Keep Sprockets in Ruby upgrade

Gemfile

@@ -16,6 +16,14 @@ gem 'config'
 gem 'delayed_job_active_record'
 gem 'daemons'
 gem 'rubystats'
+gem 'sprockets-rails', '3.4.2'
+
+# Bootstrap related gems (https://github.com/twbs/bootstrap-rubygem/tree/4.6-stable)
+gem 'bootstrap', '~> 4.6.2'
+gem 'jquery-rails', '4.6.0'
+gem 'sassc-rails', '>= 2.1.0' # Required for bootstrap, but deprecated
+
+gem 'uglifier'
 
 group :development, :test do
   # Call 'byebug' anywhere in the code to stop execution and get a debugger console

Gemfile.lock

@@ -75,9 +75,15 @@ GEM
       minitest (>= 5.1)
       mutex_m
       tzinfo (~> 2.0)
+    autoprefixer-rails (10.4.16.0)
+      execjs (~> 2)
     base64 (0.2.0)
     bigdecimal (3.1.8)
     bio (1.4.3)
+    bootstrap (4.6.2)
+      autoprefixer-rails (>= 9.1.0)
+      popper_js (>= 1.16.1, < 2)
+      sassc-rails (>= 2.0.0)
     builder (3.2.4)
     byebug (11.1.3)
     concurrent-ruby (1.2.3)
@@ -95,6 +101,8 @@ GEM
       delayed_job (>= 3.0, < 5)
     drb (2.2.1)
     erubi (1.12.0)
+    execjs (2.9.1)
+    ffi (1.16.3)
     globalid (1.2.1)
       activesupport (>= 6.1)
     haml (6.3.0)
@@ -107,6 +115,10 @@ GEM
     irb (1.13.1)
       rdoc (>= 4.0.0)
       reline (>= 0.4.2)
+    jquery-rails (4.6.0)
+      rails-dom-testing (>= 1, < 3)
+      railties (>= 4.2.0)
+      thor (>= 0.14, < 2.0)
     json (2.7.2)
     loofah (2.22.0)
       crass (~> 1.0.2)
@@ -149,6 +161,7 @@ GEM
     passenger (5.1.12)
       rack
       rake (>= 0.8.1)
+    popper_js (1.16.1)
     racc (1.7.3)
     rack (2.2.9)
     rack-cors (2.0.2)
@@ -193,20 +206,33 @@ GEM
     rdoc (4.3.0)
     reline (0.5.5)
       io-console (~> 0.5)
-    rename (1.0.10)
-      activesupport
-      rails (>= 3.0.0)
-      thor (>= 0.19.1)
     rubystats (0.4.1)
       matrix
+    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
     spring (4.2.1)
+    sprockets (4.2.1)
+      concurrent-ruby (~> 1.0)
+      rack (>= 2.2.4, < 4)
+    sprockets-rails (3.4.2)
+      actionpack (>= 5.2)
+      activesupport (>= 5.2)
+      sprockets (>= 3.0.0)
     sqlite3 (1.4.2)
     temple (0.10.3)
     thor (1.3.1)
     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)
     webrick (1.8.1)
     websocket-driver (0.7.6)
       websocket-extensions (>= 0.1.0)
@@ -223,21 +249,25 @@ PLATFORMS
 
 DEPENDENCIES
   bio (= 1.4.3)
+  bootstrap (~> 4.6.2)
   byebug
   config
   daemons
   delayed_job_active_record
   haml
+  jquery-rails (= 4.6.0)
   json
   mysql2 (= 0.4.10)
   nori
   passenger (= 5.1.12)
   rack-cors
   rails (= 7.1.3.2)
-  rename
   rubystats
+  sassc-rails (>= 2.1.0)
   spring
+  sprockets-rails (= 3.4.2)
   sqlite3 (= 1.4.2)
+  uglifier
 
