diff --git a/.github/workflows/cbrain_ci.yaml b/.github/workflows/cbrain_ci.yaml index 6495e1ec4..9f76043fb 100644 --- a/.github/workflows/cbrain_ci.yaml +++ b/.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') }} diff --git a/.travis.yml.old b/.travis.yml.old deleted file mode 100644 index bf8e7cc23..000000000 --- a/.travis.yml.old +++ /dev/null @@ -1,14 +0,0 @@ -# -# This used to be our Travis CI test script. -# This has been replaced by GitHub actions. -# -services: -- docker -script: -- bash Travis/travis_ci.sh -notifications: - slack: - rooms: - - secure: "gtJ4qanurja+/Ew0ChaeStjsZVC65nGC1uVPLEnZo05q0q8EsmMXpUCvnWSJu7xl42mrivOEmNns6xrrevGuKg0PiVZtKaj9njCGT2SRYZcvrAVZl17Q5pnNIFeRkmdiKp18sE071FKS11a8M4+K2nV1o6eupfOqNUWAWAmQAdI=" - - secure: "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" - - secure: "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" diff --git a/Bourreau/Gemfile b/Bourreau/Gemfile index cb0798fb2..3094bcea8 100644 --- a/Bourreau/Gemfile +++ b/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" diff --git a/Bourreau/app/models/bourreau_worker.rb b/Bourreau/app/models/bourreau_worker.rb index 231c0564c..f37789965 100644 --- a/Bourreau/app/models/bourreau_worker.rb +++ b/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 diff --git a/Bourreau/app/models/squashifier_en_cbrain_ssh_data_provider.rb b/Bourreau/app/models/squashifier_en_cbrain_ssh_data_provider.rb new file mode 120000 index 000000000..59016b55a --- /dev/null +++ b/Bourreau/app/models/squashifier_en_cbrain_ssh_data_provider.rb @@ -0,0 +1 @@ +../../../BrainPortal/app/models/squashifier_en_cbrain_ssh_data_provider.rb \ No newline at end of file diff --git a/Bourreau/config/initializers/validation_bourreau.rb b/Bourreau/config/initializers/validation_bourreau.rb index a43888a18..6cce6f35a 100644 --- a/Bourreau/config/initializers/validation_bourreau.rb +++ b/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}" diff --git a/Bourreau/lib/bourreau_system_checks.rb b/Bourreau/lib/bourreau_system_checks.rb index 7b13161ac..b0d243c70 100644 --- a/Bourreau/lib/bourreau_system_checks.rb +++ b/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 - diff --git a/Bourreau/lib/boutiques_collection_basenames_list_maker.rb b/Bourreau/lib/boutiques_collection_basenames_list_maker.rb new file mode 120000 index 000000000..0d8942f80 --- /dev/null +++ b/Bourreau/lib/boutiques_collection_basenames_list_maker.rb @@ -0,0 +1 @@ +../../BrainPortal/lib/boutiques_collection_basenames_list_maker.rb \ No newline at end of file diff --git a/Bourreau/lib/boutiques_ext3_capturer.rb b/Bourreau/lib/boutiques_ext3_capturer.rb new file mode 120000 index 000000000..d33b38e1c --- /dev/null +++ b/Bourreau/lib/boutiques_ext3_capturer.rb @@ -0,0 +1 @@ +../../BrainPortal/lib/boutiques_ext3_capturer.rb \ No newline at end of file diff --git a/Bourreau/lib/boutiques_input_value_fixer.rb b/Bourreau/lib/boutiques_input_value_fixer.rb new file mode 120000 index 000000000..153073c7c --- /dev/null +++ b/Bourreau/lib/boutiques_input_value_fixer.rb @@ -0,0 +1 @@ +../../BrainPortal/lib/boutiques_input_value_fixer.rb \ No newline at end of file diff --git a/Bourreau/lib/boutiques_save_std_out_std_err.rb b/Bourreau/lib/boutiques_save_std_out_std_err.rb new file mode 120000 index 000000000..7336628e0 --- /dev/null +++ b/Bourreau/lib/boutiques_save_std_out_std_err.rb @@ -0,0 +1 @@ +../../BrainPortal/lib/boutiques_save_std_out_std_err.rb \ No newline at end of file diff --git a/Bourreau/lib/boutiques_task_logs_copier.rb b/Bourreau/lib/boutiques_task_logs_copier.rb new file mode 120000 index 000000000..b84290e0c --- /dev/null +++ b/Bourreau/lib/boutiques_task_logs_copier.rb @@ -0,0 +1 @@ +../../BrainPortal/lib/boutiques_task_logs_copier.rb \ No newline at end of file diff --git a/Bourreau/lib/data_provider_test_connection_error.rb b/Bourreau/lib/data_provider_test_connection_error.rb new file mode 120000 index 000000000..ee01c5c55 --- /dev/null +++ b/Bourreau/lib/data_provider_test_connection_error.rb @@ -0,0 +1 @@ +../../BrainPortal/lib/data_provider_test_connection_error.rb \ No newline at end of file diff --git a/BrainPortal/Gemfile b/BrainPortal/Gemfile index 58571094f..95c062d97 100644 --- a/BrainPortal/Gemfile +++ b/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" diff --git a/BrainPortal/app/assets/stylesheets/cbrain.css.erb b/BrainPortal/app/assets/stylesheets/cbrain.css.erb index cc28238fb..b925a5dd2 100644 --- a/BrainPortal/app/assets/stylesheets/cbrain.css.erb +++ b/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 */ /* % ######################################################### */ diff --git a/BrainPortal/app/assets/stylesheets/neurohub.scss.erb b/BrainPortal/app/assets/stylesheets/neurohub.scss.erb index 1010e4ae1..ef6aeab25 100644 --- a/BrainPortal/app/assets/stylesheets/neurohub.scss.erb +++ b/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; diff --git a/BrainPortal/app/controllers/data_providers_controller.rb b/BrainPortal/app/controllers/data_providers_controller.rb index e1113e722..24cd5e3f7 100644 --- a/BrainPortal/app/controllers/data_providers_controller.rb +++ b/BrainPortal/app/controllers/data_providers_controller.rb @@ -2,7 +2,7 @@ # # CBRAIN Project # -# Copyright (C) 2008-2012 +# Copyright (C) 2008-2023 # The Royal Institution for the Advancement of Learning # McGill University # @@ -28,11 +28,12 @@ class DataProvidersController < ApplicationController Revision_info=CbrainFileRevision[__FILE__] #:nodoc: api_available :only => [ :index, :show, :is_alive, - :browse, :register, :unregister, :delete ] + :browse, :register, :unregister, :delete, + :create_personal, :check_personal, ] before_action :login_required before_action :manager_role_required, :only => [:new, :create] - before_action :admin_role_required, :only => [:report, :repair] + before_action :admin_role_required, :only => [:new, :create, :report, :repair] def index #:nodoc: @scope = scope_from_session @@ -61,7 +62,6 @@ def index #:nodoc: def show #:nodoc: data_provider_id = params[:id] @provider = DataProvider.find(data_provider_id) - cb_notice "Provider not accessible by current user." unless @provider.can_be_accessed_by?(current_user) respond_to do |format| @@ -86,8 +86,8 @@ def new #:nodoc: @typelist = get_type_list end - def create #:nodoc: - @provider = DataProvider.sti_new(data_provider_params) + def create #:nodoc: + @provider = DataProvider.sti_new(data_provider_params) @provider.user_id ||= current_user.id # disabled field in form DOES NOT send value! @provider.group_id ||= current_assignable_group.id @@ -110,6 +110,49 @@ def create #:nodoc: end end + def new_personal #:nodoc: + provider_group_id = current_assignable_group.id + @provider = UserkeyFlatDirSshDataProvider.new( :user_id => current_user.id, + :group_id => provider_group_id, + :online => true, + :read_only => false + ) + @groups = current_user.assignable_groups + end + + # create by normal user, only UserkeyFlatDirSshDataProvider + def create_personal + normal_params = params.require_as_params(:data_provider) + .permit(:name, :description, :group_id, + :remote_user, :remote_host, + :remote_port, :remote_dir + ) + group_id = normal_params[:group_id] + current_user.assignable_group_ids.find(group_id) # ensure assignable, not sure need check visibility etc more + @provider = UserkeyFlatDirSshDataProvider.new(normal_params) + @provider.user_id = current_user.id # prevent creation of dp on behalf of other users + + if ! @provider.save + @groups = current_user.assignable_groups + respond_to do |format| + format.html { render :action => :new_personal} + format.json { render :json => @provider.errors, :status => :unprocessable_entity } + end + return + end + + @provider.addlog_context(self, "Created by #{current_user.login}") + @provider.meta[:browse_gid] = current_user.own_group.id + flash[:notice] = "Provider successfully created. Please click the Test Configuration button."\ + " This will run tests on the current storage configuration. Note that if these tests fail,"\ + " the storage will be marked 'offline'." + + respond_to do |format| + format.html { redirect_to :action => :show, :id => @provider.id} + format.json { render :json => @provider } + end + end + def update #:nodoc: @user = current_user id = params[:id] @@ -125,35 +168,29 @@ def update #:nodoc: return end - new_data_provider_attr = data_provider_params + # hacking prevention + # this guaranties that users do not change group to something + group_id = params[:group_id] + current_user.assignable_group_ids.find(group_id) if ! current_user.has_role?(:admin_user) + + new_data_provider_attr = data_provider_params(@provider) new_data_provider_attr.delete :type # Type cannot be updated once it is set. # Fields that stay the same if the form provides a blank entry: new_data_provider_attr.delete :cloud_storage_client_token if new_data_provider_attr[:cloud_storage_client_token].blank? - if @provider.update_attributes_with_logging(new_data_provider_attr, current_user, - %w( - remote_user remote_host remote_port remote_dir - not_syncable cloud_storage_client_identifier cloud_storage_client_token - cloud_storage_client_bucket_name cloud_storage_client_path_start - cloud_storage_endpoint cloud_storage_region - datalad_repository_url datalad_relative_path - containerized_path - ) - ) + if @provider.update_attributes_with_logging(new_data_provider_attr, current_user, @provider.attributes.keys) meta_flags_for_restrictions = (params[:meta] || {}).keys.grep(/\Adp_no_copy_\d+\z|\Arr_no_sync_\d+\z/) add_meta_data_from_form(@provider, [:must_move, :no_uploads, :no_viewers, :browse_gid] + meta_flags_for_restrictions) flash[:notice] = "Provider successfully updated." respond_to do |format| format.html { redirect_to :action => :show } - format.xml { render :xml => @provider } - format.json { render :json => @provider } + format.json { render :json => @provider } end else @provider.reload respond_to do |format| format.html { render :action => 'show' } - format.xml { render :xml => @provider.errors, :status => :unprocessable_entity } format.json { render :json => @provider.errors, :status => :unprocessable_entity } end end @@ -819,9 +856,59 @@ def repair end end + # This action checks that the remote side of a Ssh DataProvider is + # accessible using SSH. Regretfully, does not guaranty that connection is possible. + # If check fails it raises an exception of class DataProviderTestConnectionError + def check_personal + id = params[:id] + @provider = DataProvider.find(id) + unless @provider.has_owner_access?(current_user) + flash[:error] = "You cannot check a provider that you do not own." + respond_to do |format| + format.html { redirect_to :action => :show } + format.xml { head :forbidden } + format.json { head :forbidden } + end + return + end + + unless @provider.is_a? SshDataProvider + flash[:error] = "Presently, detailed check is only available to ssh providers." + respond_to do |format| + format.html { redirect_to :action => :show } + format.xml { head :forbidden } + format.json { head :forbidden } + end + return + end + + # Do active checks of the connection. Will + # raise DataProviderTestConnectionError if anything is wrong. + @provider.check_connection! + + # Ok, all is well. + @provider.update_column(:online, true) + flash[:notice] = "The configuration was tested and seems to be operational." + + respond_to do |format| + format.html { redirect_to :action => :show } + format.json { render :json => 'ok' } + end + + rescue DataProviderTestConnectionError => ex + flash[:error] = ex.message + flash[:error] += "\nThis storage is marked as 'offline' until this test pass." + @provider.update_column(:online, false) + + respond_to do |format| + format.html { redirect_to :action => :show } + format.json { render :json => 'not ok' } + end + end + private - def data_provider_params #:nodoc: + def data_provider_params(for_data_provider=nil) #:nodoc: if current_user.has_role?(:admin_user) params.require_as_params(:data_provider).permit( :name, :user_id, :group_id, :remote_user, :remote_host, :alternate_host, @@ -836,17 +923,15 @@ def data_provider_params #:nodoc: :license_agreements, :containerized_path ) - else - # Normal users are not allowed to change - # some parameters that would allow them to access things - # they don't control. + elsif for_data_provider.is_a?(UserkeyFlatDirSshDataProvider) params.require_as_params(:data_provider).permit( - :name, :description, :group_id, :time_zone, - :alternate_host, + :name, :description, :group_id, + :remote_user, :remote_host, :remote_port, :remote_dir, :online, :read_only, :not_syncable, - :datalad_repository_url, :datalad_relative_path, - :license_agreements, - :containerized_path + ) + else # place for future expansion; be careful to not introduce security bugs + params.require_as_params(:data_provider).permit( + :description, ) end end @@ -855,6 +940,8 @@ def get_type_list #:nodoc: data_provider_list = [ "FlatDirSshDataProvider" ] if check_role(:site_manager) || check_role(:admin_user) data_provider_list = DataProvider.descendants.map(&:name) + data_provider_list.delete(UserkeyFlatDirSshDataProvider.name) # this type is for regular users + # not for admins end grouped_options = data_provider_list.to_a.hashed_partitions { |name| name.constantize.pretty_category_name } grouped_options.delete(nil) # data providers that can not be on this list return a category name of nil, so we remove them diff --git a/BrainPortal/app/controllers/disk_quotas_controller.rb b/BrainPortal/app/controllers/disk_quotas_controller.rb index 9eb9117b1..c111f425d 100644 --- a/BrainPortal/app/controllers/disk_quotas_controller.rb +++ b/BrainPortal/app/controllers/disk_quotas_controller.rb @@ -124,6 +124,56 @@ def destroy #:nodoc: redirect_to disk_quotas_path end + # Returns a list of users with exceeded quotas + def report #:nodoc: + quota_to_user_ids = {} # quota_obj => [uid, uid...] + + # Scan DP-wide quota objects + DiskQuota.where(:user_id => 0).all.each do |quota| + exceed_size_user_ids = Userfile + .where(:data_provider_id => quota.data_provider_id) + .group(:user_id) + .sum(:size) + .select { |user_id,size| size >= quota.max_bytes } + .keys + exceed_numfiles_user_ids = Userfile + .where(:data_provider_id => quota.data_provider_id) + .group(:user_id) + .sum(:num_files) + .select { |user_id,num_files| num_files >= quota.max_files } + .keys + union_ids = exceed_size_user_ids | exceed_numfiles_user_ids + union_ids -= DiskQuota + .where(:data_provider_id => quota.data_provider_id, :user_id => union_ids) + .pluck(:user_id) # remove user IDs that have their own quota records + quota_to_user_ids[quota] = union_ids if union_ids.size > 0 + end + + # Scan user-specific quota objects + DiskQuota.where('user_id > 0').all.each do |quota| + quota_to_user_ids[quota] = [ quota.user_id ] if quota.exceeded? + end + + # Inverse relation: user_id => [ quota, quota ] + user_id_to_quotas = {} + quota_to_user_ids.each do |quota,user_ids| + user_ids.each do |user_id| + user_id_to_quotas[user_id] ||= [] + user_id_to_quotas[user_id] << quota + end + end + + # Table content: [ [ user_id, quota ], [user_id, quota] ... ] + # Note: the rows are grouped by user_id, but not sorted in any way... + @user_id_and_quota = [] + user_id_to_quotas.each do |user_id, quotas| + quotas.each do |quota| + @user_id_and_quota << [ user_id, quota ] + end + end + + end + private def disk_quota_params #:nodoc: @@ -145,10 +195,11 @@ def base_scope #:nodoc: scope end - # Tries to turn strings like '3 mb' into 3_000_000 etc - # Supported suffixes are T, G, M, K, TB, GB, MB, KB, B (case insensitive) + # Tries to turn strings like '3 mb' into 3_000_000 etc. + # Supported suffixes are T, G, M, K, TB, GB, MB, KB, B (case insensitive). + # Negative values are parsed, but the DiskQuota model only accepts the special -1 def guess_size_units(sizestring) - match = sizestring.match /\A\s*(\d*\.?\d+)\s*([tgmk]?)\s*b?\s*\z/i + match = sizestring.match(/\A\s*(-?\d*\.?\d+)\s*([tgmk]?)\s*b?\s*\z/i) return "" unless match # parsing error number = match[1] suffix = match[2].presence&.downcase || 'u' diff --git a/BrainPortal/app/controllers/groups_controller.rb b/BrainPortal/app/controllers/groups_controller.rb index 7ee6f2c33..57fc7c093 100644 --- a/BrainPortal/app/controllers/groups_controller.rb +++ b/BrainPortal/app/controllers/groups_controller.rb @@ -48,21 +48,22 @@ def index #:nodoc: @scope.custom[:button] = true if current_user.has_role?(:normal_user) && @scope.custom[:button].nil? + view_mode = (@scope.custom[:button].present?) ? :button : :list + @base_scope = current_user.listable_groups.includes(:site) @view_scope = @scope.apply(@base_scope) - @scope.pagination ||= Scope::Pagination.from_hash({ :per_page => 50 }) - @groups = @scope.pagination.apply(@view_scope) - @groups = (@groups.to_a << 'ALL') if @scope.custom[:button] + if view_mode == :list + @scope.pagination ||= Scope::Pagination.from_hash({ :per_page => 50 }) + @groups = @scope.pagination.apply(@view_scope) + else + @groups = @view_scope.to_a + end # For regular groups @group_id_2_userfile_counts = Userfile.find_all_accessible_by_user(current_user, :access_requested => :read).group("group_id").count @group_id_2_task_counts = CbrainTask.find_all_accessible_by_user(current_user).group("group_id").count @group_id_2_user_counts = User.joins(:groups).group("group_id").count.convert_keys!(&:to_i) # .joins make keys as string - @group_id_2_tool_counts = Tool.find_all_accessible_by_user(current_user).group("group_id").count - @group_id_2_data_provider_counts = DataProvider.find_all_accessible_by_user(current_user).group("group_id").count - @group_id_2_bourreau_counts = Bourreau.find_all_accessible_by_user(current_user).group("group_id").count - @group_id_2_brain_portal_counts = BrainPortal.find_all_accessible_by_user(current_user).group("group_id").count # For `ALL` group @group_id_2_userfile_counts[nil] = Userfile.find_all_accessible_by_user(current_user, :access_requested => :read).count @@ -275,12 +276,12 @@ def group_params #:nodoc: params.require_as_params(:group).permit( :name, :description, :not_assignable, :site_id, :creator_id, :invisible, :track_usage, - :user_ids => [] + :public, :user_ids => [] ) else # non admin users params.require_as_params(:group).permit( :name, :description, :not_assignable, - :user_ids => [] + :public, :user_ids => [] ) end end diff --git a/BrainPortal/app/controllers/nh_loris_hooks_controller.rb b/BrainPortal/app/controllers/nh_loris_hooks_controller.rb index 66d4a9867..9679b9990 100644 --- a/BrainPortal/app/controllers/nh_loris_hooks_controller.rb +++ b/BrainPortal/app/controllers/nh_loris_hooks_controller.rb @@ -64,6 +64,11 @@ def file_list_maker s_group = Group.where_id_or_name(source_group_id).first if source_group_id base = Userfile.where(nil) # As seen in userfiles_controller base = Userfile.restrict_access_on_query(current_user, base, :access_requested => :read) + + extended_values = ExtendedCbrainFileList.roots_to_fullpaths(source_basenames) + source_basenames = extended_values.keys + is_extended = extended_values.any?{|parent_dir,pathlist| pathlist.present? } + userfiles = base.where(:name => source_basenames) userfiles = userfiles.where(:data_provider_id => s_dp.id) if s_dp userfiles = userfiles.where(:group_id => s_group.id) if s_group @@ -71,17 +76,22 @@ def file_list_maker # It is an error not to find exactly the same number of files as in # the params' basenames array found_names = userfiles.pluck(:name) - file_count = found_names.size - exp_count = source_basenames.size + file_count = found_names.size + exp_count = source_basenames.size if (file_count == 0) || (strict_match && (file_count != exp_count)) cb_error "Could not find an exact match for the files. Found #{file_count} of #{exp_count} files" end - # Create CbrainFileList content and save it to DP - cblist_content = CbrainFileList.create_csv_file_from_userfiles(userfiles) - - # Save result file - result = create_file_for_request(CbrainFileList, "Loris-DQT-List.cbcsv", cblist_content) + result = nil + if is_extended + new_extended = extended_values.transform_values {|relpaths| { :all_to_keep => relpaths }.to_json } + userfiles = ExtendedCbrainFileList.extended_userfiles_by_name(userfiles, new_extended) + cblist_content = ExtendedCbrainFileList.create_csv_file_from_userfiles(userfiles) + result = create_file_for_request(ExtendedCbrainFileList, "Extended-Loris-DQT-List.cbcsv", cblist_content) + else + cblist_content = CbrainFileList.create_csv_file_from_userfiles(userfiles) + result = create_file_for_request(CbrainFileList, "Loris-DQT-List.cbcsv", cblist_content) + end # Info message and unmatched entries extra_response = { diff --git a/BrainPortal/app/controllers/nh_storages_controller.rb b/BrainPortal/app/controllers/nh_storages_controller.rb index ecda963b8..be5281ec1 100644 --- a/BrainPortal/app/controllers/nh_storages_controller.rb +++ b/BrainPortal/app/controllers/nh_storages_controller.rb @@ -29,9 +29,6 @@ class NhStoragesController < NeurohubApplicationController before_action :login_required - # A private exception class when testing connectivity - class UserKeyTestConnectionError < RuntimeError ; end - def new #:nodoc: @nh_dp = UserkeyFlatDirSshDataProvider.new @nh_projects = find_nh_projects(current_user) @@ -204,70 +201,19 @@ def check @nh_dp.update_column(:online, true) - master = @nh_dp.master # This is a handler for the connection, not persistent. - tmpfile = "/tmp/dp_check.