test pr

.github/workflows/cbrain_ci.yaml

@@ -24,7 +24,7 @@ jobs:
     ###########################################################
     services:
       mariadb:
-        image: mariadb/server
+        image: mariadb
         env: # the docker container's autosetup use MYSQL_ variables
           MYSQL_ROOT_PASSWORD: that_is_nothing
           MYSQL_DATABASE:      cbrain_test
@@ -38,13 +38,13 @@ jobs:
 
       ###########################################################
       - name: Checkout CBRAIN Codebase
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
       ###########################################################
       - name: Setup Ruby
         uses: ruby/setup-ruby@v1
         with:
-          ruby-version: 2.6.6
+          ruby-version: 2.7.2
 
       ###########################################################
       - name: Setup BrainPortal And Bourreau Names
@@ -67,7 +67,7 @@ jobs:
 
       ###########################################################
       - name: Reload Cached Gems
-        uses: actions/cache@v1 # speeds up 'Prepare Ruby Gems' below
+        uses: actions/cache@v3 # speeds up 'Prepare Ruby Gems' below
         with:
           path: gem-cache
           key: ${{ runner.os }}-gems-${{ hashFiles('*/Gemfile') }}

Bourreau/Gemfile

@@ -31,6 +31,7 @@ gem 'rails', '~> 5.0.6'
 # Network components mostly
 gem "net-ssh",       :require => 'net/ssh'
 gem "net-sftp",      :require => 'net/sftp'
+gem "x25519"
 gem "rbnacl"
 gem "ed25519"
 gem "rbnacl-libsodium"
@@ -70,7 +71,8 @@ end
 group :test do
   gem "rspec"
   gem "rspec-rails"
-  gem "factory_bot_rails", :require => false
+  gem "factory_bot",       '6.4.2', :require => false
+  gem "factory_bot_rails", '6.4.2', :require => false
   gem "rails-controller-testing"
   gem "rspec-mocks"
   gem "rspec-activemodel-mocks"

Bourreau/app/models/bourreau_worker.rb

@@ -212,7 +212,9 @@ def process_task_list(tasks_todo_rel) #:nodoc:
       user_max_tasks = @rr.meta["task_limit_user_#{user_id}".to_sym]
       user_max_tasks = @rr.meta[:task_limit_user_default] if user_max_tasks.blank?
       user_max_tasks = user_max_tasks.to_i # nil, "" and "0" means unlimited
-      user_tasks     = by_user[user_id].shuffle # go through tasks in random order
+      # Go through tasks in random order, but with non-New states having higher priority
+      user_tasks     = (by_user[user_id].select { |t| t.status == 'New' }).shuffle +
+                       (by_user[user_id].select { |t| t.status != 'New' }).shuffle  # tasks are pop()ed
 
       # Loop for each task
       while user_tasks.size > 0

Bourreau/app/models/squashifier_en_cbrain_ssh_data_provider.rb

@@ -0,0 +1 @@
+../../../BrainPortal/app/models/squashifier_en_cbrain_ssh_data_provider.rb

Bourreau/config/initializers/validation_bourreau.rb

@@ -52,7 +52,10 @@
     puts "C> \t         environment variable 'CBRAIN_SKIP_VALIDATIONS' to '1'.\n"
     CbrainSystemChecks.check(:all)
     BourreauSystemChecks.check([
-      :a050_ensure_proper_cluster_management_layer_is_loaded, :z000_ensure_we_have_a_forwarded_ssh_agent,
+      :a000_ensure_models_are_preloaded,
+      :a005_ensure_boutiques_descriptors_are_loaded,
+      :a050_ensure_proper_cluster_management_layer_is_loaded,
+      :z000_ensure_we_have_a_forwarded_ssh_agent,
     ])
   end
   Process.setproctitle "CBRAIN Console #{RemoteResource.current_resource.class} #{RemoteResource.current_resource.name} #{CBRAIN::Instance_Name}"

Bourreau/lib/bourreau_system_checks.rb

@@ -484,6 +484,23 @@ def self.a100_ensure_dp_cache_symlink_exists #:nodoc:
 
 
 
+  def self.a110_ensure_task_class_git_commits_cached
+
+    #----------------------------------------------------------------------------
+    puts "C> Ensuring git commits for tasks classes are pre-cached..."
+    #----------------------------------------------------------------------------
+
+    myself = RemoteResource.current_resource
+
+    ToolConfig.where(:bourreau_id => myself.id)
+        .map {|tc| tc.cbrain_task_class rescue nil}
+        .uniq
+        .compact  # to remove the nil
+        .each { |klass| klass.revision_info.self_update }
+  end
+
+
+
   def self.z000_ensure_we_have_a_forwarded_ssh_agent #:nodoc:
 