 RUBY VERSION
    ruby 3.3.1p55

app/assets/config/manifest.js

@@ -0,0 +1,91 @@
+//= link_tree ../images
+//= link_tree ../stylesheets
+
+//= link global_tools/sweetalert.min.js
+//= link global_tools/sweetalert.css
+
+//= link main_frame/main_lib.js
+//= link main_frame/ppi_annotations.js
+//= link main_frame/import_proteins.js
+//= link main_frame/upload_data.js
+//= link main_frame/remove_annotations.js
+//= link main_frame/main_init.js
+//= link main_frame/main_inter.js
+//= link main_frame/main_style.css
+//= link main_frame/upload_data.css
+//= link main_frame/remove_annotations.css
+//= link main_frame/import_proteins.css
+//= link main_frame/fontello.css
+//= link main_frame/upload_first_step_form.css
+
+//= link sequence_viewer/jquery-1.4.2.min.js
+//= link sequence_viewer/jquery-ui-1.8.2.custom.min.js
+//= link sequence_viewer/Biojs.js
+//= link sequence_viewer/Biojs.Sequence_alignment.js
+//= link sequence_viewer/Biojs.Tooltip.js
+//= link sequence_viewer/biojs_sequence.css
+//= link sequence_frame/sequence_lib.js
+//= link sequence_frame/sequence_init.js
+//= link sequence_frame/sequence_inter.js
+
+//= link jsmol_viewer/chimeraClass.js
+//= link jsmol_viewer/JSmolClass.js
+//= link jsmol_viewer/bionotes_jsmol.js
+
+//= link jsmol_frame/jsmol_style.css
+//= link jsmol_frame/jsmol_lib.js
+//= link jsmol_frame/jsmol_init.js
+//= link jsmol_frame/jsmol_inter.js
+
+//= link annotations_frame/annotations_lib.js
+//= link annotations_frame/annotations_init.js
+//= link annotations_frame/annotations_inter.js
+//= link annotations_frame/annotations_style.css
+//= link annotations_viewer/protvista.js
+//= link annotations_viewer/featuresAnalysis.bundle.js
+//= link annotations_viewer/analyse_data.js
+//= link annotations_viewer/extendProtVista.bundle.js
+//= link annotations_viewer/extend_data.js
+//= link annotations_viewer/uniprot_viewer_main.css
+//= link annotations_viewer/features_analysis.css
+
+//= link genomic_viewer/genefeaturesviewer.js
+//= link genomic_viewer/genomic_viewer_main.css
+//= link genomic_viewer/genomic_viewer_extension.css
+//= link genomic_frame/genomic_style.css
+//= link genomic_frame/genomic_lib.js
+//= link genomic_frame/genomic_init.js
+//= link genomic_frame/genomic_inter.js
+
+//= link ppi_frame/ppi_style.css
+//= link ppi_frame/cytoscape.min.js
+//= link ppi_frame/rhill-voronoi-core.js
+//= link ppi_frame/foograph.js
+//= link ppi_frame/ppi_lib.js
+//= link ppi_frame/ppi_init.js
+//= link ppi_frame/ppi_inter.js
+//= link ppi_frame/graph_class.js
+//= link interface_viewer/interface_viewer.bundle.js
+
+//= link webserver/webserver_style.css
+//= link webserver/w3.css
+//= link webserver/help_style.css
+//= link webserver/home_style.css
+//= link webserver/webserver_lib.js
+//= link webserver/webserver_init.js
+
+//= link webserver/main.css
+//= link webserver/ekko-lightbox.css
+//= link webserver/imagemapResizer.js
+//= link webserver/carousel.js
+//= link webserver/collapse.js
+//= link webserver/ekko-lightbox.min.js
+//= link webserver/lightbox.js
+//= link covid19.js
+
+//= link webserver/viewer.css
+//= link application.css
+//= link application.js
+
+//= link_tree ../javascripts/3dbio_viewer/build
+//= link_tree ../javascripts/covid19/build

app/assets/javascripts/annotations_frame/annotations_init.js

@@ -1,4 +1,7 @@
-var $j = $.noConflict();
+//= require jquery
+//= require jquery_ujs
+
+var $j = jQuery.noConflict();
 var instance;
 
 $j(document).ready(function(){

app/assets/javascripts/application.js

@@ -1,8 +1,10 @@
-// Changed from 'sprockets' to 'webpack'
-import * as scss from "../stylesheets/application.scss";
+// Bootstrap 4 depends on jquery3, but uses of jquery
+// outside of bootstrap are not checked and we do not
+// use as much functionality in bootstrap. Please note
+// that if some bootstrap functionality is not working,
+// it could potentially be caused by this.
 
-import $ from 'jquery'
-import {} from 'jquery-ujs'
-import 'bootstrap'
-
-window.$j = $;
+//= require jquery
+//= require jquery_ujs
+//= require popper
+//= require bootstrap

app/assets/javascripts/genomic_frame/genomic_lib.js

@@ -1,4 +1,5 @@
-var $j = $.noConflict();
+//= require jquery
+var $j = jQuery.noConflict();
 var ft;
 var start_flag=true;
 

app/assets/javascripts/ppi_frame/ppi_lib.js

@@ -1,3 +1,5 @@
+//= require jquery
+
 function display_active_data(node){
   var ch = node.cyTarget.id();
   var ch_ = ch;

app/assets/javascripts/webserver/webserver_init.js

@@ -1,3 +1,4 @@
+//= require jquery
 (function (window, document, element, src, name, a, m) {
     window["GoogleAnalytics4Object"] = name;
     (window[name] =

app/assets/stylesheets/application.scss

@@ -1,3 +1,5 @@
+@import "bootstrap";
+
 protvista-tooltip table.tooltip {
     position: revert;
     display: revert;

app/assets/stylesheets/bootstrap_and_overrides.css

@@ -1,7 +1,5 @@
 /*
-  =require twitter-bootstrap-static/bootstrap
-
   Use Font Awesome icons (default)
   To use Glyphicons sprites instead of Font Awesome, replace with "require twitter-bootstrap-static/sprites"
-  =require twitter-bootstrap-static/fontawesome
-  */
+  @import twitter-bootstrap-static/fontawesome;
+  */