#{Process.pid}.#{rand(1000000)}" - - # Check #1: the SSH connection can be established - if ! master.is_alive? - test_error "Cannot establish the SSH connection. Check the configuration: username, hostname, port are valid, and SSH key is installed." - end - - # Check #2: we can run "true" on the remote site and get no output - status = master.remote_shell_command_reader("true", - :stdin => "/dev/null", - :stdout => "#{tmpfile}.out", - :stderr => "#{tmpfile}.err", - ) - stdout = File.read("#{tmpfile}.out") rescue "Error capturing stdout" - stderr = File.read("#{tmpfile}.err") rescue "Error capturing stderr" - if stdout.size != 0 - stdout.strip! if stdout.present? # just to make it pretty while still reporting whitespace-only strings - test_error "Remote shell is not clean: got some bytes on stdout: '#{stdout}'" - end - if stderr.size != 0 - stderr.strip! if stdout.present? - test_error "Remote shell is not clean: got some bytes on stderr: '#{stderr}'" - end - if ! status - test_error "Got non-zero return code when trying to run 'true' on remote side." - end - - # Check #3: the remote directory exists - master.remote_shell_command_reader "test -d #{@nh_dp.remote_dir.bash_escape} && echo DIR-OK", :stdout => tmpfile - out = File.read(tmpfile) - if out != "DIR-OK\n" - test_error "The remote directory doesn't seem to exist." - end - - # Check #4: the remote directory is readable - master.remote_shell_command_reader "test -r #{@nh_dp.remote_dir.bash_escape} && test -x #{@nh_dp.remote_dir.bash_escape} && echo DIR-READ", :stdout => tmpfile - out = File.read(tmpfile) - if out != "DIR-READ\n" - test_error "The remote directory doesn't seem to be readable" - end + # Performs an active check of the connection; will + # raise DataProviderTestConnectionError if something is wrong. + @nh_dp.check_connection! # Ok, all is well. flash[:notice] = "The configuration was tested and seems to be operational." redirect_to :action => :show - rescue UserKeyTestConnectionError => ex + rescue DataProviderTestConnectionError => ex flash[:error] = ex.message flash[:error] += "\nThis storage is marked as 'offline' until this test pass." @nh_dp.update_column(:online, false) redirect_to :action => :show - - ensure - File.unlink "#{tmpfile}.out" rescue true - File.unlink "#{tmpfile}.err" rescue true - - end - - private - - # Utility method to raise an exception - # when testing for a DP's configuration. - def test_error(message) #:nodoc: - raise UserKeyTestConnectionError.new(message) end end diff --git a/BrainPortal/app/controllers/noc_controller.rb b/BrainPortal/app/controllers/noc_controller.rb index 4c84835a3..6414c4dd9 100644 --- a/BrainPortal/app/controllers/noc_controller.rb +++ b/BrainPortal/app/controllers/noc_controller.rb @@ -255,7 +255,7 @@ def gather_info(since_when) #:nodoc: # Count of active statuses info[:status_counts] = b.is_a?(BrainPortal) ? [] : - b.cbrain_tasks.where(["updated_at > ?", since_when ]) + b.cbrain_tasks.where(["updated_at > ? or status in (?)", since_when, CbrainTask::RUNNING_STATUS ]) .group(:status) .count .to_a # [ [ status, count ], [ status, count ] ... ] diff --git a/BrainPortal/app/controllers/portal_controller.rb b/BrainPortal/app/controllers/portal_controller.rb index 86b410585..fdb65b600 100644 --- a/BrainPortal/app/controllers/portal_controller.rb +++ b/BrainPortal/app/controllers/portal_controller.rb @@ -27,9 +27,9 @@ class PortalController < ApplicationController include DateRangeRestriction - api_available :only => [ :swagger ] # GET /swagger returns the .json specification + api_available :only => [ :swagger, :stats ] # GET /swagger returns the .json specification - before_action :login_required, :except => [ :credits, :about_us, :welcome, :swagger, :available ] # welcome is here so that the redirect to the login page doesn't show the error message + before_action :login_required, :except => [ :credits, :about_us, :welcome, :swagger, :available, :stats ] # welcome is here so that the redirect to the login page doesn't show the error message before_action :admin_role_required, :only => :portal_log # Display a user's home page with information about their account. @@ -253,7 +253,6 @@ def available #:nodoc: .select { |t| t.tool_configs.to_a.any? { |tc| tc.bourreau_id.present? && tc.bourreau_id > 0 && - tc.bourreau.try(:online) && # comment out to show them all tc.version_name.present? } } @@ -444,6 +443,22 @@ def swagger end end + # Return information about the usage of the platform. + def stats + @stats = RemoteResource.current_resource.meta[:stats] || {} + @stats_by_client = @stats[:UserAgents] || {} + @stats_by_contr_action = compile_total_stats(@stats) + + @last_reset = (RemoteResource.current_resource.meta.md_for_key(:stats).created_at || Time.at(0)).utc.iso8601 + @stats[:lastReset] = @last_reset + + respond_to do |format| + format.html + format.xml { render :xml => @stats } + format.json { render :json => @stats } + end + end + private def merge_vals_as_array(*sub_reports) #:nodoc: @@ -486,4 +501,26 @@ def colorize_logs(data) #:nodoc: data end + # From the raw stats accumulated for all clients, + # controllers and actions, compile two other + # secondary stats: the sums by clients, and + # the sums by pair "controller,service". + def compile_total_stats(stats={}) #:nodoc: + stats_by_contr_action = {} + + # stats['AllAgents'] is { 'controller' => { 'action' => [1,2] , ... }, ... } + all_agents = stats['AllAgents'] || stats[:AllAgents] || {} + all_agents.each do |controller, by_action| + by_action.each do |action, counts| + # By controller and action + contr_action = "#{controller},#{action}" + stats_by_contr_action[contr_action] ||= [0,0] + stats_by_contr_action[contr_action][0] += counts[0] + stats_by_contr_action[contr_action][1] += counts[1] + end + end + + return stats_by_contr_action + end + end diff --git a/BrainPortal/app/controllers/service_controller.rb b/BrainPortal/app/controllers/service_controller.rb deleted file mode 100644 index 0269d3fa6..000000000 --- a/BrainPortal/app/controllers/service_controller.rb +++ /dev/null @@ -1,222 +0,0 @@ - -# -# CBRAIN Project -# -# Copyright (C) 2008-2012 -# The Royal Institution for the Advancement of Learning -# McGill University -# -# This program is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation, either version 3 of the License, or -# (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with this program. If not, see . -# - -# Controller for the Service. -# Implement actions as defined by the CANARIE Web Service Monitoring API. -# -# By default, all these actions are commented out in the route.rb file, -# so for most installations this controller is NOT USED at all. -class ServiceController < ApplicationController - - Revision_info=CbrainFileRevision[__FILE__] #:nodoc: - - api_available - - # Return basic identification and provenance - # information about the platform - def info - @info = { :name => "CBRAIN Data Platform", - :synopsis => <<-SYNOPSYS.strip.gsub(/\s\s+/, " "), # the ugly gsub is because of CANARIE - - The CBRAIN platform is a web-based, collaborative research platform - designed to address major issues in "Big Data" research through a - single consistent framework by providing researchers the ability - to easily execute large-scale pipelines for computational research. - The platform's primary objective is to provide a user-friendly, - extensible, integrated, and robust yet lightweight collaborative - neuroimaging research platform providing transparent access to the - heterogeneous computing and data resources available across Canada - and around the world. - - SYNOPSYS - :version => CbrainFileRevision.cbrain_head_tag, - :institution => "McGill University", - :releaseTime => Time.parse(CbrainFileRevision.cbrain_head_revinfo.datetime).utc.iso8601, - :researchSubject => "Multi-discipline", - :supportEmail => RemoteResource.current_resource.support_email, - :tags => [ "neurology", "CBRAIN", "data transfer", "cluster", - "supercomputer", "task", "data modeling", "visualization", - ], - } - - respond_to do |format| - format.html - format.xml { render :xml => @info } - format.json { render :json => @info } - end - end - - # Return information about the usage of the platform. - def stats - stats = RemoteResource.current_resource.meta[:stats] || {} - stats_by_contr_action = compile_total_stats(stats) - - @summary_stats = stats['UserAgents'].dup - @last_reset = (RemoteResource.current_resource.meta.md_for_key(:stats).try(:created_at) || Time.now).utc.iso8601 - authenticated_actions = count_authenticated_actions(stats_by_contr_action) - @summary_stats["TotalActions"] = authenticated_actions - @summary_stats["lastReset"] = @last_reset - - # CANARIE only wants TWO fields. :-( - @json_stats = { - "Total Actions" => authenticated_actions, - "lastReset" => @last_reset, - } - - respond_to do |format| - format.html - format.xml { render :xml => @summary_stats } - format.json { render :json => @json_stats } - end - end - - # Return the online documentation. - def doc - redirect_to 'https://github.com/aces/cbrain/wiki' - end - - # Return release note describing the current version - # of the platform APIs. - def releasenotes - redirect_to 'https://github.com/aces/cbrain/blob/master/Release-Notes.md' - end - - # Provides information on how to get support - # for the platform. - def support - about_us_url = url_for(:controller => :portal, :action => :about_us) - @support = { :supportEmail => RemoteResource.current_resource.support_email, - :aboutUs => about_us_url, - :helpUrl => RemoteResource.current_resource.help_url, - } - - respond_to do |format| - format.html - format.xml { render :xml => @support } - format.json { render :json => @support } - end - end - - # Return link to the source code of the platform - def source - redirect_to 'https://github.com/aces/cbrain' - end - - # Redirects to the main login page. - def tryme - redirect_to '/login' - end - - # Allows users to view platform's - # licencing/usage term. - def licence - respond_to do |format| - format.html { redirect_to :controller => :portal, :action => :about_us } - format.xml { head :not_acceptable } - format.json { head :not_acceptable } - end - end - - # Allows user to view the software provenance - def provenance - respond_to do |format| - format.html { render 'portal/provenance' } - format.xml { head :not_acceptable } - format.json { head :not_acceptable } - end - end - - # Base information - def factsheet - respond_to do |format| - format.html { redirect_to :controller => :portal, :action => :about_us } - format.xml { head :not_acceptable } - format.json { head :not_acceptable } - end - end - - # Return information about the usage of the platform. - def detailed_stats - @stats = RemoteResource.current_resource.meta[:stats] || {} - @stats_by_client = @stats[:UserAgents] || {} - @stats_by_contr_action = compile_total_stats(@stats) - - @last_reset = (RemoteResource.current_resource.meta.md_for_key(:stats).created_at || Time.at(0)).utc.iso8601 - @stats[:lastReset] = @last_reset - - respond_to do |format| - format.html - format.xml { render :xml => @stats } - format.json { render :json => @stats } - end - end - - private - - # From the raw stats accumulated for all clients, - # controllers and actions, compile two other - # secondary stats: the sums by clients, and - # the sums by pair "controller,service". - def compile_total_stats(stats={}) #:nodoc: - stats_by_contr_action = {} - - # stats['AllAgents'] is { 'controller' => { 'action' => [1,2] , ... }, ... } - all_agents = stats['AllAgents'] || stats[:AllAgents] || {} - all_agents.each do |controller, by_action| - by_action.each do |action, counts| - # By controller and action - contr_action = "#{controller},#{action}" - stats_by_contr_action[contr_action] ||= [0,0] - stats_by_contr_action[contr_action][0] += counts[0] - stats_by_contr_action[contr_action][1] += counts[1] - end - end - - return stats_by_contr_action - end - - # Returns a count of all actions that require - # being authenticated; there is a built-in - # exception list to ignore actions that can - # be invoked externally without authentication - # (for instance, /service/* or /portal/welcome) - # Returns the sum of successful and unsuccessful - # actions. - def count_authenticated_actions(stats_by_contr_action = {}) #:nodoc: - tot = 0; - stats_by_contr_action.keys.sort.each do |contr_action| - next if contr_action == 'portal,welcome' - next if contr_action == 'portal,credits' - next if contr_action == 'portal,about_us' - controller = contr_action.split(",").first - next if controller == 'service' # all of them - next if controller == 'controls' # show - next if controller == 'sessions' # new, show, destroy, create - next if controller == 'nh_sessions' - next if controller == 'noc' - counts = stats_by_contr_action[contr_action] || [0,0] - tot += counts[0] + counts[1] # OK + FAIL - end - tot - end - -end diff --git a/BrainPortal/app/controllers/sessions_controller.rb b/BrainPortal/app/controllers/sessions_controller.rb index 0b254994d..8410ca194 100644 --- a/BrainPortal/app/controllers/sessions_controller.rb +++ b/BrainPortal/app/controllers/sessions_controller.rb @@ -331,7 +331,7 @@ def user_tracking(portal,origin='CBRAIN') #:nodoc: # the same information afterwards. Thus the weird style alignment. user.addlog( "Logged in on #{portal.name}/#{origin} with #{authentication_mechanism} from #{pretty_host} using #{pretty_brow}") portal.addlog("User #{user.login} logged in on #{origin} with #{authentication_mechanism} from #{pretty_host} using #{pretty_brow}") - user.update_attribute(:last_connected_at, Time.now) + user.update_column(:last_connected_at, Time.now) # Admin users start with some differences in behavior if user.has_role?(:admin_user) diff --git a/BrainPortal/app/controllers/tasks_controller.rb b/BrainPortal/app/controllers/tasks_controller.rb index 5a0fabb11..c6d6a2319 100644 --- a/BrainPortal/app/controllers/tasks_controller.rb +++ b/BrainPortal/app/controllers/tasks_controller.rb @@ -187,7 +187,7 @@ def new #:nodoc: if tool_config_id # the prefered method @tool_config = ToolConfig.find(tool_config_id) if ! @tool_config.can_be_accessed_by?(current_user) - raise ActiveRecord::RecordNotFound("Cannot access ToolConfig ##{tool_config_id}") + raise ActiveRecord::RecordNotFound.new("Cannot access ToolConfig ##{tool_config_id}") end else # Try to propose a version; usually that's when we get just a tool_id if tool_id.blank? @@ -197,7 +197,7 @@ def new #:nodoc: end tool = Tool.find(tool_id) if ! tool.can_be_accessed_by?(current_user) - raise ActiveRecord::RecordNotFound("Cannot access Tool ##{tool_id}") + raise ActiveRecord::RecordNotFound.new("Cannot access Tool ##{tool_id}") end bourreau_id = Bourreau.find_all_accessible_by_user(current_user).where(:online => true).pluck(:id) if bourreau_id.nil? # try them all toolconfigs = ToolConfig.where( @@ -1502,6 +1502,8 @@ def handle_preset_actions #:nodoc: if (! preset_id.blank?) && preset = CbrainTask.where(:id => preset_id, :status => [ 'Preset', 'SitePreset' ]).first old_params = @task.params.clone @task.params = preset.params + @task.description = @task.description || "" + @task.description += "\n\nDescription from preset configuration:\n\n#{preset.description}" if preset.description.present? @task.restore_untouchable_attributes(old_params, :include_unpresetable => true) if preset.group && preset.group.can_be_accessed_by?(current_user) @task.group = preset.group diff --git a/BrainPortal/app/controllers/tool_configs_controller.rb b/BrainPortal/app/controllers/tool_configs_controller.rb index d287c23ec..d71b2f6da 100644 --- a/BrainPortal/app/controllers/tool_configs_controller.rb +++ b/BrainPortal/app/controllers/tool_configs_controller.rb @@ -238,9 +238,16 @@ def update #:nodoc: respond_to do |format| new_record = @tool_config.new_record? - if @tool_config.save_with_logging(current_user, %w( env_array script_prologue script_epilogue ncpus extra_qsub_args - container_image_userfile_id containerhub_image_name - container_engine container_index_location )) + if @tool_config.save_with_logging(current_user, + %w( version_name env_array script_prologue script_epilogue ncpus extra_qsub_args + container_image_userfile_id containerhub_image_name + container_engine container_index_location container_exec_args + inputs_readonly + singularity_overlays_specs singularity_use_short_workdir + boutiques_descriptor_path + ) + ) + if new_record flash[:notice] = "Tool configuration is successfully created." else @@ -298,6 +305,7 @@ def tool_config_params #:nodoc: :group_id, :ncpus, :container_image_userfile_id, :containerhub_image_name, :container_index_location, :inputs_readonly, :container_engine, :extra_qsub_args, :singularity_overlays_specs, :container_exec_args, + :singularity_use_short_workdir, :boutiques_descriptor_path, # The configuration of a tool in a VM managed by a # ScirCloud Bourreau is defined by the following diff --git a/BrainPortal/app/controllers/userfiles_controller.rb b/BrainPortal/app/controllers/userfiles_controller.rb index f9869e118..3204b36d5 100644 --- a/BrainPortal/app/controllers/userfiles_controller.rb +++ b/BrainPortal/app/controllers/userfiles_controller.rb @@ -239,7 +239,7 @@ def stream # Find and validate target userfile @userfile = Userfile.find_accessible_by_user(userfile_id, current_user, :access_requested => :read) if @userfile.nil? - raise ActiveRecord::RecordNotFound("Could not retrieve a userfile with ID: #{userfile_id}") + raise ActiveRecord::RecordNotFound.new("Could not retrieve a userfile with ID: #{userfile_id}") end # If it's a SingleFile @@ -433,8 +433,16 @@ def sync_multiple #:nodoc: SyncStatus.where(:userfile_id => @userfiles.map(&:id), :status => [ "InSync" ]).all.each do |ss| updated += 1 if ss.status_transition(ss.status,"ProvNewer") end - flash[:notice] = "Marked #{updated} files as newer on their Data Provider." - redirect_to :action => :index + respond_to do |format| + format.html do + flash[:notice] = "Marked #{updated} files as newer on their Data Provider." + redirect_to :action => :index + end + format.json do + render :json => { :notice => "Marked #{updated} files as newer on provider" }, + :status => :ok + end + end return end @@ -1091,7 +1099,7 @@ def change_provider #:nodoc: next if orig_provider.id == data_provider_id # no support for copy to same provider in the interface, yet. res = nil if task == :move - raise "not owner" unless u.has_owner_access?(current_user) + raise RuntimeError.new("Not owner") unless u.has_owner_access?(current_user) res = u.provider_move_to_otherprovider(new_provider, :crush_destination => crush_destination) else # task is :copy my_group_id = current_assignable_group.id @@ -1145,10 +1153,15 @@ def delete_files #:nodoc: failed_list = {} CBRAIN.spawn_with_active_records_if(! api_request?, current_user, "Delete files") do idlist = to_delete.raw_first_column(:id).shuffle + reset_dpids = {} idlist.each_with_index do |userfile_id,count| userfile = Userfile.find(userfile_id) rescue nil # that way we instantiate one record at a time next unless userfile # in case it was destroyed externally Process.setproctitle "Delete ID=#{userfile.id} #{count+1}/#{idlist.size}" + if ! reset_dpids[userfile.data_provider_id] + userfile.data_provider.reset_connection if userfile.data_provider.respond_to?