     #----------------------------------------------------------------------------
@@ -501,4 +518,3 @@ def self.z000_ensure_we_have_a_forwarded_ssh_agent #:nodoc:
   end
 
 end
-

Bourreau/lib/boutiques_collection_basenames_list_maker.rb

@@ -0,0 +1 @@
+../../BrainPortal/lib/boutiques_collection_basenames_list_maker.rb

Bourreau/lib/boutiques_ext3_capturer.rb

@@ -0,0 +1 @@
+../../BrainPortal/lib/boutiques_ext3_capturer.rb

Bourreau/lib/boutiques_input_value_fixer.rb

@@ -0,0 +1 @@
+../../BrainPortal/lib/boutiques_input_value_fixer.rb

Bourreau/lib/boutiques_save_std_out_std_err.rb

@@ -0,0 +1 @@
+../../BrainPortal/lib/boutiques_save_std_out_std_err.rb

Bourreau/lib/boutiques_task_logs_copier.rb

@@ -0,0 +1 @@
+../../BrainPortal/lib/boutiques_task_logs_copier.rb

Bourreau/lib/data_provider_test_connection_error.rb

@@ -0,0 +1 @@
+../../BrainPortal/lib/data_provider_test_connection_error.rb

BrainPortal/Gemfile

@@ -31,10 +31,13 @@ gem 'rails', '~> 5.0.6'
 # Network components mostly
 gem "net-ssh",       :require => 'net/ssh'
 gem "net-sftp",      :require => 'net/sftp'
-gem "rbnacl"
+gem "x25519"
 gem "ed25519"
-gem "rbnacl-libsodium"
 gem "bcrypt_pbkdf"
+# You can comment-out the following two gems if you don't mind not having 'userkey' data providers.
+# They are usually the most tricky to compile and integrate into the app.
+gem "rbnacl"
+gem "rbnacl-libsodium"
 
 # Other utilities
 gem "sys-proctable", '~> 1.2.0'
@@ -46,6 +49,7 @@ gem "json-schema"
 gem "aws-sdk-s3", '~> 1'
 gem 'zenodo_client', '>= 1.0.0', :git => 'https://github.com/aces/zenodo-client-gem'
 gem 'jwt'
+gem "rack-cors"
 
 # User interface gems
 gem "will_paginate"
@@ -65,7 +69,7 @@ gem "activemodel-serializers-xml"
 
 gem 'sassc-rails' # "rake assets:precompile" fails if this gems is put into the :assets group
 group :assets do
-  gem 'therubyracer'
+  #gem 'therubyracer'  # very old; consider installing ANY other JS engine, like 'node'. If not, try 'mini_racer'.
   gem 'coffee-rails'
   gem 'uglifier'
 end
@@ -90,7 +94,8 @@ end
 group :test do
   gem "rspec"
   gem "rspec-rails"
-  gem "factory_bot_rails", :require => false
+  gem "factory_bot",       '6.4.2', :require => false
+  gem "factory_bot_rails", '6.4.2', :require => false
   gem "rails-controller-testing"
   gem "rspec-mocks"
   gem "rspec-activemodel-mocks"

BrainPortal/app/assets/stylesheets/cbrain.css.erb

@@ -3,7 +3,7 @@
 #
 # CBRAIN Project
 #
-# Copyright (C) 2008-2012
+# Copyright (C) 2008-2023
 # The Royal Institution for the Advancement of Learning
 # McGill University
 #
@@ -441,9 +441,9 @@ table.bordered {
 
 table.public_tools_list {
   border: 0px;
-  margin-left: auto;
-  margin-right: auto;
-  margin-bottom: 2em;
+  display: table-cell;
+  padding-bottom: 1em;
+  padding-right: 1em;
 }
 
 table.public_tools_list tr {
@@ -458,7 +458,7 @@ table.public_tools_list th {
 table.public_tools_list td {
   border: 0px;
   border-bottom: 0.2em solid #999;
-  max-width: 60em;
+  max-width: 30em;
 }
 
 
@@ -804,6 +804,10 @@ pre {
   line-height: 1.3em;
   border: 0.2em solid black;
   padding: 0.4em;
+  word-break: break-all;
+  overflow-wrap: break-word;
+  text-align: left;
+  table-layout: fixed;
 }
 
