-    newrelic_rpm (9.4.2)
-    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)
+    newrelic_rpm (9.6.0)
+      base64
+    nio4r (2.6.0)
+    nokogiri (1.15.5-x86_64-darwin)
       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)
     psych (3.3.4)
-    public_suffix (5.0.3)
-    racc (1.7.1)
+    public_suffix (5.0.4)
+    racc (1.7.3)
     rack (2.2.8)
     rack-mini-profiler (3.1.1)
       rack (>= 1.2.0)
@@ -272,14 +269,14 @@ GEM
       rake (>= 12.2)
       thor (~> 1.0)
     rainbow (3.1.1)
-    rake (13.0.6)
+    rake (13.1.0)
     rb-fsevent (0.11.2)
     rb-inotify (0.10.1)
       ffi (~> 1.0)
     rdoc (6.3.3)
     recaptcha (5.9.0)
       json
-    regexp_parser (2.8.1)
+    regexp_parser (2.8.2)
     rest-client (2.1.0)
       http-accept (>= 1.7.0, < 2.0)
       http-cookie (>= 1.0.2, < 2.0)
@@ -303,19 +300,18 @@ 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)
       rubocop-ast (>= 1.28.1, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 2.4.0, < 3.0)
-    rubocop-ast (1.29.0)
+    rubocop-ast (1.30.0)
       parser (>= 3.2.1.0)
     ruby-progressbar (1.13.0)
     ruby2_keywords (0.0.5)
@@ -332,6 +328,14 @@ 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)
@@ -342,42 +346,40 @@ GEM
       actionpack (>= 5.2)
       activesupport (>= 5.2)
       sprockets (>= 3.0.0)
-    sshkit (1.21.5)
+    sshkit (1.21.6)
       net-scp (>= 1.1.2)
       net-ssh (>= 2.8.0)
     stackprof (0.2.25)
-    temple (0.10.2)
+    temple (0.10.3)
+    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)
-    timeout (0.4.0)
+    thor (1.3.0)
+    tilt (2.3.0)
+    timeout (0.4.1)
     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)
-    unicode-display_width (2.4.2)
+    unicode-display_width (2.5.0)
     websocket-driver (0.7.6)
       websocket-extensions (>= 0.1.0)
     websocket-extensions (0.1.5)
     will_paginate (3.3.1)
     xpath (3.2.0)
       nokogiri (~> 1.8)
-    zeitwerk (2.6.11)
+    zeitwerk (2.6.12)
 
 PLATFORMS
   arm64-darwin-22
   x86_64-darwin-21
   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 +394,7 @@ DEPENDENCIES
   dalli
   ed25519 (>= 1.2, < 2.0)
   flamegraph
+  graphql (~> 2.0.27)
   graphql-client
   haml (~> 5.1)
   html2haml
@@ -420,9 +423,9 @@ 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_notes.js

@@ -341,13 +341,14 @@ function subscribeToNotes(button) {
   var ontologyId = jQuery(button).attr("data-bp_ontology_id");
   var isSubbed = jQuery(button).attr("data-bp_is_subbed");
   var userId = jQuery(button).attr("data-bp_user_id");
+  let encodedUserId = encodeURIComponent(userId);
 
   jQuery(".notes_sub_error").html("");
   jQuery(".notes_subscribe_spinner").show();
 
   jQuery.ajax({
     type: "POST",
-    url: "/subscriptions?user_id="+userId+"&ontology_id="+ontologyId+"&subbed="+isSubbed,
+    url: `/subscriptions?user_id=${encodedUserId}&ontology_id=${ontologyId}&subbed=${isSubbed}`,
     dataType: "json",
     success: function(data) {
       jQuery(".notes_subscribe_spinner").hide();
@@ -356,10 +357,17 @@ function subscribeToNotes(button) {
       var subbedVal = (isSubbed == "true") ? "false" : "true";
       jQuery("a.subscribe_to_notes").attr("data-bp_is_subbed", subbedVal);
 
-      // Change button text
-      var txt = jQuery("a.subscribe_to_notes span.ui-button-text").html();
-      var newButtonText = txt.match("Unsubscribe") ? txt.replace("Unsubscribe", "Subscribe") : txt.replace("Subscribe", "Unsubscribe");
-      jQuery("a.subscribe_to_notes span.ui-button-text").html(newButtonText);
+      /*
+       * Update link text.
+       * Note that there are two links that allow users to subscribe/unsubscribe from notes emails. Given any ontology,
+       * one link is located on the top-level Notes tab, and the other link is located on the Notes sub-tab on the
+       * right-hand side of the Classes tab. Both links are handled by the subscriptions controller, and the text of
+       * both should be updated on success.
+       */
+      const matches = document.querySelectorAll('a.subscribe_to_notes');
+      matches.forEach(match => {
+        match.textContent = (subbedVal === 'true') ? 'Unsubscribe from notes emails' : 'Subscribe to notes emails';
+      });
     },
     error: function(data) {
       jQuery(".notes_subscribe_spinner").hide();

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') {