(:reset_connection) + reset_dpids[userfile.data_provider_id] = true + end begin userfile.destroy deleted_success_list << userfile @@ -1703,13 +1716,13 @@ def extract_from_archive(archive_file_name, file_type = nil, attributes = {}) #: :variable_text => report ) end - rescue => e - Message.send_message(current_user, - :message_type => 'error', - :header => "File extraction failed", - :description => "Some errors occurred while extracting files from archive '#{archive_file_name}'", - :variable_text => e.message - ) + rescue => e + Message.send_message(current_user, + :message_type => 'error', + :header => "File extraction failed", + :description => "Some errors occurred while extracting files from archive '#{archive_file_name}'", + :variable_text => e.message + ) end # This method creates a tar file of the userfiles listed @@ -2103,7 +2116,7 @@ def userfile_for_viewer # Otherwise we want to view a file inside a FileCollection. # Create a fake Userfile to pass information to the viewer sub_file_info = @top_userfile.provider_collection_index.detect { |u| u.name == sub_file_name } - raise ActiveRecord::RecordNotFound("Could not retrieve a file with the name #{sub_file_name} inside the FileCollection") if !sub_file_info + raise ActiveRecord::RecordNotFound.new("Could not retrieve a file with the name #{sub_file_name} inside the FileCollection") if !sub_file_info # Find the class for the new userfile object that will be used for viewing viewer_userfile_class = viewer_class_name.try(:constantize) || @top_userfile.class diff --git a/BrainPortal/app/helpers/basic_helper.rb b/BrainPortal/app/helpers/basic_helper.rb index a17570719..fa1f68526 100644 --- a/BrainPortal/app/helpers/basic_helper.rb +++ b/BrainPortal/app/helpers/basic_helper.rb @@ -80,5 +80,12 @@ def tree_view_icon(level = 0) (' ' * 4 * (level.presence || 0) + '↳').html_safe end + # Renders 1234567 as 1,234,567 + def number_with_commas(number) + s = number.to_s + return s if s !~ /\A\d+\z/ # anything not a series of digits is just returned as is + s.reverse.gsub(/(\d\d\d)(?=\d)/, '\1,').reverse + end + end diff --git a/BrainPortal/app/helpers/disk_quotas_helper.rb b/BrainPortal/app/helpers/disk_quotas_helper.rb new file mode 100644 index 000000000..60810c2d2 --- /dev/null +++ b/BrainPortal/app/helpers/disk_quotas_helper.rb @@ -0,0 +1,38 @@ + +# +# CBRAIN Project +# +# Copyright (C) 2008-2023 +# The Royal Institution for the Advancement of Learning +# McGill University +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +# + +# Helper methods for Disk Quota views. +module DiskQuotasHelper + + Revision_info=CbrainFileRevision[__FILE__] #:nodoc: + + # Returns a DiskQuota max_bytes in pretty form: 'None allowed' in red, or '126 MB' etc (colored) + def pretty_quota_max_bytes(quota) + quota.none_allowed? ? red_if(true, 'None allowed') : colored_pretty_size(quota.max_bytes) + end + + # Returns a DiskQuota max_files in pretty form: 'None allowed' in red, or just a number + def pretty_quota_max_files(quota) + quota.none_allowed? ? red_if(true, 'None allowed') : number_with_commas(quota.max_files) + end + +end diff --git a/BrainPortal/app/helpers/dynamic_form_helper.rb b/BrainPortal/app/helpers/dynamic_form_helper.rb index 3aa1da1ce..238580ebe 100644 --- a/BrainPortal/app/helpers/dynamic_form_helper.rb +++ b/BrainPortal/app/helpers/dynamic_form_helper.rb @@ -49,15 +49,18 @@ def submit_button(value, options = {}) # Create a checkbox that will select or deselect all checkboxes on the page # of class +checkbox_class+. # Most +options+ are just treated as HTML attributes. - # Except +options[:persistant_name]+; if provided, - # an additional hidden input will be added to track - # the state of the select_all checkbox. + # + # Except: + # - +options[:persistant_name]+: if provided, an additional hidden + # input will be added to track the state of the select_all checkbox. def select_all_checkbox(checkbox_class, options = {}) options[:class] ||= "" options[:class] += " select_all" - options["data-checkbox-class"] = checkbox_class - atts = options.reject{|x| x.to_s === "persistant_name"}.to_html_attributes + options["data-checkbox-class"] = checkbox_class + options["data-persistant-name"] = options[:persistant_name].present? + + atts = options.reject { |x| x.to_s == "persistant_name" }.to_html_attributes # Most common case just the select_all input input = "".html_safe @@ -66,11 +69,11 @@ def select_all_checkbox(checkbox_class, options = {}) # Add the hidden input; javascript code will update # its value as needed. hidden_options = { - :name => options[:persistant_name], + :name => options[:persistant_name], "data-checkbox-class" => checkbox_class, :class => "select_all_hidden" - } - + } + hidden_atts = hidden_options.to_html_attributes hidden_input = "".html_safe inputs = "#{input} #{hidden_input}".html_safe diff --git a/BrainPortal/app/helpers/groups_helper.rb b/BrainPortal/app/helpers/groups_helper.rb index a53aefdd2..edaff110c 100644 --- a/BrainPortal/app/helpers/groups_helper.rb +++ b/BrainPortal/app/helpers/groups_helper.rb @@ -33,24 +33,15 @@ def css_group_type(group, group_user_count = nil) return group.to_s.downcase unless group.is_a?(Group) # SystemGroup subclasses; UserGroup => "user", EveryoneGroup => "everyone" - return group.class.name.demodulize.match(/\A([A-Z][a-z]+)/).to_s.downcase if group.is_a?(SystemGroup) + return "user" if group.is_a?(UserGroup) + return "everyone" if group.is_a?(EveryoneGroup) + return "site" if group.is_a?(SiteGroup) group_user_count ||= group.users.count - return "invisible" if group.invisible? return "public" if group.public? - return "empty" if group_user_count == 0 return "shared" if group_user_count > 1 - return "personal" + return "private" end - # Produces a centered legend for every distinct group type in +groups+ - def group_legend(groups) - return if groups.blank? - - center_legend(nil, groups.map { |g| css_group_type(g) }.uniq.map { |g| - # 9675: UTF8 white circle, 9679: UTF8 black circle - ["&##{g == "all" ? "x25ef" : "x2b24"};", "#{g.titleize} Project"] - }) - end end diff --git a/BrainPortal/app/helpers/select_box_helper.rb b/BrainPortal/app/helpers/select_box_helper.rb index 63ca15f7b..bea85d59e 100644 --- a/BrainPortal/app/helpers/select_box_helper.rb +++ b/BrainPortal/app/helpers/select_box_helper.rb @@ -152,7 +152,7 @@ def group_select(parameter_name = "group_id", options = {}, select_tag_options = end # Step 3: Other project categories, in that order - [ "Shared Work Projects", "Empty Work Projects", "Site Projects", "User Projects", "System Projects", "Invisible Projects", "Everyone Projects" ].each do |proj| + [ "Shared Work Projects", "Empty Work Projects", "Site Projects", "User Projects", "System Projects", "Invisible Projects", "Everyone Projects", "Public Projects" ].each do |proj| ordered_category_grouped << [ proj, category_grouped_pairs.delete(proj) ] if category_grouped_pairs[proj] end diff --git a/BrainPortal/app/helpers/userfiles_helper.rb b/BrainPortal/app/helpers/userfiles_helper.rb index 493d7eaa8..ad0eb5089 100644 --- a/BrainPortal/app/helpers/userfiles_helper.rb +++ b/BrainPortal/app/helpers/userfiles_helper.rb @@ -79,7 +79,7 @@ def file_link_table(previous_userfile, next_userfile, sort_index, options = {}) # Generates links to pretty file content for files inside FileCollections. # Generates a download link if no viewer code can be found for the files. - def data_link(file_name, userfile) + def data_link(file_name, userfile, replace_div_id="sub_viewer_filecollection_cbrain") full_path_name = Pathname.new(userfile.cache_full_path.dirname + file_name) display_name = full_path_name.basename.to_s @@ -87,9 +87,12 @@ def data_link(file_name, userfile) file_lstat = full_path_name.lstat # lstat doesn't follow symlinks, so we can tell if it is one - return h(display_name) unless file_lstat.file? + # return if userfile class is a FileCollection and file is not a file (i.e. a directory) + return h(display_name) if userfile.is_a?(FileCollection) && !file_lstat.file? + + matched_class = SingleFile.descendants.unshift(SingleFile).find { |c| file_name =~ c.file_name_pattern } + matched_class ||= userfile.class if userfile.is_a?(SingleFile) - matched_class = SingleFile.descendants.unshift(SingleFile).find { |c| file_name =~ c.file_name_pattern } viewer = matched_class.class_viewers.first.partial rescue nil if matched_class && viewer @@ -100,7 +103,7 @@ def data_link(file_name, userfile) :viewer => viewer, :viewer_userfile_class => matched_class ), - :replace => "sub_viewer_filecollection_cbrain", + :replace => replace_div_id, } ) do (""+display_name+"").html_safe diff --git a/BrainPortal/app/models/application_record.rb b/BrainPortal/app/models/application_record.rb index 6bf174128..7689f069e 100644 --- a/BrainPortal/app/models/application_record.rb +++ b/BrainPortal/app/models/application_record.rb @@ -96,6 +96,8 @@ def self.default_api_limit #:nodoc: end # Useful generic scopes for console users. + scope :uhour, -> { where [ "#{self.quoted_table_name}.updated_at >= ?", 1.hour.ago ] } + scope :chour, -> { where [ "#{self.quoted_table_name}.created_at >= ?", 1.hour.ago ] } scope :utoday, -> { where [ "#{self.quoted_table_name}.updated_at >= ?", Time.now.at_beginning_of_day ] } scope :ctoday, -> { where [ "#{self.quoted_table_name}.created_at >= ?", Time.now.at_beginning_of_day ] } # Note: the following two scopes imply that the week starts on Monday morning diff --git a/BrainPortal/app/models/bourreau.rb b/BrainPortal/app/models/bourreau.rb index 31622acbb..2124e9e65 100644 --- a/BrainPortal/app/models/bourreau.rb +++ b/BrainPortal/app/models/bourreau.rb @@ -454,7 +454,11 @@ def self.process_command_alter_tasks(command) CBRAIN.spawn_with_active_records(:admin, "AlterTask #{newstatus}") do + signaled_finish = false # set to true when receiving TERM + Signal.trap("TERM") { signaled_finish = true } + taskids.shuffle.each_with_index do |task_id,count| + break if signaled_finish # ends the entire task ID list Process.setproctitle "AlterTask #{newstatus} ID=#{task_id} #{count+1}/#{taskids.size}" task = CbrainTask.where(:id => task_id, :bourreau_id => myself.id).first next unless task # doesn't even exist? just ignore it diff --git a/BrainPortal/app/models/boutiques_cluster_task.rb b/BrainPortal/app/models/boutiques_cluster_task.rb index b8a0a9a25..be695e44e 100644 --- a/BrainPortal/app/models/boutiques_cluster_task.rb +++ b/BrainPortal/app/models/boutiques_cluster_task.rb @@ -137,7 +137,6 @@ def cluster_commands #:nodoc: end # Write down the file with the boutiques descriptor itself - boutiques_json_basename = "boutiques.#{self.run_id}.json" File.open(boutiques_json_basename, "w") do |fh| cleaned_desc = descriptor.dup cleaned_desc.delete("groups") if cleaned_desc.groups.size == 0 # bosh is picky @@ -152,7 +151,11 @@ def cluster_commands #:nodoc: #{boutiques_json_basename.bash_escape} SIMULATE simulate_com.gsub!("\n"," ") - simulout = IO.popen(simulate_com) { |fh| fh.read } + begin + simulout = IO.popen(simulate_com) { |fh| fh.read } + rescue => ex + cb_error "The 'bosh exec simulate' command failed: #{ex.class} #{ex.message}" + end simul_status = $? # a Process::Status object if ! simul_status.success? cb_error "The 'bosh exec simulate' command failed with return code #{simul_status.exitstatus}" @@ -161,7 +164,9 @@ def cluster_commands #:nodoc: commands = <<-COMMANDS # Main tool command, generated with bosh exec simulate #{simulout.strip} - echo $? > #{exit_status_filename.bash_escape} + status=$? + echo $status > #{exit_status_filename.bash_escape} + bash -c "exit $status" # clumsy but I can't think of any better way COMMANDS else # exec launch mode # The bosh launch command. This is all a single line, but broken up @@ -171,7 +176,9 @@ def cluster_commands #:nodoc: bosh exec launch \\ #{boutiques_json_basename.bash_escape} \\ #{self.invoke_json_basename.bash_escape} - echo $? > #{exit_status_filename.bash_escape} + status=$? + echo $status > #{exit_status_filename.bash_escape} + bash -c "exit $status" # clumsy but I can't think of any better way COMMANDS end commands.gsub!(/(\S) +(\S)/,'\1 \2') # make pretty @@ -245,8 +252,13 @@ def save_results #:nodoc: self.addlog("Attempting to save result file #{path}") name, userfile_class = name_and_type_for_output_file(output, path) - # Save the file (possible overwrite if race condition) + # Select an alternative and safe output type when guessing it produces a mismatch + userfile_class = SingleFile if File.file?(path) && !(userfile_class <= SingleFile) + userfile_class = FileCollection if File.directory?(path) && !(userfile_class <= FileCollection) + + # Save the file outfile = safe_userfile_find_or_new(userfile_class, :name => name) + new_out = outfile.new_record? unless outfile.save messages = outfile.errors.full_messages.join("; ") @@ -257,17 +269,22 @@ def save_results #:nodoc: end # Transfer content to DataProvider + self.addlog("Created result file '#{name}' (ID #{outfile.id})") if new_out + self.addlog("Reused result file '#{name}' (ID #{outfile.id})") if ! new_out + self.addlog("Uploading content to #{outfile.data_provider.type} '#{outfile.data_provider.name}' (ID #{outfile.data_provider_id})") outfile.cache_copy_from_local_file(path) + self.addlog("Content uploaded") + + # Record ID of output file in task's params params["_cbrain_output_#{output.id}"] ||= [] params["_cbrain_output_#{output.id}"] |= [ outfile.id ] - self.addlog("Saved result file #{name}") # Add provenance logs all_file_input_ids = descriptor.file_inputs.map do |input| invoke_params[input.id] end.compact.uniq parent_userfiles = Userfile.where(:id => all_file_input_ids).to_a - self.addlog_to_userfiles_these_created_these(parent_userfiles, [outfile]) if parent_userfiles.present? + self.addlog_to_userfiles_these_created_these(parent_userfiles, [outfile], "", 2) if parent_userfiles.present? # If there is only one input file, we move the output under it if parent_userfiles.size == 1 @@ -295,7 +312,7 @@ def save_results #:nodoc: self.addlog "Attempting to update input '#{userfile.name}' on DataProvider '#{userfile.data_provider.name}'" userfile.cache_is_newer userfile.sync_to_provider - self.addlog_to_userfiles_processed(userfile, "(content modified in place)") + self.addlog_to_userfiles_processed(userfile, "(content modified in place)", 1) end end @@ -323,7 +340,8 @@ def name_and_type_for_output_file(output, pathname) desc = descriptor_for_save_results custom = desc.custom || {} # 'custom' is not packaged as an object, just a hash idlist = custom['cbrain:no-run-id-for-outputs'].presence # list of IDs where no run id inserted - no_run_id = true if idlist && idlist.include?(output.id) + # We allow no_run_id only if the dest DP is MultiLevel, presumably the output goes to "a/b/c/basename_without_id" + no_run_id = true if idlist && idlist.include?(output.id) && self.results_data_provider.has_browse_path_capabilities? # Get basename, use it to guess the class name = File.basename(pathname) @@ -393,7 +411,13 @@ def boutiques_bosh_exec_mode # Returns the basename of the JSON file # that holds the 'invoke' structure for bosh. def invoke_json_basename - "invoke.#{self.run_id}.json" + ".invoke.#{self.run_id}.json" + end + + # Returns the basename of the JSON file + # that holds the boutiques descriptor for bosh. + def boutiques_json_basename + ".boutiques.#{self.run_id}.json" end # Return true or false depending on if diff --git a/BrainPortal/app/models/boutiques_portal_task.rb b/BrainPortal/app/models/boutiques_portal_task.rb index 4b525e653..d2bc2f900 100644 --- a/BrainPortal/app/models/boutiques_portal_task.rb +++ b/BrainPortal/app/models/boutiques_portal_task.rb @@ -27,7 +27,9 @@ class BoutiquesPortalTask < PortalTask # This method returns the BoutiquesDescriptor # directly associated with the ToolConfig for the task def boutiques_descriptor - self.tool_config.boutiques_descriptor + self.tool_config.boutiques_descriptor || + self.find_compatible_placeholder_descriptor || # Workaround #1 for misconfigured portal + self.generate_placeholder_descriptor # Workaround #2 for misconfigured portal end # This method returns the same descriptor as @@ -218,7 +220,7 @@ def after_form # Check the content of all CbrainFileLists (cbcsv) # ------------------------------------------------ # Get all the input cbcsv files - cbcsvs = self.cbcsv_files + cbcsvs = self.cbcsv_files # [ [input, cbcsv_userfile], [input, cbcsv_userfile], ... ] numRows = nil # Keep track of number of files per cbcsv # Validate each cbcsv (all columns match per row, user has access to the file) for input, cbcsv in cbcsvs @@ -230,8 +232,8 @@ def after_form # If the number of rows does not match, error # We need only check this for inputs that are not "list". if ! input.list - currNumRows = (cbcsv.ordered_raw_ids || []).length - numRows = numRows.nil? ? currNumRows : numRows + currNumRows = (cbcsv.ordered_raw_ids || []).length + numRows ||= currNumRows if currNumRows != numRows params_errors.add(invokename, " does not have the same number of files (#{currNumRows}) as in other present cbcsvs (#{numRows})") next @@ -263,6 +265,18 @@ def self.add_pretty_params_names(inputs) def final_task_list #:nodoc: descriptor = self.descriptor_for_final_task_list self.addlog(descriptor.file_revision_info.format("%f rev. %s %a %d")) + valid_input_keys = descriptor.inputs.map(&:id) + + # Add author(s) information + authors = Array(descriptor.custom['cbrain:author']) + authors = authors.empty? ? "No CBRAIN author information" : + authors.join(", ") + self.addlog("CBRAIN Author(s): #{authors}") + + # Add information about Boutiques module + boutiques_module_information().each do |log_info| + self.addlog(log_info) + end # -------------------------------------- # Special case where there is a single file input @@ -277,27 +291,36 @@ def final_task_list #:nodoc: if descriptor.file_inputs.size == 1 input = descriptor.file_inputs.first - fillTask = lambda do |userfile,tsk| - tsk.invoke_params[input.id] = userfile.id + fillTask = lambda do |userfile,tsk,extra_params=nil| + tsk.params[:interface_userfile_ids] |= [ userfile.id.to_s ] + tsk.invoke_params[input.id] = userfile.id tsk.sanitize_param(input) - tsk.description ||= '' - tsk.description += " #{input.id}: #{userfile.name}" + tsk.description = "#{input.id}: #{userfile.name}\n#{tsk.description}".strip + tsk.invoke_params.merge!(extra_params.slice(*valid_input_keys)) if extra_params tsk.description.strip! tsk end - tasklist = self.params[:interface_userfile_ids].map do |userfile_id| + original_userfiles_ids = self.params[:interface_userfile_ids].dup + self.params[:interface_userfile_ids] = [] # zap it; we'll re-introduce each userfile.id as needed + tasklist = original_userfiles_ids.map do |userfile_id| f = Userfile.find_accessible_by_user( userfile_id, self.user, :access_requested => file_access_symbol() ) # One task for that file if (! f.is_a?( CbrainFileList ) || input.list) # in case of a list input, we *do* assign it the CbFileList task = self.dup fillTask.( f, task ) - else # One task per userfile in the CbrainFileList - ufiles = f.userfiles_accessible_by_user!( self.user, nil, nil, file_access_symbol() ) - # Skip files that are purposefully nil (e.g. given id 0 by the user) - subtasks = ufiles.select { |u| ! u.nil? }.map { |u| fillTask.( u, self.dup ) } + ufiles = f.userfiles_accessible_by_user!( self.user, nil, nil, file_access_symbol() ) + ordered_extra_params = f.is_a?(ExtendedCbrainFileList) ? f.ordered_params : [] + + # Fill subtasks array + subtasks = [] + ufiles.each_with_index do |u, index| + next if u.nil? + subtasks << fillTask.( u, self.dup, ordered_extra_params[index]) + end + subtasks # an array of tasks end end @@ -311,7 +334,7 @@ def final_task_list #:nodoc: # -------------------------------------- # Grab all the cbcsv input files - cbcsvs = self.cbcsv_files(descriptor) + cbcsvs = self.cbcsv_files(descriptor) # [ [input, cbcsv_userfile], [input, cbcsv_userfile], ... ] cbcsvs.reject! { |pair| pair[0].list } # ignore file inputs with list=true; they just get the CBCSV directly # Default case: just return self as a single task @@ -322,9 +345,17 @@ def final_task_list #:nodoc: # Array with the actual userfiles corresponding to the cbcsv mapCbcsvToUserfiles = cbcsvs.map { |f| f[1].ordered_raw_ids.map { |i| (i==0) ? nil : i } } + # Array with the actual extra json_params corresponding to the cbcsv + mapCbcsvToParams = cbcsvs.map do |f| + cbcsv = f[1] + cbcsv.is_a?