 .script_preview {
@@ -880,7 +884,7 @@ pre {
 }
 
 .errorExplanation {
-  width: 400px;
+  width: 600px;
   border: 2px solid red;
   padding: 7px;
   padding-bottom: 12px;
@@ -1138,18 +1142,16 @@ pre {
   float: left;
   text-align: center;
   text-decoration: none;
-  color: white;
   padding: 0.4em;
   margin: 2em ;
   width: 18em;
   height: 9em;
-  border: 0.4em gray solid;
+  border: 0.5em black solid;
   border-radius: 1em;
   cursor: pointer;
 }
 
-.project_button h4{
-  color: white;
+.project_button h4 {
   font-weight: bold;
   border-bottom: none;
   margin-bottom: 0;
@@ -1163,13 +1165,24 @@ pre {
 
 .project_button_bottom_link {
   font-size: 10px;
-  color: white;
   font-weight: bold;
   text-decoration: none;
   position: absolute;
   bottom: 1px;
 }
 
+.project_user_count {
+  color: #660000;
+}
+
+.project_files_count {
+  color: #006600;
+}
+
+.project_tasks_count {
+  color: #000066;
+}
+
 .project_button_description {
   font-style: italic;
   line-height: 1.2em;
@@ -1180,48 +1193,30 @@ pre {
 }
 
 .project_edit_button {
-  left: 5px;
+  left: 1em;
 }
 
 .project_delete_button {
-  right: 5px;
+  right: 1em;
 }
 
-.system_project_point     { color:      #d41c1c; }
-.system_project           { background: #d41c1c; }
-.system_project:active    { background: #d41c1c; }
-
-.everyone_project_point   { color:      #af0b0b; }
-.everyone_project         { background: #af0b0b; }
-.everyone_project:active  { background: #af0b0b; }
-
-.site_project_point       { color:      #8c0953; }
-.site_project             { background: #8c0953; }
-.site_project:active      { background: #8c0953; }
+.everyone_project         { background: #bbbbbb; }
+.everyone_project:active  { background: #bbbbbb; }
 
-.user_project_point       { color:      #500d75; }
-.user_project             { background: #500d75; }
-.user_project:active      { background: #500d75; }
+.site_project             { background: #dbf7cc; }
+.site_project:active      { background: #dbf7cc; }
 
-.shared_project_point     { color:      #00bf09; }
-.shared_project           { background: #00bf09; }
-.shared_project:active    { background: #00bf09; }
+.user_project             { background: #bbbbbb; }
+.user_project:active      { background: #bbbbbb; }
 
-.public_project_point     { color:      #9e5400; }
-.public_project           { background: #9e5400; }
-.public_project:active    { background: #9e5400; }
+.shared_project           { background: #A5D1DF; }
+.shared_project:active    { background: #A5D1DF; }
 
-.personal_project_point   { color:      #008686; }
-.personal_project         { background: #008686; }
-.personal_project:active  { background: #008686; }
+.public_project           { background: #fdcece; }
+.public_project:active    { background: #fdcece; }
 
-.invisible_project_point  { color:      #2b97c1; }
-.invisible_project        { background: #2b97c1; }
-.invisible_project:active { background: #2b97c1; }
-
-.empty_project_point      { color:      #d7ca0a; }
-.empty_project            { background: #d7ca0a; }
-.empty_project:active     { background: #d7ca0a; }
+.private_project          { background: #eeeeee; }
+.private_project:active   { background: #eeeeee; }
 
 .giant {
   margin-top: 0.3em;
@@ -2460,6 +2455,7 @@ img {
   color: black;
   padding: 5px;
   border: 1px solid black;
+  max-width: 42em;
 }
 
 .white_bg {
@@ -2623,6 +2619,26 @@ img {
   display: table-cell;
 }
 
+/* % ######################################################### */
+/* % Disk Quota Styles */
+/* % ######################################################### */
+
+.disk_quota_user_quota_highlight {
+  background-color: #ffd; /* light yellow */
+}
+
+.disk_quota_dp_quota_highlight {
+  background-color: #ffd; /* light yellow */
+}
+
+.disk_quota_exceed_bytes {
+  background-color: #fdd; /* light pink */
+}
+
+.disk_quota_exceed_files {
+  background-color: #fdd; /* light pink */
+}
+
 /* % ######################################################### */
 /* % Report Generator Styles */
 /* % ######################################################### */

BrainPortal/app/assets/stylesheets/neurohub.scss.erb

@@ -3220,6 +3220,7 @@ $DASHBOARD_CARD_MIN_WIDTH: 25;
     border: 1px solid $DEFAULT_ALT;
     border-radius: 2px;
     overflow: scroll;
+    box-sizing: border-box;
   }
   .license-list {
     background: $PRIMARY_WASH;