(ExtendedCbrainFileList) ? + cbcsv.ordered_params : [] + end + # Task list to fill and total number of tasks to output - tasklist = [] - nTasks = mapCbcsvToUserfiles[0].length + tasklist = [] + nTasks = mapCbcsvToUserfiles[0].length + # Iterate over each task that needs to be generated for i in 0..(nTasks - 1) # Clone this task @@ -335,6 +366,8 @@ def final_task_list #:nodoc: #currTask.params[:interface_userfile_ids] << mapCbcsvToUserfiles unless currId.nil? currTask.invoke_params[cinput.id] = currId # If id = 0 or nil, currId = nil currTask.invoke_params.delete(cinput.id) if currId.nil? + extra_params_from_Cbcsv = mapCbcsvToParams[j][i] || {} + currTask.invoke_params.merge!(extra_params_from_Cbcsv.slice(*valid_input_keys)) end # Add the new task to our tasklist tasklist << currTask @@ -385,7 +418,7 @@ def isInactive(input) ( val.nil? || # most of the time, the interface sends NO value at all, which is what we prefer (type == 'Flag' && val == "0") || # checkboxes send their values as strings 0 and 1, - (type == 'Flag' && val == false) # but normally they are transformed into bool in sanitize_params + (type == 'Flag' && val == false) # but normally they are transformed into bool in sanitize_param() ) end @@ -408,6 +441,7 @@ def ascertainCbcsvUserAccess(f,id) msg2 = lambda { |e| " cbcsv accessibility error in #{f.name}! Possibly due to cbcsv malformation. (Received error: #{e.inspect})" } errFlag = true # Whether the error checking found a problem begin # Check that the user has access to all of the files in the cbcsv + f.sync_to_cache # We need the content of the cbcsv f.userfiles_accessible_by_user!(self.user, nil, nil, file_access_symbol()) # side effect: cache entries within f for i in f.ordered_raw_ids.select{ |r| (! r.nil?) && (r.to_s != '0') } accessible = Userfile.find_accessible_by_user( i, self.user, :access_requested => file_access_symbol() ) rescue nil @@ -448,6 +482,11 @@ def sanitize_param(input) name = input.id type = input.type.downcase.to_sym # old code convention from previous integrator + # For strings, we support a special list of parameters + # that can be empty strings. + descriptor = self.descriptor_for_after_form + empty_string_allowed = Array(descriptor.custom['cbrain:allow_empty_strings']).include?(name) + # Taken userfile names. An error will be raised if two input files have the # same name. @taken_files ||= Set.new @@ -476,18 +515,17 @@ def sanitize_param(input) when :string value = value.to_s if value.is_a?(Symbol) params_errors.add(invokename, " not a string (#{value})") unless value.is_a?(String) - params_errors.add(invokename, " is blank") if value.blank? + params_errors.add(invokename, " is blank") if value.blank? && !empty_string_allowed # The following two checks are to prevent cases when # a string param is used as a path params_errors.add(invokename, " cannot contain newlines") if value.to_s =~ /[\n\r]/ params_errors.add(invokename, " cannot start with this character") if value.to_s =~ /^[\.\/]+/ + params_errors.add(invokename, " cannot move up dirs") if value.to_s.include? "/../" # Try to match against various common representation of true and false when :flag - if value.is_a?(String) - value = true if value =~ /\A(true|t|yes|y|on|1)\z/i - value = false if value =~ /\A(false|f|no|n|off|0|)\z/i - end + value = true if value.to_s =~ /\A(true|t|yes|y|on|1)\z/i + value = false if value.to_s =~ /\A(false|f|no|n|off|0|)\z/i if ! [ true, false ].include?(value) params_errors.add(invokename, ": not true or false (#{value})") @@ -622,4 +660,118 @@ def file_access_symbol @_file_access ||= (self.class.properties[:readonly_input_files].present? || self.tool_config.try(:inputs_readonly) ? :read : :write) end + # In the case of a misconfiguration of the portal, or if the file for + # the Boutiques descriptor has disappeared, this method will look at + # other ToolConfigs associated with the tool of the task and try find + # a replacement descriptor. It's not garanteed that this descriptor + # is compatible with the params of the task but it's probably good + # enough to show the task to the user. + # + # The task object itself will get a permanent ActiveRecord + # error added to its base to prevent any saving/editing/launching. + # + # See also the method generate_placeholder_descriptor which, in case + # we can't find a descriptor here, is called to create a fake + # descriptor out of thin air. + # + # Known limitations: if the original task was integrated with + # special modules that have custom entries that are different + # than the ones in the found descriptor, the callback methods + # setup(), before_form() etc might crash. + def find_compatible_placeholder_descriptor + + # Build a list of tool configs to scan + tool_configs = self.tool.tool_configs.order("created_at desc").to_a + + # Find the most recently created one (hopefully, backwards compatible) + compat_tool_config = tool_configs.detect { |tc| tc.boutiques_descriptor } # first one is the one we use + return nil if ! compat_tool_config + + # Add persistent errors, to make sure the task cannot be touched. + if self.errors.blank? + cur_version = self.tool_config.version_name + alt_version = compat_tool_config.version_name + self.errors.add(:base, "The Boutiques Descriptor for version '#{cur_version}' of this task has disappeared. This is a configuration error, contact the administrators.") + self.errors.add(:base, "A descriptor from another version ('#{alt_version}') is currently in use to allow you to view the parameters.") + self.errors.add(:unsavable, ": The parameters for this task cannot be modified.") # this special error prevents the save button from working + end + + compat_tool_config.boutiques_descriptor + end + + # In the case of a misconfiguration of the portal, or if the file for + # the Boutiques descriptor has disappeared, this method will look at the + # current params of the task and create out of thin air a new fake + # descriptor for it. This allows the user to (at least) view the task + # in the interface. + # + # The task object itself will get a permanent ActiveRecord + # error added to its base to prevent any saving/editing/launching. + # + # Known limitations: if the original task was integrated with + # special modules that require custom entries in the descriptor, + # the callback methods setup(), before_form() etc might crash. + # That's because the descriptor generated here contains an empty + # "custom" entry. + def generate_placeholder_descriptor + + # Add persistent errors, to make sure the task cannot be touched. + if self.errors.blank? + cur_version = self.tool_config.version_name + self.errors.add(:base, "The Boutiques Descriptor for version '#{cur_version}' of this task has disappeared. This is a configuration error, contact the administrators.") + self.errors.add(:base, "A replacement descriptor is currently in use to allow you to view the parameters.") + self.errors.add(:base, "Because the type information for the parameters is missing, they are all shown as strings.") + self.errors.add(:unsavable, ": The parameters for this task cannot be modified.") # this special error prevents the save button from working + end + + # Main descriptor + fake = BoutiquesSupport::BoutiquesDescriptor.new( + :name => self.pretty_type, + :description => 'Missing Boutiques Descriptor Placeholder', + "tool-version" => self.tool_config.version_name, + "schema-version" => "0.5", + "command-line" => "false", # as in, the unix command 'false' + :custom => { 'cbrain:integrator_modules' => {} }, # we can't do better than that + ) + + # Create fake inputs for files + (self.params[:interface_userfile_ids] || []).each do |userfile_id| + fake.inputs << BoutiquesSupport::Input.new( + :id => "inputfile-#{userfile_id}", + :name => "inputfile-#{userfile_id}", + :type => 'File', + :description => "Fake input file", + ) + end + + # Create fake inputs for all other params (including those that are files) + (self.invoke_params || {}).keys.each do |input_id| + fake.inputs << BoutiquesSupport::Input.new( + :id => input_id, + :name => input_id, + :type => 'String', + :description => "Fake string input for key '#{input_id}'", + ) + end + + fake + end + + private + + # Prepare an array with revision information of + # all the Boutiques integrator modules used by the + # tools. + def boutiques_module_information #:nodoc: + descriptor = self.descriptor_for_final_task_list + + integrator_modules = descriptor.custom['cbrain:integrator_modules'] || {} + + integrator_modules.map do |module_name, _| + module_name = module_name.constantize + rev_info = module_name::Revision_info + rev_info.format("%f rev. %s %a %d") + end + end + end diff --git a/BrainPortal/app/models/cbrain_task.rb b/BrainPortal/app/models/cbrain_task.rb index acf752f91..56578bc9d 100644 --- a/BrainPortal/app/models/cbrain_task.rb +++ b/BrainPortal/app/models/cbrain_task.rb @@ -98,10 +98,15 @@ class CbrainTask < ApplicationRecord else value = s end - where(:status => value) + where("cbrain_tasks.status" => value) } - scope :active, lambda { status( :active ) } + scope :active, -> { status( :active ) } + scope :failed, -> { status( :failed ) } + scope :failed_setup, -> { where( "cbrain_tasks.status" => 'Failed To Setup' ) } + scope :failed_cluster, -> { where( "cbrain_tasks.status" => 'Failed On Cluster' ) } + scope :failed_post, -> { where( "cbrain_tasks.status" => 'Failed To PostProcess' ) } + scope :completed, -> { where( "cbrain_tasks.status" => 'Completed' ) } scope :real_tasks, -> { where( "cbrain_tasks.status <> 'Preset' AND cbrain_tasks.status <> 'SitePreset'" ) } diff --git a/BrainPortal/app/models/cluster_task.rb b/BrainPortal/app/models/cluster_task.rb index 5ffad9202..e2623f0c2 100644 --- a/BrainPortal/app/models/cluster_task.rb +++ b/BrainPortal/app/models/cluster_task.rb @@ -20,12 +20,6 @@ # along with this program. If not, see . # -require 'stringio' -require 'base64' -require 'fileutils' -require 'json' -require 'json-schema' - #Abstract model representing a job running on a cluster. This is the core class for #launching GridEngine/PBS/MOAB/UNIX jobs (etc) using Scir. # @@ -521,14 +515,14 @@ def path_is_in_workdir?(path) #:nodoc: # and add a log entry to each userfile identifying that # it was processed by the current task. An optional # comment can be appended to the message. - def addlog_to_userfiles_processed(userfiles,comment = "") + def addlog_to_userfiles_processed(userfiles, comment = "", caller_level=0) userfiles = [ userfiles ] unless userfiles.is_a?(Array) myname = self.fullname mylink = "/tasks/#{self.id}" # can't use show_task_path() on Bourreau side mymarkup = "[[#{myname}][#{mylink}]]" userfiles.each do |u| next unless u.is_a?(Userfile) && u.id - u.addlog_context(self,"Processed by task #{mymarkup} #{comment}",3) + u.addlog_context(self,"Processed by task #{mymarkup} #{comment}",3+caller_level) end end @@ -536,14 +530,14 @@ def addlog_to_userfiles_processed(userfiles,comment = "") # and add a log entry to each userfile identifying that # it was created by the current task. An optional # comment can be appended to the message. - def addlog_to_userfiles_created(userfiles,comment = "") + def addlog_to_userfiles_created(userfiles, comment = "", caller_level=0) userfiles = [ userfiles ] unless userfiles.is_a?(Array) myname = self.fullname mylink = "/tasks/#{self.id}" # can't use show_task_path() on Bourreau side mymarkup = "[[#{myname}][#{mylink}]]" userfiles.each do |u| next unless u.is_a?(Userfile) && u.id - u.addlog_context(self,"Created/updated by #{mymarkup} #{comment}",3) + u.addlog_context(self,"Created/updated by #{mymarkup} #{comment}",3+caller_level) end end @@ -552,7 +546,7 @@ def addlog_to_userfiles_created(userfiles,comment = "") # and records for each created file what were the creators, and for # each creator file what files were created, along with a link # to the task itself. An optional comment can be appended to the header message. - def addlog_to_userfiles_these_created_these(creatorlist, createdlist, comment = "") + def addlog_to_userfiles_these_created_these(creatorlist, createdlist, comment="", caller_level=0) # Two lists of userfiles. Make sure their contents are OK. creatorlist = Array(creatorlist).select { |u| u.is_a?(Userfile) && u.id } @@ -570,9 +564,9 @@ def addlog_to_userfiles_these_created_these(creatorlist, createdlist, comment = # Add an entry to each creator files, listing created files creatorlist.each do |creator| if createdlist.size == 1 # a common case; create shorter log entry then. - creator.addlog_context(self, "Used by task #{mymarkup} to create #{createdMarkups[0]}. #{comment}", 4) + creator.addlog_context(self, "Used by task #{mymarkup} to create #{createdMarkups[0]}. #{comment}", 4+caller_level) else - creator.addlog_context(self, "Used by task #{mymarkup}, list of #{createdlist.size} created files follow. #{comment}", 4) + creator.addlog_context(self, "Used by task #{mymarkup}, list of #{createdlist.size} created files follow. #{comment}", 4+caller_level) createdMarkups.each_slice(5).each do |files_4| creator.addlog(files_4.join(", ")) end @@ -582,9 +576,9 @@ def addlog_to_userfiles_these_created_these(creatorlist, createdlist, comment = # Add an entry to each created files, listing creators createdlist.each do |created| if creatorlist.size == 1 # a common case; create shorter log entry then. - created.addlog_context(self, "Created/updated by task #{mymarkup} from file #{creatorMarkups[0]}. #{comment}", 4) + created.addlog_context(self, "Created/updated by task #{mymarkup} from file #{creatorMarkups[0]}. #{comment}", 4+caller_level) else - created.addlog_context(self, "Created/updated by task #{mymarkup}, list of #{creatorlist.size} used files follow. #{comment}", 4) + created.addlog_context(self, "Created/updated by task #{mymarkup}, list of #{creatorlist.size} used files follow. #{comment}", 4+caller_level) creatorMarkups.each_slice(5).each do |files_4| created.addlog(files_4.join(", ")) end @@ -624,10 +618,14 @@ def tool_config_system(command) # Build script script = "" + # flag to guaranty propagation of env variables to the singularity/apptainer + # as far I know only needed to reverse effect of --cleanenv option, and otherwise all vars are copied to the container + # yet potentially more cases may be identified + propagate = self.use_singularity? # Add prologues in specialization order - script += bourreau_glob_config.to_bash_prologue if bourreau_glob_config - script += tool_glob_config.to_bash_prologue if tool_glob_config - script += tool_config.to_bash_prologue if tool_config + script += bourreau_glob_config.to_bash_prologue propagate if bourreau_glob_config + script += tool_glob_config.to_bash_prologue propagate if tool_glob_config + script += tool_config.to_bash_prologue propagate if tool_config # Add CBRAIN special inits script += self.supplemental_cbrain_tool_config_init # Add the command @@ -775,11 +773,11 @@ def post_process saveok = saveok && self.save_results self.meta[:no_end_keyword_check] = nil end - self.update_size_of_cluster_workdir if ! saveok self.status_transition(self.status, "Failed On Cluster") self.addlog("Data processing failed on the cluster.") else + self.update_size_of_cluster_workdir # callbacks and modules might have cleaned up the files by now self.addlog("Post processing completed.") self.status_transition(self.status, "Completed") end @@ -1780,27 +1778,16 @@ def submit_cluster_job # Joined version of all the lines in the scientific script command_script = commands.join("\n") - # Add HOME switching back and forth - command_script = <<-HOME_SWITCHING -# Preserve system HOME, then switch it to the task's workdir -_cbrain_home_="$HOME" -export HOME=#{self.full_cluster_workdir.bash_escape} - -#{command_script} - -# Restore system HOME (while preserving the latest exit code) -_cbrain_status_="$?" -export HOME="$_cbrain_home_" -bash -c "exit $_cbrain_status_" - HOME_SWITCHING - # In case of Docker or Singularity, we rewrite the scientific script inside # yet another wrapper script. if self.use_docker? + command_script = wrap_new_HOME(command_script, self.full_cluster_workdir) command_script = self.docker_commands(command_script) elsif self.use_singularity? load_singularity_image - command_script = self.singularity_commands(command_script) + command_script = self.singularity_commands(command_script) # note: invokes wrap_new_HOME itself + else + command_script = wrap_new_HOME(command_script, self.full_cluster_workdir) end # Create a bash science script out of the text @@ -1813,9 +1800,9 @@ def submit_cluster_job # by ClusterTask # #{ClusterTask.revision_info.to_s} -#{bourreau_glob_config ? bourreau_glob_config.to_bash_prologue : ""} -#{tool_glob_config ? tool_glob_config.to_bash_prologue : ""} -#{tool_config ? tool_config.to_bash_prologue : ""} +#{bourreau_glob_config ? bourreau_glob_config.to_bash_prologue(self.use_singularity?) : ""} +#{tool_glob_config ? tool_glob_config.to_bash_prologue(self.use_singularity?) : ""} +#{tool_config ? tool_config.to_bash_prologue(self.use_singularity?) : ""} #{self.supplemental_cbrain_tool_config_init} # CbrainTask '#{self.name}' commands section @@ -1862,13 +1849,38 @@ def submit_cluster_job # Record runtime environment bash #{Rails.root.to_s.bash_escape}/vendor/cbrain/bin/runtime_info.sh > #{runtime_info_basename} -# stdout and stderr captured below will be re-substituted in -# the output and error of this script. -bash '#{sciencefile}' > #{science_stdout_basename} 2> #{science_stderr_basename} &2 # where stderr captured below will be substituted +# With apptainer/singularity jobs, we sometimes get an error booting the container, +# so we try up to five times. +for singularity_attempts in 1 2 3 4 5 ; do # note: the number 5 is used a bit below in an 'if' + SECONDS=0 # this is a special bash variable, see the doc + + # stdout and stderr captured below will be re-substituted in + # the output and error of this script here (this one!) + bash '#{sciencefile}' >> #{science_stdout_basename} 2>> #{science_stderr_basename} /dev/null ; then + break # move on, for any other error or even non zero successes + fi + + # Detect that final attempt to boot failed + if test $singularity_attempts -eq 5 ; then + echo "Apptainer container boot attempts all failed, giving up." + status=99 # why not + break + fi + + # Cleanup and try again + echo "Apptainer boot attempt number $singularity_attempts failed, trying again." + grep -v -i 'FATAL.*container.*creation.*failed' < #{science_stderr_basename} > #{science_stderr_basename}.clean + mv -f #{science_stderr_basename}.clean #{science_stderr_basename} +done + +echo '__CBRAIN_CAPTURE_PLACEHOLDER__' # where stdout captured above will be substituted +echo '__CBRAIN_CAPTURE_PLACEHOLDER__' 1>&2 # where stderr captured above will be substituted date "+CBRAIN Task Ending With Status $status After $SECONDS seconds, at %s : %F %T" date "+CBRAIN Task Ending With Status $status After $SECONDS seconds, at %s : %F %T" 1>&2 @@ -2305,9 +2317,7 @@ def load_docker_image_cmd #:nodoc: # Returns true if the task's ToolConfig is configured to point to a singularity image # for the task's processing. def use_singularity? - return self.tool_config.container_engine == "Singularity" && - ( self.tool_config.containerhub_image_name.present? || - self.tool_config.container_image_userfile_id.present? ) + return self.tool_config.use_singularity? end # Return the 'singularity' command to be used for the task; this is fetched @@ -2316,6 +2326,12 @@ def singularity_executable_name return self.bourreau.singularity_executable_name.presence || "singularity" end + # Returns true if the admin has configured this option in the + # task's ToolConfig attributes. + def use_singularity_short_workdir? + self.tool_config.singularity_use_short_workdir + end + # Returns the command line(s) associated with the task, wrapped in # a Singularity call if a Singularity image has to be used. +command_script+ # is the raw scientific bash script. @@ -2328,17 +2344,34 @@ def singularity_commands(command_script) # Numbers in (paren) correspond to the comment # block in the script, well below. + # (7) The path to the task's work directory + task_workdir = self.full_cluster_workdir # a string + short_workdir = "/T#{self.id}" # only used in short workdir mode + effect_workdir = use_singularity_short_workdir? ? short_workdir : task_workdir + # (1) additional singularity execution command options defined in ToolConfig container_exec_args = self.tool_config.container_exec_args.presence - # (2) The root of the shared area for all CBRAIN tasks - gridshare_dir = self.bourreau.cms_shared_dir + # (2) The root of the DataProvider cache + cache_dir = self.bourreau.dp_cache_dir - # (3) The root of the DataProvider cache - cache_dir = self.bourreau.dp_cache_dir + # (3) The root of the GridShare area (all tasks workdirs) + gridshare_dir = self.bourreau.cms_shared_dir # not mounted explicitely - # (6) The path to the task's work directory - task_workdir = self.full_cluster_workdir + # (6) Ext3 capture mounts, if any. + # These will look like "-B .capt_abcd.ext3:/path/workdir/abcd:image-src=/" + # While we are building these options, we're also creating + # the ext3 filesystems at the same time, if needed. + esc_capture_mounts = ext3capture_basenames().inject("") do |sing_opts,(basename,size)| + fs_name = ".capt_#{basename}.ext3" # e.g. .capt_work.ext3 + mountpoint = "#{effect_workdir}/#{basename}" # e.g. /path/to/workdir/work or /T123/work + install_ext3fs_filesystem(fs_name,size) + safe_mkdir(basename) + "#{sing_opts} -B #{fs_name.bash_escape}:#{mountpoint.bash_escape}:image-src=/" + end + # This list will be used to make a device number check: all components + # must be on a device different from the one for the work directory. + capture_basenames = ext3capture_basenames.map { |basename,_| basename } # (4) More -B (bind mounts) for all the local data providers. # This will be a string "-B path1 -B path2 -B path3" etc. @@ -2359,9 +2392,28 @@ def singularity_commands(command_script) "#{sing_opts} --overlay=#{path.bash_escape}:ro" end + # Wrap new HOME environment + command_script = wrap_new_HOME(command_script, effect_workdir) + # Set singularity command singularity_commands = <<-SINGULARITY_COMMANDS +# Note to developers: +# During a standard CBRAIN task, this script is invoked with no arguments +# at all. For debugging situations, an admin can invoke it with the single +# argument "shell" to bypass the tool's execution and launch a convenient +# interactive shell inside the container. + +# These two variables control the mode switching at the end of the script. +mode="exec" +sing_basename=./#{singularity_wrapper_basename.bash_escape} # note: the ./ is necessary + +# In 'shell' mode we replace them with other things. +if test $# -eq 1 -a "X$1" = "Xshell" ; then + mode="shell" + sing_basename="" +fi + # Build a local wrapper script to run in a singularity container cat << \"SINGULARITYJOB\" > #{singularity_wrapper_basename.bash_escape} #!/bin/bash @@ -2390,13 +2442,40 @@ def singularity_commands(command_script) exit 2 fi - # CBRAIN internal consistency test 4: must have the gridshare_dir mounted inside the container if test ! -d #{gridshare_dir.bash_escape} ; then echo "Container missing mount point for gridshare directory:" #{gridshare_dir.bash_escape} exit 2 fi +# CBRAIN internal consistency test 5: short task workdir (optional). +# It's possible the path below will be the same as the task workdir if no shortening +# is configured, so the test becomes trivially like test 2. +if test ! -d #{effect_workdir.bash_escape} ; then + echo "Container missing shortened task work directory:" #{effect_workdir.bash_escape} + exit 2 +fi + +# Make sure we are in the task's workdir now. +cd #{effect_workdir.bash_escape} || exit 2 + +# CBRAIN internal consistency test 6: all mounted ext3 filesystems should be +# on a device different from the task's workdir. Otherwise something went +# wrong with the mounts. Singularity or Apptainer can sometimes do that +# if the command is improperly built (order of mounts args etc). +workdir_devid=$(stat -c %d .) # dev number of task workdir +for mount in #{capture_basenames.map(&:bash_escape).join(" ")} ; do + mnt_devid=$(stat -c %d $mount 2>/dev/null) + if test -z "$mnt_devid" ; then + echo "Container missing mount point for '$mount'." + exit 2 + fi + if test "$workdir_devid" -eq "$mnt_devid" ; then + echo "Container has mount point for '$mount' but it is not mounted to an external filesystem." + exit 2 + fi +done + # Scientific commands start here #{command_script} @@ -2404,28 +2483,31 @@ def singularity_commands(command_script) # Make sure it is executable chmod 755 #{singularity_wrapper_basename.bash_escape} -# Other should have executable right on all components -# of the path in order to be mounted by singularity. -chmod o+x . .. ../.. ../../.. # Invoke Singularity with our wrapper script above. # Tricks used here: # 1) we supply (if any) additional options for the exec command -# 2) we mount the gridshare root directory -# 3) we mount the local data provider cache root directory -# 4) we mount each (if any) of the root directory for local data providers -# 5) we mount (if any) file system overlays -# 6) with -H we set the task's work directory as the singularity $HOME directory +# 2) we mount the local data provider cache root directory +# a) at its original cluster full path +# b) at /DP_Cache (used only when shortening workdir) +# 3) we mount the root of the gridshare area (for all tasks) +# 4) we mount each (if any) of the root directories for local data providers +# 5) we mount (if any) other fixed file system overlays +# 6) we mount (if any) capture ext3 filesystems +# 7) with -H we set the task's work directory as the singularity $HOME directory #{singularity_executable_name} \\ - exec \\ + $mode \\ #{container_exec_args} \\ - -B #{gridshare_dir.bash_escape} \\ -B #{cache_dir.bash_escape} \\ + -B #{cache_dir.bash_escape}:/DP_Cache \\ + -B #{gridshare_dir.bash_escape} \\ #{esc_local_dp_mountpoints} \\ #{overlay_mounts} \\ - -H #{task_workdir.bash_escape} \\ + -B #{task_workdir.bash_escape}:#{effect_workdir.bash_escape} \\ + #{esc_capture_mounts} \\ + -H #{effect_workdir.bash_escape} \\ #{container_image_name.bash_escape} \\ - ./#{singularity_wrapper_basename.bash_escape} + $sing_basename SINGULARITY_COMMANDS @@ -2440,6 +2522,24 @@ def singularity_commands(command_script) private + # Add HOME switching back and forth to a bash script; + # preserve the status returned by the script too. + def wrap_new_HOME(script, new_home) + new_home_script = <<-HOME_SWITCHING +# Preserve system HOME, then switch it +_cbrain_home_="$HOME" +export HOME=#{new_home.bash_escape} + +#{script} + +# Restore system HOME (while preserving the latest exit code) +_cbrain_status_="$?" +export HOME="$_cbrain_home_" +bash -c "exit $_cbrain_status_" + HOME_SWITCHING + new_home_script + end + # Returns an array of directory paths for all # online data providers that are local to the current # system (including smart ones). This is often needed @@ -2455,6 +2555,43 @@ def local_dp_storage_paths #:nodoc: dirs end + # Just invokes the same method on the task's ToolConfig. + def ext3capture_basenames + self.tool_config.ext3capture_basenames + end + + # This method creates an empty +filename+ with +size+ bytes + # (where size is specified like what the unix 'truncate' command accepts) + # and then formats it with a ext3 filesystem. If the filename already exists, + # nothing is done. + def install_ext3fs_filesystem(filename,size) #:nodoc: + if File.file?(filename) # already exists, all ok + self.addlog("EXT3 filesystem file '#{filename}' already exists") + return true + end + + self.addlog("Creating EXT3 filesystem in '#{filename}' with size=#{size}") + + # Create an empty file of the proper size + system("truncate -s #{size.bash_escape} #{filename.bash_escape}") + status = $? # A Process::Status object + if ! status.success? + cb_error "Cannot create EXT3 filesystem file '#{filename}': #{status.to_s}" + end + + # Format it. Only works on linux obviously + system("echo y | mkfs.ext3 -t ext3 -m 0 -q -E root_owner #{filename.bash_escape}") + status = $? # A Process::Status object + if ! status.success? + cb_error "Cannot format EXT3 filesystem file '#{filename}': #{status.to_s}" + end + + true + rescue => ex + File.unlink(filename) rescue nil # keep directory clean of broken ext3 file + raise ex + end + ################################################################## diff --git a/BrainPortal/app/models/data_provider.rb b/BrainPortal/app/models/data_provider.rb index 1fc072b47..96e0f22e6 100644 --- a/BrainPortal/app/models/data_provider.rb +++ b/BrainPortal/app/models/data_provider.rb @@ -238,6 +238,8 @@ class DataProvider < ApplicationRecord :message => 'is invalid as only paths with simple characters are valid: a-z, A-Z, 0-9, _, +, =, . and of course /', :allow_blank => true + validate :owner_is_appropriate + belongs_to :user belongs_to :group has_many :userfiles, :dependent => :restrict_with_exception @@ -731,6 +733,9 @@ def provider_move_to_otherprovider(userfile, otherprovider, options = {}) return false unless Userfile.is_legal_filename?(new_name) return false unless userfile.id # must be a fully saved file + # Check quota at destination + DiskQuota.exceeded!(new_user_id, otherprovider.id) + # Find existing destination, if any target_exists = Userfile.where( :name => new_name, @@ -828,6 +833,9 @@ def provider_copy_to_otherprovider(userfile, otherprovider, options = {}) return false unless Userfile.is_legal_filename?(new_name) return false unless userfile.id # must be a fully saved file + # Check quota at destination + DiskQuota.exceeded!(new_user_id, otherprovider.id) + # Find existing destination, if any target_exists = Userfile.where( :name => new_name, @@ -1059,6 +1067,21 @@ def for_api + ################################################################# + # Model Callbacks + ################################################################# + + # This verifies that the user_id matches an Admin user. + # For security reason, no data providers should by default + # be owned by normal users. + # + # This method can be overrided in subclasses. + def owner_is_appropriate #:nodoc: + return true if User.where(:id => self.user_id).first.is_a?(AdminUser) + self.errors.add(:user_id, 'must be an administrator') + return false + end + ################################################################# # Class-level cache-handling methods ################################################################# diff --git a/BrainPortal/app/models/disk_quota.rb b/BrainPortal/app/models/disk_quota.rb index a29696cb8..2e31c9ace 100644 --- a/BrainPortal/app/models/disk_quota.rb +++ b/BrainPortal/app/models/disk_quota.rb @@ -20,7 +20,23 @@ # along with this program. If not, see . # -# Model representing disk quotas +# Model representing disk quotas. +# +# We have two type of quota records: +# 1) User-specific quotas on a specific DP (user_id > 0) +# 2) DP-wide quotas applying for all users (user_id == 0) +# +# Quotas are verified by callbacks in the Userfile model. +# The methods here will try to fetch and process and +# user's specific quota (user_id and data_provider_id both set) +# before it falls back to the DP-wise quota (user_id == 0) +# +# The two main attributes are :max_size and :max_files +# which puts limit to the sum(size) and sum(num_files) +# of all the userfiles owned by a user on a specific DP. +# +# A quota record can be configuered with -1,-1, which prevents +# a user from creating any file at all on a DP. class DiskQuota < ApplicationRecord Revision_info=CbrainFileRevision[__FILE__] #:nodoc: @@ -29,6 +45,7 @@ class DiskQuota < ApplicationRecord validates_presence_of :data_provider_id validates_presence_of :max_bytes validates_presence_of :max_files + validate :limits_are_reasonable belongs_to :user, :optional => true # the value can be 0 but not nil belongs_to :data_provider, :optional => false @@ -39,11 +56,23 @@ class DiskQuota < ApplicationRecord attr_reader :cursize, :curfiles # values are filled when performing a check + def is_for_dp? #:nodoc: + self.user_id == 0 + end + + def is_for_user? #:nodoc: + self.user_id != 0 + end + + def none_allowed? #:nodoc: + self.max_files == -1 + end + # Returns true if currently, the user specified by +user_id+ # uses more disk space or more total files on +data_provider_id+ than # the quota limit configured by the admin. # - # The quota record for the limites is first looked up specifically for the pair + # The quota record for the limits is first looked up specifically for the pair # (user, data_provider); if no quota record is found, the pair (0, data_provider) # will be fetched instead (meaning a default quota for all users on that DP) # @@ -70,7 +99,7 @@ def self.exceeded!(user_id, data_provider_id) # Returns true if currently, the user specified by +user+ (specified by id) # uses more disk space or more total files on than configured in the limits # of this quota object. Since a quota object can contain '0' for the user attribute - # (meaning it's a default for all users), a user_id musy be given explicitely + # (meaning it's a default for all users), a user_id must be given explicitely # in argument in that case. def exceeded?(user_id = self.user_id) @@ -108,4 +137,35 @@ def exceeded!(user_id = self.user_id) raise CbrainDiskQuotaExceeded.new(user_id, self.data_provider_id) end + ##################################################### + # Validations callbacks + ##################################################### + + # Checks that both limits have proper values. + # 1) Both values are >= 0 : all OK + # 2) max_bytes == -1 and max_files == -1 : locked quota (no other negative numbers are allowed) + # + # Note that a value of 0 will still allow a user to create ONE userfile entry, + # because quota failures happen only after the quota is exceeded. That's + # why a value of -1 exists, it prevents any files from being created. + # + # A DP-wode quota of (-1,-1) will prevent ALL users from creating files on a DP + # (similar than having the DP set to read-only) but you can give special privileges + # to individual users by creating user-specific quota records. + def limits_are_reasonable + + # Already checked by other validate_presence callbacks + return false if self.max_bytes.blank? || self.max_files.blank? + + # All quotas are OK with this rule + return true if (self.max_bytes >= 0 && self.max_files >= 0) + # Only -1 in both fields is allowed if using negative numbers + return true if (self.max_bytes == -1 && self.max_files == -1) + + # Log errors + self.errors.add(:max_bytes, "must be -1, 0 or > 0") if self.max_bytes < -1 + self.errors.add(:max_files, "must be -1, 0 or > 0") if self.max_files < -1 + self.errors.add(:base, "when using -1, both limits must be set to -1") if self.max_bytes == -1 || self.max_files == -1 + end + end diff --git a/BrainPortal/app/models/remote_resource.rb b/BrainPortal/app/models/remote_resource.rb index 0ee6efdb3..750eb45e6 100644 --- a/BrainPortal/app/models/remote_resource.rb +++ b/BrainPortal/app/models/remote_resource.rb @@ -58,7 +58,6 @@ class RemoteResource < ApplicationRecord # can only be set by the admin using the Rails console; leaving them blank # means the mailers use whatever is configured in the Rails environment config. serialize :email_delivery_options - serialize :nh_email_delivery_options validates :name, :uniqueness => true, @@ -525,8 +524,8 @@ def get_ssh_public_key #:nodoc: cb_error "SSH public key only accessible for the current resource." unless self.id == self.class.current_resource.id return @ssh_public_key if @ssh_public_key home = CBRAIN::Rails_UserHome - if File.exists?("#{home}/.ssh/id_cbrain_portal.pub") - @ssh_public_key = File.read("#{home}/.ssh/id_cbrain_portal.pub") rescue "" + if File.exists?("#{home}/.ssh/id_cbrain_ed25519.pub") + @ssh_public_key = File.read("#{home}/.ssh/id_cbrain_ed25519.pub") rescue "" else @ssh_public_key = "" end diff --git a/BrainPortal/app/models/s3_flat_data_provider.rb b/BrainPortal/app/models/s3_flat_data_provider.rb index d0a297b51..dc4b42a35 100644 --- a/BrainPortal/app/models/s3_flat_data_provider.rb +++ b/BrainPortal/app/models/s3_flat_data_provider.rb @@ -77,6 +77,11 @@ def s3_connection ) end + def reset_connection #:nodoc: + Aws.empty_connection_pools! rescue nil + @s3_connection = nil + end + def impl_is_alive? #:nodoc: return true if s3_connection.connected? # Try to create the bucket once @@ -302,9 +307,11 @@ def cache_recursive_fileinfos(userfile) #:nodoc: cache_parent = cache_fullpath.parent parent_length = "#{cache_parent}/".length # used in substr below glob_pattern = userfile.is_a?(FileCollection) ? "/**/*" : "" - Dir.glob("#{userfile.cache_full_path}#{glob_pattern}").map do |fullpath| # /path/to/userfilebase/d1/d2/f1.txt - stats = File.lstat(fullpath) # not stat() ! - relpath = fullpath[parent_length,999999] # userfilebase/d1/d2/f1.txt + Dir.glob("#{userfile.cache_full_path}#{glob_pattern}", File::FNM_DOTMATCH).map do |fullpath| # /path/to/userfilebase/d1/d2/f1.txt + next if fullpath.ends_with? "/." # skip spurious entries for self-referencing sub directories + next if fullpath.ends_with? "/.." # skip spurious entries for referencing parent directories (never happens?) + stats = File.lstat(fullpath) # not stat() ! + relpath = fullpath[parent_length,999999] # userfilebase/d1/d2/f1.txt # This struct is defined in DataProvider FileInfo.new( :name => relpath, @@ -321,7 +328,7 @@ def cache_recursive_fileinfos(userfile) #:nodoc: :ctime => stats.ctime, :mtime => stats.mtime, ) - end.compact # the compact is in case we ever insert a 'next' in the map() above + end.compact end # Scan the Amazon bucket and returns a list of FileInfo objects @@ -390,8 +397,25 @@ def rsync_emulation(src_fileinfos,dst_fileinfos) #:nodoc: src_idx = src_fileinfos.index_by { |fi| fi.name } dst_idx = dst_fileinfos.index_by { |fi| fi.name } + # Hash of all possible directory prefixes at source + all_src_prefixes = src_idx + .keys # names of all source files and dirs + .map { |path| File.dirname(path) } # parents of all of them + .uniq + .map do |dirpath| + prefixes = [ dirpath ] + while (parent=File.dirname(dirpath)) != '.' + raise "Woh, got an absolute path back to root filesystem?!?" if parent == '/' + prefixes << parent + dirpath = parent + end + prefixes + end + .flatten + .index_by(&:itself) # will also do uniq + # Build two lists - delete_dest = dst_fileinfos.select { |fi| ! src_idx[fi.name] } + delete_dest = dst_fileinfos.select { |fi| ! src_idx[fi.name] && ! all_src_prefixes[fi.name] } delete_dest += dst_fileinfos.select { |fi| src_idx[fi.name] && src_idx[fi.name].symbolic_type != fi.symbolic_type } add_dest = src_fileinfos.select do |src_fi| diff --git a/BrainPortal/app/models/sing_bindmount_data_provider.rb b/BrainPortal/app/models/sing_bindmount_data_provider.rb index 8799a7f8b..516c70df4 100644 --- a/BrainPortal/app/models/sing_bindmount_data_provider.rb +++ b/BrainPortal/app/models/sing_bindmount_data_provider.rb @@ -160,10 +160,9 @@ def impl_sync_to_cache(userfile) #:nodoc: # As of rsync 3.1.2, rsync does the escaping of the remote path properly itself source_escaped = remotefull.to_s.bash_escape if self.class.local_rsync_protects_args? text = bash_this("#{rsync} -a -l --no-g --chmod=u=rwX,g=rX,Dg+s,o=r --delete #{self.rsync_excludes} #{source_colon}#{source_escaped}#{sourceslash} #{shell_escape(localfull)} 2>&1") - text.sub!(/Warning: Permanently added[^\n]+known hosts.\s*/i,"") # a common annoying warning - cb_error "Error syncing userfile to local cache, rsync returned:\n#{text}" unless text.blank? + cb_error "Error syncing userfile ##{userfile.id} to local cache, rsync returned:\n#{text}" unless text.blank? unless File.exist?(localfull) - cb_error "Error syncing userfile to local cache: no destination file found after rsync?\n" + + cb_error "Error syncing userfile ##{userfile.id} to local cache: no destination file found after rsync?\n" + "Make sure you are running rsync 3.0.6 or greater!" end true diff --git a/BrainPortal/app/models/sing_squashfs_data_provider.rb b/BrainPortal/app/models/sing_squashfs_data_provider.rb index d41e9dce4..f2c352321 100644 --- a/BrainPortal/app/models/sing_squashfs_data_provider.rb +++ b/BrainPortal/app/models/sing_squashfs_data_provider.rb @@ -128,11 +128,13 @@ def impl_sync_to_cache(userfile) #:nodoc: source_escaped = provider_is_remote ? remote_shell_escape(remotefull) : remotefull.to_s.bash_escape # As of rsync 3.1.2, rsync does the escaping of the remote path properly itself source_escaped = remotefull.to_s.bash_escape if self.class.local_rsync_protects_args? + # We need the SSH agent even when doing local transfers + CBRAIN.with_unlocked_agent + text = bash_this("#{rsync} -a -l --no-g --chmod=u=rwX,g=rX,Dg+s,o=r --delete #{self.rsync_excludes} #{source_colon}#{source_escaped}#{sourceslash} #{shell_escape(localfull)} 2>&1") - text.sub!(/Warning: Permanently added[^\n]+known hosts.\s*/i,"") # a common annoying warning - cb_error "Error syncing userfile to local cache, rsync returned:\n#{text}" unless text.blank? + cb_error "Error syncing userfile ##{userfile.id} to local cache, rsync returned:\n#{text}" unless text.blank? unless File.exist?(localfull) - cb_error "Error syncing userfile to local cache: no destination file found after rsync?\n" + + cb_error "Error syncing userfile ##{userfile.id} to local cache: no destination file found after rsync?\n" + "Make sure you are running rsync 3.0.6 or greater!" end true @@ -279,7 +281,7 @@ def get_squashfs_basenames(force = false) #:nodoc: remote_cmd = "cd #{self.remote_dir.bash_escape} && ls -1" text = self.remote_bash_this(remote_cmd) lines = text.split("\n") - @sq_files = lines.select { |l| l =~ /\A\S+\.(squashfs|sqs)\z/ }.sort + @sq_files = lines.select { |l| l =~ /\A\S+\.(squashfs|sqs|sqfs)\z/ }.sort self.meta[:squashfs_basenames] = @sq_files end diff --git a/BrainPortal/app/models/squashifier_en_cbrain_ssh_data_provider.rb b/BrainPortal/app/models/squashifier_en_cbrain_ssh_data_provider.rb new file mode 100644 index 000000000..26135a1c4 --- /dev/null +++ b/BrainPortal/app/models/squashifier_en_cbrain_ssh_data_provider.rb @@ -0,0 +1,170 @@ + +# +# CBRAIN Project +# +# Copyright (C) 2008-2023 +# The Royal Institution for the Advancement of Learning +# McGill University +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +# + +# This DataProvider class implements a remote SSH-accessible data provider +# using the EnCbrainSshDataProvider file structure, but with an added +# functionality: +# +# 1) the content of any FileCollection will be locally +# squashed with the command 'mksquashfs' before being sent to the +# data provider side (aka synchronizing to the provider). +# +# 2) Conversely a FileCollection's content will be unsquashed with +# the command 'unsquashfs' when synchronizing to the cache. +# +# This DP requires the Rails application to have access to these +# two commands, of course. +# +# Note that this DP cannot be made into a 'Smart' version, since the +# content on the DP side is always different from the content on th +# cache side, even when working with both under the same host. So +# there will always be a SSH upload and download operation whenever +# syncing to or from the cache. +# +# TODO refactor to avoid code duplication. That would require creating a new +# base-class abstract method cache_full_path_for_upload() and +# cache_full_path_for_download() (suggested names) that DP subclasses +# would use to implement their data transfer methods, distinct from +# cache_full_pathname() +class SquashifierEnCbrainSshDataProvider < EnCbrainSshDataProvider + + Revision_info=CbrainFileRevision[__FILE__] #:nodoc: + + # Name of the squashfs file that will contain a filecollection's squashified content + # This is a constant name independant of what the collection's own name is. + SQ_BASENAME = "CBRAIN_SquashedContent.squashfs" + + # This returns the category of the data provider + def self.pretty_category_name #:nodoc: + "Squashifier Enhanced SSH CBRAIN" + end + + def impl_sync_to_cache(userfile) #:nodoc: + return super if userfile.is_a?(SingleFile) + + # Normal code will fetch (remote) basename/basename.squashfs into (local) basename/basename.squashfs + super + + # Then we unsquash it all + fullpath = cache_full_path(userfile) # path to dir; in it is the .squashfs file + cacheparent = fullpath.parent + basename = userfile.name + tmpdirbase = ".tmp.unsq.#{Process.pid}" + unsqu_out = bash_this( + "cd #{cacheparent.to_s.bash_escape} && " + + "mv #{basename.bash_escape} #{tmpdirbase} && " + + "unsquashfs -f -n -p 1 -no-xattrs -d #{basename.bash_escape} #{tmpdirbase.bash_escape}/#{SQ_BASENAME.bash_escape} 2>&1 1>/dev/null && " + + "rm -rf #{tmpdirbase}" + ) + # Perform cleanup of expected messages (stupid unsquashfs program is too verbose) + #[ + # # In the following regexps, the trailing .* match anything to NL (but not including it) + # /^Parallel unsquashfs: Using \d+ processor.*/i, + # /^\d+ inodes.*to write.*/i, + # /^created \d+.*/i, + #].each { |regex| unsqu_out.sub!(regex,"") } + unsqu_out.strip! # remove all blanks on each side, whatever's left is the culprit + cb_error "Error syncing userfile ##{userfile.id} to local cache, unsquashfs commands returned:\n#{unsqu_out}" unless unsqu_out.blank? + true + end + + def impl_sync_to_provider(userfile) #:nodoc: + return super if userfile.is_a?(SingleFile) + + fullpath = cache_full_path(userfile) # without SQEXT + cacheparent = fullpath.parent + basename = userfile.name + tmpdirbase = ".tmp.mksq.#{Process.pid}" + # Note about the mksquashfs command: by supplying a single source argument ('basename'), the + # *content* of that directory is put directly at the top of the created squashfs filesystem. + mem_opt = self.class.mksquashfs_has_mem_option? ? "-mem 64m" : "" + mksqu_out = bash_this( + "cd #{cacheparent.to_s.bash_escape} && " + + "mkdir -p #{tmpdirbase.bash_escape} && " + + "mksquashfs #{basename.bash_escape} #{tmpdirbase.bash_escape}/#{SQ_BASENAME.bash_escape} -processors 1 -no-progress -noappend -no-xattrs -noD -noI -noF #{mem_opt} 2>&1 1>/dev/null || echo mksquashfs command failed" + ) + # Perform cleanup of expected messages (stupid mksquashfs program is too verbose) + #[ + # # In the following regexps, the trailing .* match anything to NL (but not including it) + # /^created \d+.*/i, + #].each { |regex| unsqu_out.sub!(regex,"") } + mksqu_out.strip! + cb_error "Error syncing userfile ##{userfile.id} to provider, mksquashfs commands returned:\n#{mksqu_out}" unless mksqu_out.blank? + + # Invoke the normal code; duplicated from superclasses unfortunately + + # ------- + # Prep code from EnCbrainSshDataProvider (simplified a little) + # ------- + threelevels = cache_subdirs_from_id(userfile.id) + remcachedir = Pathname.new(remote_dir) + threelevels[0] + threelevels[1] + threelevels[2] + mkdir_command = "mkdir -p #{remcachedir.to_s.bash_escape} >/dev/null 2>&1" + remote_bash_this(mkdir_command) + # ------- + # End of EnCbrainSshDataProvider code + # ------- + + # ------- + # rsync upload code from SshDataProvider, adjusted + # ------- + localfull = cacheparent + tmpdirbase + remotefull = provider_full_path(userfile) + cb_error "Error: directory #{localfull} does not exist in local cache!" unless File.exist?(localfull) + + sourceslash = "/" # constant this time + rsync = rsync_over_ssh_prefix(userfile.user, userfile) + + # Double escaping for old rsyncs + dest_escaped = remote_shell_escape(remotefull) + # As of rsync 3.1.2, rsync does the escaping of the remote path properly itself + dest_escaped = remotefull.to_s.bash_escape if self.class.local_rsync_protects_args? + + # It's IMPORTANT that the destination be specified with a bare ':' in front. + text = bash_this("#{rsync} -a -l --no-g --chmod=u=rwX,g=rX,Dg+s,o=r --delete #{self.rsync_excludes} #{shell_escape(localfull)}#{sourceslash} :#{dest_escaped} 2>&1") + cb_error "Error syncing userfile ##{userfile.id} to data provider, rsync returned:\n#{text}" unless text.blank? + unless self.provider_file_exists?(userfile).to_s =~ /file|dir/ + cb_error "Error syncing userfile ##{userfile.id} to data provider: no destination file found after rsync?\n" + + "Make sure you are running rsync 3.0.6 or greater!\n" + end + # ------- + # End of SshDataProvider code + # ------- + + true + ensure + # Cleanup local squashfs file no matter what + if cacheparent.to_s.present? && tmpdirbase.present? && File.directory?("#{cacheparent.to_s.bash_escape}/#{tmpdirbase.bash_escape}") + system "rm -rf #{cacheparent.to_s.bash_escape}/#{tmpdirbase.bash_escape}" + end + end + + # Check the capabilities of the local mksquashfs program. + # Returns true if it has -mem . Value cached in class variable. + def self.mksquashfs_has_mem_option? + return @_mksquashfs_mem_ if defined?(@_mksquashfs_mem_) + system "mksquashfs 2>&1 | grep -e -mem >/dev/null" + @_mksquashfs_mem_ = $?.success? + @_mksquashfs_mem_ + end + +end + diff --git a/BrainPortal/app/models/ssh_data_provider.rb b/BrainPortal/app/models/ssh_data_provider.rb index 60d6b0863..5bcd23252 100644 --- a/BrainPortal/app/models/ssh_data_provider.rb +++ b/BrainPortal/app/models/ssh_data_provider.rb @@ -87,10 +87,9 @@ def impl_sync_to_cache(userfile) #:nodoc: # It's IMPORTANT that the source be specified with a bare ':' in front. text = bash_this("#{rsync} -a -l --no-g --chmod=u=rwX,g=rX,Dg+s,o=r --delete #{self.rsync_excludes} :#{source_escaped}#{sourceslash} #{shell_escape(localfull)} 2>&1") - text.sub!(/Warning: Permanently added[^\n]+known hosts.\s*/i,"") # a common annoying warning - cb_error "Error syncing userfile to local cache, rsync returned:\n#{text}" unless text.blank? + cb_error "Error syncing userfile ##{userfile.id} to local cache, rsync returned:\n#{text}" unless text.blank? unless File.exist?(localfull) - cb_error "Error syncing userfile to local cache: no destination file found after rsync?\n" + + cb_error "Error syncing userfile ##{userfile.id} to local cache: no destination file found after rsync?\n" + "Make sure you are running rsync 3.0.6 or greater!" end true @@ -112,9 +111,9 @@ def impl_sync_to_provider(userfile) #:nodoc: # It's IMPORTANT that the destination be specified with a bare ':' in front. text = bash_this("#{rsync} -a -l --no-g --chmod=u=rwX,g=rX,Dg+s,o=r --delete #{self.rsync_excludes} #{shell_escape(localfull)}#{sourceslash} :#{dest_escaped} 2>&1") text.sub!(/Warning: Permanently added[^\n]+known hosts.\s*/i,"") # a common annoying warning - cb_error "Error syncing userfile to data provider, rsync returned:\n#{text}" unless text.blank? + cb_error "Error syncing userfile ##{userfile.id} to data provider, rsync returned:\n#{text}" unless text.blank? unless self.provider_file_exists?(userfile).to_s =~ /file|dir/ - cb_error "Error syncing userfile to data provider: no destination file found after rsync?\n" + + cb_error "Error syncing userfile ##{userfile.id} to data provider: no destination file found after rsync?\n" + "Make sure you are running rsync 3.0.6 or greater!\n" end true @@ -298,8 +297,68 @@ def impl_provider_repair(issue) #:nodoc: super(issue) end + # Checks connection and other common problems. + # Raises exception DataProviderTestConnectionError if connection is down or + # common config issues detected. Returns true if everything is OK. + def check_connection! + err_message = self.find_connection_issues + raise DataProviderTestConnectionError.new(err_message) if err_message.present? + true + end + protected + # Verifies the configuration and returns a string with a descriptive + # error message if something is wrong. + def find_connection_issues + master = self.master # This is a handler for the connection, not persistent. + tmpfile = "/tmp/dp_check.#{Process.pid}.#{rand(1000000)}" # prefix for .out and .err capture files + + # Check #1: the SSH connection can be established + if ! master.is_alive? + return "Cannot establish the SSH connection. Check the configuration: username, hostname, port are valid, and SSH key is installed." + end + + # Check #2: we can run "true" on the remote site and get no output + status = master.remote_shell_command_reader("true", + :stdin => "/dev/null", + :stdout => "#{tmpfile}.out", + :stderr => "#{tmpfile}.err" + ) + stdout = File.read("#{tmpfile}.out") rescue "Error capturing stdout" + stderr = File.read("#{tmpfile}.err") rescue "Error capturing stderr" + if stdout.size != 0 + stdout.strip! if stdout.present? # just to make it pretty while still reporting whitespace-only strings + return "Remote shell is not clean: got some bytes on stdout: '#{stdout}'" + end + if stderr.size != 0 + stderr.strip! if stdout.present? + return "Remote shell is not clean: got some bytes on stderr: '#{stderr}'" + end + if !status + return "Got non-zero return code when trying to run 'true' on remote side." + end + + # Check #3: the remote directory exists + master.remote_shell_command_reader "test -d #{self.remote_dir.bash_escape} && echo DIR-OK", :stdout => "#{tmpfile}.out" + out = File.read("#{tmpfile}.out") + if out != "DIR-OK\n" + return "The remote directory doesn't seem to exist." + end + + # Check #4: the remote directory is readable + master.remote_shell_command_reader "test -r #{self.remote_dir.bash_escape} && test -x #{self.remote_dir.bash_escape} && echo DIR-READ", :stdout => "#{tmpfile}.out" + out = File.read("#{tmpfile}.out") + if out != "DIR-READ\n" + return "The remote directory doesn't seem to be readable" + end + + return nil # No error messages means all is OK + ensure + File.unlink("#{tmpfile}.out") rescue nil + File.unlink("#{tmpfile}.err") rescue nil + end + # Returns a list of all files in remote directory +dirname+, with all their # associated metadata; size, permissions, access times, owner, group, etc. def remote_dir_entries(dirname, user = nil, userfile = nil) diff --git a/BrainPortal/app/models/ssh_data_provider_base.rb b/BrainPortal/app/models/ssh_data_provider_base.rb index d0dc188c9..d2b002e16 100644 --- a/BrainPortal/app/models/ssh_data_provider_base.rb +++ b/BrainPortal/app/models/ssh_data_provider_base.rb @@ -107,6 +107,29 @@ def remote_bash_this(command, user = nil, userfile = nil) self.master(user, userfile).remote_shell_command_reader(command, :stdin => '/dev/null') do |fh| text = fh.read end + + filter_out_ssh_stderr_messages(text) + end + + # Same as superclass, but because we sometimes issue local commands + # that indirectly connect through ssh, we also filter out the same error + # messages as in remote_bash_this(). + def bash_this(command) #:nodoc: + text = super + filter_out_ssh_stderr_messages(text) + end + + private + + # Remove common warning messages generally printed on stderr... + def filter_out_ssh_stderr_messages(text) + # 1) From ssh + text.sub!(/^Warning: Permanently added[^\n]+known hosts.\s*/i,"") # a common annoying warning + + # 1) From ssh-keysign when ssh to localhost from a different GID + text.sub!(/^setresgid \d+: Operation not permitted\s*/i,"") + text.sub!(/^ssh_keysign: no reply\s*/i,"") + text.sub!(/^sign using hostkey.*failed\s*/i,"") text end diff --git a/BrainPortal/app/models/sync_status.rb b/BrainPortal/app/models/sync_status.rb index 643f723e6..11bedf11c 100644 --- a/BrainPortal/app/models/sync_status.rb +++ b/BrainPortal/app/models/sync_status.rb @@ -126,42 +126,51 @@ def self.ready_to_copy_to_cache(userfile) unless userfile_id return yield end + prettyfile = "'#{userfile.name}' (##{userfile_id})" # for messages state = self.get_or_create_status(userfile_id) puts "SYNC: ToCache: #{state.pretty} Enter" if DebugMessages - # Wait until no other local client is copying the file's content - # in one direction or the other. - allok = repeat_every_formax_untilblock(CheckInterval,CheckMaxWait) do - state.reload - state.invalidate_old_status - puts "SYNC: ToCache: #{state.pretty} Check" if DebugMessages - state.status !~ /^To/ # no ToProvider or ToCache - end - puts "SYNC: ToCache: #{state.pretty} Proceed" if DebugMessages + # This loops attempts to wait for and then lock out other + # processes on the same server. + 2.times do + + # Wait until no other local client is copying the file's content + # in one direction or the other. + allok = repeat_every_formax_untilblock(CheckInterval,CheckMaxWait) do + state.reload + state.invalidate_old_status + puts "SYNC: ToCache: #{state.pretty} Check" if DebugMessages + state.status !~ /^To/ # no ToProvider or ToCache + end + puts "SYNC: ToCache: #{state.pretty} Proceed" if DebugMessages - if ! allok # means timeout occurred - oldstate = state.status - #state.status_transition(oldstate, "ProvNewer") # do our best; not needed? - raise "Sync error: timeout waiting for file '#{userfile_id}' " + - "in '#{oldstate}' for operation 'ToCache'." - end + if ! allok # means timeout occurred + oldstate = state.status + raise "Sync error: timeout waiting for #{prettyfile} in '#{oldstate}' for operation 'ToCache'." + end - # No need to do anything if the data is already in sync! - if state.status == "InSync" - state.update_attributes( :accessed_at => Time.now ) - return true - end + # No need to do anything if the data is already in sync! + if state.status == "InSync" + state.update_attributes( :accessed_at => Time.now ) + return true + end - if state.status == "Corrupted" - raise "Sync error: file '#{userfile_id}' marked 'Corrupted' " + - "for operation 'ToCache'." - end + # This can be set by invalidate_old_status above + if state.status == "Corrupted" + raise "Sync error: #{prettyfile} marked 'Corrupted' for operation 'ToCache'." + end + + # Adjust state to let all other processes know what + # WE want to do now. This will lock out other clients. + break if state.status_transition(state.status, "ToCache") # if we fail here, race condition + + end # loop 2 times - # Adjust state to let all other processes know what - # WE want to do now. This will lock out other clients. - state.status_transition!(state.status, "ToCache") # if we fail here, race condition puts "SYNC: ToCache: #{state.pretty} Update" if DebugMessages + if state.status != 'ToCache' + raise "Sync error: #{prettyfile} cannot be fetched after two attempts. Status=#{state.status}" + end # Wait until all other clients out there are done # transferring content to the DP side. We don't care @@ -175,8 +184,7 @@ def self.ready_to_copy_to_cache(userfile) if ! allok # means timeout occurred state.status_transition("ToCache", "ProvNewer") # checked OK - raise "Sync error: timeout waiting for other clients for " + - "file '#{userfile_id}' for operation 'ToCache'." + raise "Sync error: timeout waiting for other clients for #{prettyfile} for operation 'ToCache'." end # Now, perform the sync_to_cache operation. @@ -220,37 +228,46 @@ def self.ready_to_copy_to_dp(userfile) unless userfile_id return yield end + prettyfile = "'#{userfile.name}' (##{userfile_id})" # for messages state = self.get_or_create_status(userfile_id) puts "SYNC: ToProv: #{state.pretty} Enter" if DebugMessages - # Wait until no other local client is copying the file's content - # in one direction or the other. - allok = repeat_every_formax_untilblock(CheckInterval,CheckMaxWait) do - state.reload - state.invalidate_old_status - puts "SYNC: ToProv: #{state.pretty} Check" if DebugMessages - state.status !~ /^To/ # no ToProvider or ToCache - end - puts "SYNC: ToProv: #{state.pretty} Proceed" if DebugMessages + # This loops attempts to wait for and then lock out other + # processes on the same server. + 2.times do + + # Wait until no other local client is copying the file's content + # in one direction or the other. + allok = repeat_every_formax_untilblock(CheckInterval,CheckMaxWait) do + state.reload + state.invalidate_old_status + puts "SYNC: ToProv: #{state.pretty} Check" if DebugMessages + state.status !~ /^To/ # no ToProvider or ToCache + end + puts "SYNC: ToProv: #{state.pretty} Proceed" if DebugMessages - if ! allok # means timeout occurred - oldstate = state.status - #state.status_transition(oldstate, "CacheNewer") # do our best; not needed? - raise "Sync error: timeout waiting for file '#{userfile_id}' " + - "in '#{oldstate}' for operation 'ToProvider'." - end + if ! allok # means timeout occurred + oldstate = state.status + raise "Sync error: timeout waiting for #{prettyfile} in '#{oldstate}' for operation 'ToProvider'." + end - # No need to do anything if the data is already in sync! - if state.status == "InSync" - state.update_attributes( :accessed_at => Time.now ) - return true - end + # No need to do anything if the data is already in sync! + if state.status == "InSync" + state.update_attributes( :accessed_at => Time.now ) + return true + end + + # Adjust state to let all other processes know what + # WE want to do now. This will lock out other clients. + break if state.status_transition(state.status, "ToProvider") # if we fail, race condition + + end # loop 2 times - # Adjust state to let all other processes know what - # WE want to do now. This will lock out other clients. - state.status_transition!(state.status, "ToProvider") # if we fail, race condition puts "SYNC: ToProv: #{state.pretty} Update" if DebugMessages + if state.status != 'ToProvider' + raise "Sync error: #{prettyfile} cannot be uploaded after two attempts. Status=#{state.status}" + end # Wait until all other clients out there are done # transferring content to/from the provider, one way or the other. @@ -263,8 +280,7 @@ def self.ready_to_copy_to_dp(userfile) if ! allok # means timeout occurred state.status_transition("ToProvider", "CacheNewer") # checked OK - raise "Sync error: timeout waiting for other clients for " + - "file '#{userfile_id}' for operation 'ToProvider'." + raise "Sync error: timeout waiting for other clients for #{prettyfile} for operation 'ToProvider'." end # Now, perform the ToProvider operation. @@ -318,33 +334,43 @@ def self.ready_to_modify_cache(userfile, final_status = 'CacheNewer') unless userfile_id return yield end + prettyfile = "'#{userfile.name}' (##{userfile_id})" # for messages state = self.get_or_create_status(userfile_id) puts "SYNC: ModCache: #{state.pretty} Enter" if DebugMessages - # Wait until no other local client is copying the file's content - # in one direction or the other. - allok = repeat_every_formax_untilblock(CheckInterval,CheckMaxWait) do - state.reload - state.invalidate_old_status - puts "SYNC: ModCache: #{state.pretty} Check" if DebugMessages - state.status !~ /^To/ # no ToProvider or ToCache - end - puts "SYNC: ModCache: #{state.pretty} Proceed" if DebugMessages + # This loops attempts to wait for and then lock out other + # processes on the same server. + 2.times do + + # Wait until no other local client is copying the file's content + # in one direction or the other. + allok = repeat_every_formax_untilblock(CheckInterval,CheckMaxWait) do + state.reload + state.invalidate_old_status + puts "SYNC: ModCache: #{state.pretty} Check" if DebugMessages + state.status !~ /^To/ # no ToProvider or ToCache + end + puts "SYNC: ModCache: #{state.pretty} Proceed" if DebugMessages - if ! allok # means timeout occurred - oldstate = state.status - raise "Sync error: timeout waiting for file '#{userfile_id}' " + - "in '#{oldstate}' for operation 'ModifyCache'." - end + if ! allok # means timeout occurred + oldstate = state.status + raise "Sync error: timeout waiting for #{prettyfile} in '#{oldstate}' for operation 'ModifyCache'." + end + + # Adjust state to let all other processes know that + # we want to modify the cache. "ToCache" is not exactly + # true, as we are not copying from the DP, but it will + # still lock out other processes trying to start data + # operations, which is what we want. + break if state.status_transition(state.status, "ToCache") # if we fail, race condition + + end # loop 2 times - # Adjust state to let all other processes know that - # we want to modify the cache. "ToCache" is not exactly - # true, as we are not copying from the DP, but it will - # still lock out other processes trying to start data - # operations, which is what we want. - state.status_transition!(state.status, "ToCache") # if we fail, race condition puts "SYNC: ModCache: #{state.pretty} Update" if DebugMessages + if state.status != 'ToCache' + raise "Sync error: cache for #{prettyfile} cannot be updated after two attempts. Status=#{state.status}" + end # Now, perform the ModifyCache operation self.wrap_block( @@ -390,34 +416,43 @@ def self.ready_to_modify_dp(userfile) unless userfile_id return yield end + prettyfile = "'#{userfile.name}' (##{userfile_id})" # for messages state = self.get_or_create_status(userfile_id) puts "SYNC: ModProv: #{state.pretty} Entering" if DebugMessages - # Wait until no other local client is copying the file's content - # in one direction or the other. - allok = repeat_every_formax_untilblock(CheckInterval,CheckMaxWait) do - state.reload - state.invalidate_old_status - puts "SYNC: ModProv: #{state.pretty} Check" if DebugMessages - state.status !~ /^To/ # no ToProvider or ToCache - end - puts "SYNC: ModProv: #{state.pretty} Proceed" if DebugMessages + # This loops attempts to wait for and then lock out other + # processes on the same server. + 2.times do + + # Wait until no other local client is copying the file's content + # in one direction or the other. + allok = repeat_every_formax_untilblock(CheckInterval,CheckMaxWait) do + state.reload + state.invalidate_old_status + puts "SYNC: ModProv: #{state.pretty} Check" if DebugMessages + state.status !~ /^To/ # no ToProvider or ToCache + end + puts "SYNC: ModProv: #{state.pretty} Proceed" if DebugMessages - if ! allok # means timeout occurred - oldstate = state.status - #state.status_transition(oldstate, "CacheNewer") # do our best; not needed? - raise "Sync error: timeout waiting for file '#{userfile_id}' " + - "in '#{oldstate}' for operation 'ModifyProvider'." - end + if ! allok # means timeout occurred + oldstate = state.status + raise "Sync error: timeout waiting for #{prettyfile} in '#{oldstate}' for operation 'ModifyProvider'." + end + + # Adjust state to let all other processes know that + # we want to modify the provider side. "ToProvider" is not + # exactly true, as we are not copying to the DP, but it will + # still lock out other processes trying to start data + # operations, which is what we want. + break if state.status_transition(state.status, "ToProvider") # if we fail, race condition + + end # loop 2 times - # Adjust state to let all other processes know that - # we want to modify the provider side. "ToProvider" is not - # exactly true, as we are not copying to the DP, but it will - # still lock out other processes trying to start data - # operations, which is what we want. - state.status_transition!(state.status, "ToProvider") # if we fail, race condition puts "SYNC: ModProv: #{state.pretty} Update" if DebugMessages + if state.status != 'ToProvider' + raise "Sync error: provider content for #{prettyfile} cannot be modified after two attempts. Status=#{state.status}" + end # Wait until all other clients out there are done # transferring content to/from the provider, one way or the other. @@ -429,8 +464,7 @@ def self.ready_to_modify_dp(userfile) end if ! allok # means timeout occurred - raise "Sync error: timeout waiting for other clients for " + - "file '#{userfile_id}' for operation 'ModifyProvider'." + raise "Sync error: timeout waiting for other clients for #{prettyfile} for operation 'ModifyProvider'." end # Now, perform the ModifyProvider operation. @@ -479,11 +513,13 @@ def self.ready_to_modify_dp(userfile) def invalidate_old_status # "InSync" state is too old for current RemoteResource - myself = RemoteResource.current_resource - expire = myself.cache_trust_expire # in seconds before now - expire = nil if expire && expire < 3600 # we don't accept thresholds less than one hour - expire = 2.years.to_i if expire && expire > 2.years.to_i - if expire and self.status == "InSync" && self.synced_at < Time.now - expire + if @expire.nil? # this value is global for the current APP (Bourreau or Portal) + myself = RemoteResource.current_resource + @expire = myself.cache_trust_expire || 0 # in seconds before now + @expire = 0 if @expire < 3600 # we don't accept thresholds less than one hour + @expire = 2.years.to_i if @expire > 2.years.to_i + end + if @expire > 0 and self.status == "InSync" && self.synced_at < Time.now - @expire puts "SYNC: Invalid: #{self.pretty} InSync Is Too Old" if DebugMessages self.status_transition(self.status, "ProvNewer") return @@ -504,7 +540,7 @@ def pretty #:nodoc: end # This method changes the status attribute - # in the current task object to +to_state+ but + # in the current sync_status object to +to_state+ but # also makes sure the current value is +from_state+ . # The change is performed in a transaction where # the record is locked, to ensure the transition is diff --git a/BrainPortal/app/models/tool_config.rb b/BrainPortal/app/models/tool_config.rb index 8d4229f16..8f85347cc 100644 --- a/BrainPortal/app/models/tool_config.rb +++ b/BrainPortal/app/models/tool_config.rb @@ -67,6 +67,21 @@ class ToolConfig < ApplicationRecord api_attr_visible :version_name, :description, :tool_id, :bourreau_id, :group_id, :ncpus + # given array of pairs variable/value builds export script, a prefix is added to variables options + def vars_to_export_script(varprefix="") + env = self.env_array || [] + commands = "" + env.each do |name_val| + name = name_val[0] + val = name_val[1] + name.strip! + #val.gsub!(/'/,"'\''") + commands += "export #{varprefix}#{name}=\"#{val}\"\n" + end + commands += "\n" if env.size > 0 + commands + end + # To make it somewhat compatible with the ResourceAccess module, # here's this model's own method for checking if it's visible to a user. def can_be_accessed_by?(user) @@ -154,8 +169,10 @@ def extended_environment # Generates a partial BASH script that initializes environment # variables and is followed a the script prologue stored in the - # object. - def to_bash_prologue + # object. For singularity prologues, special prefixes are added to + # variable names to ensure they will be propagated to the container + # even in presence of --cleanenv parameteres and such + def to_bash_prologue(singularity=false) tool = self.tool bourreau = self.bourreau group = self.group @@ -194,17 +211,25 @@ def to_bash_prologue #--------------------------------------------------- ENV_HEADER - env.each do |name_val| - name = name_val[0] - val = name_val[1] - name.strip! - #val.gsub!(/'/,"'\''") - script += "export #{name}=\"#{val}\"\n" + script += vars_to_export_script + + if singularity + script += <<-ENV_HEADER +#--------------------------------------------------- +# Ensuring that environment variables are propagated:#{env.size == 0 ? " (NONE DEFINED)" : ""} +#--------------------------------------------------- + + ENV_HEADER + script += vars_to_export_script("SINGULARITYENV_") + script += vars_to_export_script("APPTAINERENV_") # SINGULARITYENV is to be depricated + end script += "\n" if env.size > 0 prologue = self.script_prologue || "" - script += <<-SCRIPT_HEADER + script += <<-SCRIPT_HEADER + + #--------------------------------------------------- # Script Prologue:#{prologue.blank? ? " (NONE SUPPLIED)" : ""} #--------------------------------------------------- @@ -291,6 +316,13 @@ def is_at_least_version(version) end end + # true if singularity image is defined + def use_singularity? + return self.container_engine == "Singularity" && + ( self.containerhub_image_name.present? || + self.container_image_userfile_id.present? ) + end + # This method calls any custom compare_versions() method defined # in the CbrainTask subclass for the tool of the current tool_config. # Returns true if the version_name of the current tool_config @@ -333,6 +365,8 @@ def cbrain_task_class # dp:1234 # # CBRAIN db registered file # userfile:1234 + # # A ext3 capture filesystem, will NOT be returned here as an overlay + # ext3capture:basename=12G def singularity_overlays_full_paths specs = parsed_overlay_specs specs.map do |knd, id_or_name| @@ -356,6 +390,8 @@ def singularity_overlays_full_paths cb_error "Userfile with id '#{id_or_name}' for overlay fetching not found." if ! userfile userfile.sync_to_cache() rescue cb_error "Userfile with id '#{id_or_name}' for fetching overlay failed to synchronize." userfile.cache_full_path() + when 'ext3capture' + [] # flatten will remove all that else cb_error "Invalid '#{knd}:#{id_or_name}' overlay." end @@ -374,6 +410,16 @@ def data_providers_with_overlays end.compact end + # Returns pairs [ [ basename, size], ...] as in [ [ 'work', '28g' ] + def ext3capture_basenames + specs = parsed_overlay_specs + return [] if specs.empty? + specs + .map { |pair| pair[1] if pair[0] == 'ext3capture' } + .compact + .map { |basename_and_size| basename_and_size.split("=") } + end + ################################################################# # Validation methods ################################################################# @@ -429,6 +475,9 @@ def parsed_overlay_specs # userfile:333 # dp:123 # dp:dp_name + # ext3capture:basename=SIZE + # ext3capture:work=30G + # ext3capture:tool_1.1.2=15M # def validate_overlays_specs #:nodoc: specs = parsed_overlay_specs @@ -444,9 +493,9 @@ def validate_overlays_specs #:nodoc: case kind # different validations rules for file, userfile and dp specs when 'file', 'old style file' # full path specification for a local file, e.g. "file:/myfiles/c.sqs" - if id_or_name !~ /^\/\S+\.(sqs|squashfs)$/i + if id_or_name !~ /^\/\S+\.(sqs|sqfs|squashfs)$/ self.errors.add(:singularity_overlays_specs, - " contains invalid #{kind} named '#{id_or_name}'. It should be a full path that ends in .squashfs or .sqs") + " contains invalid #{kind} named '#{id_or_name}'. It should be a full path that ends in .squashfs, .sqs or .sqfs") end when 'userfile' # db-registered file spec, e.g. "userfile:42" @@ -461,9 +510,9 @@ def validate_overlays_specs #:nodoc: self.errors.add(:singularity_overlays_specs, %{" contains invalid userfile id '#{id_or_name}'. The file with id '#{id_or_name}' is not found."} ) - elsif ! userfile.name.end_with?('.sqs') && ! userfile.name.end_with?('.squashfs') + elsif userfile.name.to_s !~ /\.(sqs|sqfs|squashfs)$/ self.errors.add(:singularity_overlays_specs, - " contains invalid userfile with id '#{id_or_name}' and name '#{userfile.name}'. File name should end in .squashfs or .sqs") + " contains invalid userfile with id '#{id_or_name}' and name '#{userfile.name}'. File name should end in .squashfs, .sqs or .sqfs") # todo maybe or/and check file type? end @@ -475,6 +524,12 @@ def validate_overlays_specs #:nodoc: self.errors.add(:singularity_overlays_specs, "DataProvider '#{id_or_name}' is not a SingSquashfsDataProvider") end + when 'ext3capture' # ext3 filesystem as a basename with an initial size + # The basename is limited to letters, digits, numbers and dashes; the =SIZE suffix must end with G or M + if id_or_name !~ /\A\w[\w\.-]+=([1-9]\d*)[mg]\z/i + self.errors.add(:singularity_overlays_specs, "contains invalid ext3capture specification (must be like ext3capture:basename=1g or 2m etc)") + end + else # Other errors self.errors.add(:singularity_overlays_specs, "contains invalid specification '#{kind}:#{id_or_name}'") @@ -573,10 +628,12 @@ def self.create_from_descriptor(bourreau, tool, descriptor, record_path=false) container_info = descriptor.container_image || {} container_engine = container_info['type'].presence.try(:capitalize) - container_engine = "Singularity" if (container_engine == "Docker" && + container_engine = "Singularity" if (container_engine == "Docker" && !bourreau.docker_present? && bourreau.singularity_present? ) + container_index = container_info['index'].presence + container_index = 'docker://' if container_index == 'index.docker.io' # old convention tc = ToolConfig.create!( # Main three keys :tool_id => tool.id, @@ -593,7 +650,7 @@ def self.create_from_descriptor(bourreau, tool, descriptor, record_path=false) :boutiques_descriptor_path => (record_path.presence && descriptor.from_file), # The following three attributes are for containerization; not sure about values :container_engine => container_engine, - :container_index_location => container_info['index'].presence, + :container_index_location => container_index, :containerhub_image_name => container_info['image'].presence, ) diff --git a/BrainPortal/app/models/user.rb b/BrainPortal/app/models/user.rb index c06063e17..9b966bb6e 100644 --- a/BrainPortal/app/models/user.rb +++ b/BrainPortal/app/models/user.rb @@ -382,7 +382,7 @@ def destroy_user_sessions # If option +create_it+ is true, create the key files if necessary. # If option +ok_no_files+ is true, will return the object even if # the key files don't exist yet (default it to raise an exception) - def ssh_key(options = { :create_id => false, :ok_no_files => false }) + def ssh_key(options = { :create_it => false, :ok_no_files => false }) name = "u#{self.id}" # Avoiding username in ssh filenames or in comment. return SshKey.find_or_create(name) if options[:create_it] return SshKey.new(name) if options[:ok_no_files] diff --git a/BrainPortal/app/models/userfile.rb b/BrainPortal/app/models/userfile.rb index a15d5e2ac..0c04fea29 100644 --- a/BrainPortal/app/models/userfile.rb +++ b/BrainPortal/app/models/userfile.rb @@ -649,11 +649,11 @@ def available? # local userfile, and get to the cache quickly if it's already there. # # The +attributes+ describes a userfile's attribute for tracking - # the data; normally only the 'name' is required is should be specific + # the data. Normally only the 'name' is required and it should be specific # enough to represent a particular piece of data (e.g. a container # image name with full version in it). A block must be given to the - # method, and it will be invoked if the data is not already cached; - # it will receive a single argument, the path to the caching subsystem + # method, and it will be invoked if the data is not already cached. + # The block will receive a single argument, the path to the caching subsystem # where the userfile's data should be installed (the path is the same # as that returned by 'DataProvider#cache_full_path()'. The block is # expected to fill this path with appropriate files and/or directories. @@ -1155,7 +1155,7 @@ def validate_browse_path # This method is invoked before the creation of any file. # It will raise an CbrainDiskQuotaExceeded exception if the - # user has exceeded a quota (space, or number of files) for the DP. + # user has already exceeded a quota (space, or number of files) for the DP. def check_exceeded_quota! DiskQuota.exceeded!(self.user_id, self.data_provider_id) true diff --git a/BrainPortal/app/models/userkey_flat_dir_ssh_data_provider.rb b/BrainPortal/app/models/userkey_flat_dir_ssh_data_provider.rb index 54c56863f..8cf27ec66 100644 --- a/BrainPortal/app/models/userkey_flat_dir_ssh_data_provider.rb +++ b/BrainPortal/app/models/userkey_flat_dir_ssh_data_provider.rb @@ -88,5 +88,15 @@ def ssh_shared_options(user = nil, userfile = nil) #:nodoc: self.master(user, userfile).ssh_shared_options end + ################################################################# + # Model Callbacks + ################################################################# + + # Normally, DPs can only be owned by admins. However, this DP class + # is meant to be owned by normal users. + def owner_is_appropriate #:nodoc: + return true + end + end diff --git a/BrainPortal/app/models/work_group.rb b/BrainPortal/app/models/work_group.rb index c7f1851fe..fde5cf535 100644 --- a/BrainPortal/app/models/work_group.rb +++ b/BrainPortal/app/models/work_group.rb @@ -31,7 +31,7 @@ class WorkGroup < Group # This method optimizes the DB lookups necessary to # create the pretty_category_name of a set of WorkGroups def self.prepare_pretty_category_names(groups = [], as_user = nil) - wgs = Array(groups).select { |g| g.is_a?(WorkGroup) && !g.invisible? } + wgs = Array(groups).select { |g| g.is_a?(WorkGroup) && !g.invisible? && !g.public?} wg_ids = wgs.map(&:id) wg_ucnt = WorkGroup.joins("LEFT JOIN groups_users ON groups_users.group_id=groups.id LEFT JOIN users ON users.id=groups_users.user_id").where('groups.id' => wg_ids).group('groups.id').count('users.login') # how many users per workgroup diff --git a/BrainPortal/app/views/access_profiles/show.html.erb b/BrainPortal/app/views/access_profiles/show.html.erb index 7ce15ff9f..52bd6966b 100644 --- a/BrainPortal/app/views/access_profiles/show.html.erb +++ b/BrainPortal/app/views/access_profiles/show.html.erb @@ -65,7 +65,7 @@ <%= show_table(@access_profile, :form_helper => cf, :edit_condition => check_role(:admin_user), :header => @access_profile.new_record? ? 'Project Membership' : 'Projects In This Profile') do |t| %> <% group_names = (@access_profile.groups.sort_by(&:name).map { |g| link_to_group_if_accessible(g) }.join(", ").html_safe.presence) || "(None)" %> - <% t.edit_cell(:group_ids, :show_width => 2, :no_header => "Projects", :content => group_names) do %> + <% t.edit_cell(:group_ids, :show_width => 2, :no_header => "Projects", :td_options => { :class => "wrap" }, :content => group_names) do %> <%= render :partial => 'shared/group_tables', :locals => { :model => @access_profile } %> diff --git a/BrainPortal/app/views/bourreaux/_notes.html.erb b/BrainPortal/app/views/bourreaux/_notes.html.erb index 023251f1c..7511958df 100644 --- a/BrainPortal/app/views/bourreaux/_notes.html.erb +++ b/BrainPortal/app/views/bourreaux/_notes.html.erb @@ -18,7 +18,7 @@ # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License -# along with this program. If not, see . +# along with this program. If not, see . # -%> @@ -46,89 +46,5 @@ are several ways that the BrainPortal can be told how to connect to and manage the Execution Server, which explains all the fields in this form. -

-

Hardcoded DB and ActiveResource

-

- - In the most ordinary case, an Execution Server is installed and deployed - manually by a CBRAIN administrator; this requires choosing the - listen port (the port argument to its script/server - -p port command when it's started) and creating its - database.yml file. For such a manual installation, the - only two required field in this form will be those in the box - ActiveResource Configuration. Note that these - two fields are completely ignored if the ActiveResource connection - is being tunnelled (see below). - -

-

Hardcoded, But With Remote Control

-

- - If the fields in the section SSH Remote Control - Configuration are filled and describe the deployment - remote account of the Execution Server, then the BrainPortal will have the - ability to establish a persistent SSH master connection to that - host and allow the administrator to start and stop the Server - right from the WEB interface. Note that the UNIX user under which - the BrainPortal runs must have the proper SSH public keys for that - remote account installed. - -

-

Remote Control And Optional Tunnels

-

- - It's possible the further deviate from the standard hardcoded - Execution Server by having the BrainPortal set up SSH tunnels for - either (or both) of the ActiveResource connection and the - Database Server connection. This can be turned on by entering - port numbers in the two fields in the section Tunnelling - Configuration. For this to work, the SSH Remote - Control Configuration must be operational (see above). The - port numbers specified here must both be public TCP port that are - free on the Execution Server's host; they can be arbitrary numbers between - 1024 and 65530, not used by other services. - -

- - Tunnelling the ActiveResource connection: Entering - a port number here will tell the BrainPortal to select this - port for the Execution Server's Rails listening port (the port - argument to its script/server -p port command when it's - started). When starting the Execution Server using the interface, a SSH - tunnel will be established between a local port (not shown here - anywhere) on the BrainPortal side and the listening HTTP port - of the Server selected here. This means that the two fields in - the form's section ActiveResource Configuration - will be completely ignored. - -

- - Tunnelling the DB server connection: Entering a port - number here will tell the BrainPortal to select this port for the - Execution Server's Rails DB connection; more accurately, by doing this, the - BrainPortal will create from scratch a new database.yml - file, send it over to the Execution Server side, and force it to use - it. This database.yml will tell the Server to connect - to host 127.0.0.1 on the port number specified here. This port - will be configured to tunnel back to the BrainPortal all the way - to the DB server used by the BrainPortal itself. Note that this - can only work if the BrainPortal is connecting to its DB via a IP - domain connection, not a file socket. For MySQL for instance, - it means the BrainPortal's database.yml file must NOT - have the value localhost for the Host - field. Also, it's likely that you'll need to comment out the entry - "bind-address" in the server's my.cnf file. - -

- - A side effect of tunnelling the DB server is that any - database.yml file already present on the Execution Server side will - be backed up, and also that the newly created database.yml - file will be DELETED after the Server is started. This provides a - high security context for the DB server's connection as if there - were no database.yml file at all. And if there were, - and tunnelling is disabled by blanking out the port field, then - the backup database.yml will be restored. - diff --git a/BrainPortal/app/views/data_providers/_data_providers_table.html.erb b/BrainPortal/app/views/data_providers/_data_providers_table.html.erb index b9e168029..aa253354f 100644 --- a/BrainPortal/app/views/data_providers/_data_providers_table.html.erb +++ b/BrainPortal/app/views/data_providers/_data_providers_table.html.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 # @@ -30,10 +30,14 @@

<% if check_role(:site_manager) || check_role(:admin_user) %> - <%= link_to "Create New Data Provider", new_data_provider_path, :class => "button menu_button" %> + <%= link_to "Create New System Data Provider", new_data_provider_path, :class => "button menu_button" %> <% end %> - <%= link_to "Check All", nil, {:class => "button check_all_dp",} %> + <%= link_to "Create Personal Data Provider", new_personal_data_providers_path, :class => "button menu_button" %> + + <% if check_role(:admin_user) %> + <%= link_to "Check All", nil, {:class => "button check_all_dp",} %> + <% end %> <%= link_to "User Access Report", {:controller => :data_providers, :action => :dp_access}, diff --git a/BrainPortal/app/views/data_providers/_show_user_key.html.erb b/BrainPortal/app/views/data_providers/_show_user_key.html.erb new file mode 100644 index 000000000..a0fb0e184 --- /dev/null +++ b/BrainPortal/app/views/data_providers/_show_user_key.html.erb @@ -0,0 +1,63 @@ + +<%- +# +# CBRAIN Project +# +# Copyright (C) 2008-2023 +# The Royal Institution for the Advancement of Learning +# McGill University +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +# +-%> + + + + + + + + + + + + + + + + + +
SSH Key Configuration Instructions
+ The box below shows your personal, public SSH key that the CBRAIN system will use + to connect to your Data Provider. It is one line of text that needs to be installed + in your home directory on the remote host you configured for your Data Provider. +

+ For experts: if you are already familiar with this type of setup, you can simply cut-and-paste the + key with a text editor in the file .ssh/authorized_keys on the remote system. + Make sure permissions on the folder .ssh are 'rwx------' and on the file authorized_keys are 'rw-------'. +

+ For newcomers: consider downloading the key using the link below and saving it as a file 'mykey.pub' on + your current computer (or any computer). Then in a bash shell, run the 'ssh-copy-id' command as + explained below and it will automatically connect to the remote host + and install the key for you. The full command is:

+

+ 
ssh-copy-id -f -i mykey.pub -p <%= @provider.remote_port.presence || '22' %> <%= @provider.remote_user.presence || '[username_from_config_above]' %>@<%= @provider.remote_host.presence || '[hostname_from_config_above]' %>
+
+ Note that revealing this key's content to other people causes no security risks. + The information in this key is meant to be public and people cannot use it to access your information. +
Your Personal CBRAIN Public SSH Key
<%= pretty_ssh_key @provider.user.ssh_key(create_it: true).public_key rescue "Error fetching public key" %>
+ Download link: + <%= link_to "mykey.pub", "data:plain;charset=utf-8,#{url_encode(@provider.user.ssh_key(create_it: true).public_key) rescue "Error fetching public key" }" , download: "mykey.pub" %> +
+ diff --git a/BrainPortal/app/views/data_providers/new_personal.html.erb b/BrainPortal/app/views/data_providers/new_personal.html.erb new file mode 100644 index 000000000..56eab5b18 --- /dev/null +++ b/BrainPortal/app/views/data_providers/new_personal.html.erb @@ -0,0 +1,100 @@ + +<%- +# +# CBRAIN Project +# +# Copyright (C) 2008-2023 +# The Royal Institution for the Advancement of Learning +# McGill University +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +# +-%> + +<% title 'Add New Personal Data Provider' %> + +

Add New Personal SSH-based Data Provider

+ +<%= error_messages_for(@provider) %> + +<%= form_for @provider, :as => :data_provider, :url => { :action => "create_personal" }, :datatype => "script" do |f| -%> + +
+ +
+ <%= f.label :name, "Name" %>
+ <%= f.text_field :name %> +
This should be a simple identifier with no special characters or spaces
+
+ +

+ +

+ <%= f.label :description, "Description" %>
+ <%= f.text_area :description, :rows => 3, :cols => 85 %> +
The first line should be a short summary, and the rest are for any special notes for the users.
+
+ +

+ +

+ <%= f.label :group_id, "Project" %>
+ <%= group_select("data_provider[group_id]", { :groups => @groups, :selector => @provider.group_id.to_s }) %> +
This will control which users within CBRAIN can view and access the files on your storage. The default and recommended project is your own private project, '<%= current_user.own_group.name %>'.
+
+ +

+ +

+ SSH parameters + +
+ <%= f.label :remote_host, "Remote Hostname" %>
+ <%= f.text_field :remote_host, :size => 40 %> +
+ +

+ +

+ <%= f.label :remote_user, "Remote Username" %>
+ <%= f.text_field :remote_user, :size => 40 %> +
+ +

+ +

+ <%= f.label :remote_port, "Remote Port Number" %>
+ <%= f.text_field :remote_port, :size => 6 %> +
+ +

+ +

+ <%= f.label :remote_dir, "Full Directory Path" %>
+ <%= f.text_field :remote_dir, :size => 80 %> +
+ +
+
+ +

+ + <%= render :partial => 'show_user_key' %> + +

+ + <%= submit_tag 'Create New Data Provider' %>

+ +<% end %> + diff --git a/BrainPortal/app/views/data_providers/show.html.erb b/BrainPortal/app/views/data_providers/show.html.erb index c215d7c83..fd5de1b3d 100644 --- a/BrainPortal/app/views/data_providers/show.html.erb +++ b/BrainPortal/app/views/data_providers/show.html.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 # @@ -24,6 +24,10 @@ <% title 'Data Provider Info' %> +<% has_owner_access = (check_role(:admin_user) || @provider.user_id == current_user.id) %> +<% is_userkey_dp = @provider.is_a?(UserkeyFlatDirSshDataProvider) %> +<% needs_ssh_config = @provider.is_a?(SshDataProvider) || @provider.is_a?(SmartDataProviderInterface) %> +
<% if @provider.is_browsable?(current_user) && @provider.online? %> @@ -34,17 +38,23 @@ <%= link_to 'Inconsistency Report', report_data_provider_path(@provider), :class => "button" %> <% end %> - <%= link_to 'File Registration Statistics', report_path( - :table_name => 'userfiles.combined_file_rep', - :data_provider_id => @provider.id, - :row_type => :user_id , - :col_type => :type, - :generate => "ok" - ), :class => "button" %> + <% if @provider.userfiles.count > 0 %> + <%= link_to 'File Registration Statistics', report_path( + :table_name => 'userfiles.combined_file_rep', + :data_provider_id => @provider.id, + :row_type => :user_id , + :col_type => :type, + :generate => "ok" + ), :class => "button" %> + <% end %> - <% if check_role(:admin_user) || @provider.user_id == current_user.id %> - <%= link_to 'Delete', data_provider_path(@provider), { :data => { :confirm => "Are you sure you want to delete '#{@provider.name}' ?" }, :method => :delete, :class => "button" } %> - <% end %> + <% if @provider.respond_to?(:check_connection!) %> + <%= link_to "Test Configuration", check_personal_data_provider_path(@provider), :method => :post, :class => "button" %> + <% end %> + + <% if has_owner_access %> + <%= link_to 'Delete', data_provider_path(@provider), { :data => { :confirm => "Are you sure you want to delete '#{@provider.name}' ?" }, :method => :delete, :class => "button" } %> + <% end %>
@@ -54,7 +64,7 @@
- <%= show_table(@provider, :as => :data_provider, :edit_condition => (check_role(:admin_user) || @provider.user_id == current_user.id)) do |t| %> + <%= show_table(@provider, :as => :data_provider, :edit_condition => has_owner_access) do |t| %> <% t.edit_cell(:name) do |f| %> <%= f.text_field :name %> @@ -64,7 +74,7 @@ <%= f.text_area :description, :rows => 10, :cols => 40 %>
<% end %> - <% if check_role(:admin_user) || @provider.user_id == current_user.id %> + <% if has_owner_access %> <% t.attribute_cell(:type) %> <% else %> <% t.empty_cell %> @@ -90,63 +100,65 @@ <%= f.select :not_syncable, [["Fully syncable", false], ["NOT syncable", true]] %> <% end %> - <% t.cell("Site") { link_to_site_if_accessible(@provider.site) } %> - - <% if check_role(:admin_user) || @provider.user_id == current_user.id %> - <% t.cell("Revision Info (DataProvider)") { DataProvider.revision_info.format() } %> - <% else %> - <% t.empty_cell %> - <% end %> - <% joint_licenses = @provider.license_agreements.join("\n") %> - <% licenses = @provider.license_agreements.count == 0 ? "(None)": @provider.license_agreements.join("\n") %> - <% t.edit_cell(:license_agreements, :content => licenses) do |f| %> - <%= f.text_area :license_agreements, :value => joint_licenses, :content => joint_licenses, :rows => 5, :cols => 40 %>
-
Enter one agreement name per line. Note that only alphanumeric characters, underscores (_) and dashes (-) are accepted.
- <% end %> - - <% t.edit_cell(:time_zone, :content => (@provider.time_zone || "(Unset)") ) do |f| %> - <%= f.select :time_zone, time_zone_options_for_select(@provider.time_zone, /canada/i), :include_blank => true %> + <% if current_user.has_role?(:admin_user) %> + <% t.cell("Revision Info (DataProvider)", :show_width => 2) { DataProvider.revision_info.format() } %> + <% t.cell("Revision Info (#{@provider.type})", :show_width => 2) { @provider.revision_info.format() } %> <% end %> - <% if check_role(:admin_user) || @provider.user_id == current_user.id %> - <% t.cell("Revision Info (#{@provider.type})") { @provider.revision_info.format() } %> - <% else %> - <% t.empty_cell %> + <% if ! is_userkey_dp %> + <% t.edit_cell(:time_zone, :content => (@provider.time_zone || "(Unset)"), :show_width => 2 ) do |f| %> + <%= f.select :time_zone, time_zone_options_for_select(@provider.time_zone, /canada/i), :include_blank => true %> + <% end %> <% end %> - <% if check_role(:admin_user) || @provider.user_id == current_user.id %> + <% if has_owner_access %> <% t.edit_cell(:remote_dir, :header => "Physical Data Location", :show_width => 2) do |f| %> <%= f.text_field :remote_dir, :size => 80 %> <% end %> <% end %> + <% if current_user.has_role?(:admin_user) %> + <% joint_licenses = @provider.license_agreements.join("\n") %> + <% licenses = @provider.license_agreements.count == 0 ? "(None)": @provider.license_agreements.join("\n") %> + <% t.edit_cell(:license_agreements, :content => licenses, :show_width => 2) do |f| %> + <%= f.text_area :license_agreements, :value => joint_licenses, :content => joint_licenses, :rows => 5, :cols => 40 %>
+
Enter one agreement name per line. Note that only alphanumeric characters, underscores (_) and dashes (-) are accepted.
+ <% end %> + <% else %> + <% t.empty_cell %> + <% end %> + <% end %> - <% if check_role(:admin_user) || @provider.user_id == current_user.id %> - <%= show_table(@provider, :as => :data_provider, :header => "SSH parameters for remote Data Providers", :edit_condition => true) do |t| %> - <% t.edit_cell(:remote_host) do |f| %> - <%= f.text_field :remote_host %> + <% if has_owner_access && needs_ssh_config %> + <%= show_table(@provider, :as => :data_provider, :header => "SSH parameters", :edit_condition => true) do |t| %> + <% t.edit_cell(:remote_host, :show_width => 2) do |f| %> + <%= f.text_field :remote_host, :size => 40 %> <% end %> - <% t.edit_cell(:alternate_host, :header => "Alternate hostname(s)") do |f| %> - <%= f.text_field :alternate_host, :size => 60 %>
-
Comma-separated list of alternate hostnames; hostname1,hostname2,hostname3,...
+ <% if check_role(:admin_user) %> + <% t.edit_cell(:alternate_host, :show_width => 2, :header => "Alternate hostname(s)") do |f| %> + <%= f.text_field :alternate_host, :size => 100 %>
+
Comma-separated list of alternate hostnames; hostname1,hostname2,hostname3,...
+ <% end %> + <% end %> + <% t.edit_cell(:remote_user) do |f| %> + <%= f.text_field :remote_user, :size => 40 %> <% end %> <% t.edit_cell(:remote_port) do |f| %> <%= f.text_field :remote_port, :size => 6 %> <% end %> - <% t.edit_cell(:remote_user) do |f| %> - <%= f.text_field :remote_user %> - <% end %> <% end %> + <% end %> - <% if @provider.is_a?(SingSquashfsDataProvider) || @provider.is_a?(SingBindmountDataProvider) %> + <% if @provider.is_a?(SingSquashfsDataProvider) || @provider.is_a?(SingBindmountDataProvider) %> <%= show_table(@provider, :as => :data_provider, :header => "Containerized Storage Configuration", :edit_condition => true) do |t| %> <% t.edit_cell(:containerized_path, :header => 'Containerized Data Path', :show_width => 2) do %> <%= text_field_tag "data_provider[containerized_path]", @provider.containerized_path, :size => 80 %> <% end %> <% end %> - <% end %> + <% end %> + <% if @provider.is_a?(S3DataProvider) || @provider.is_a?(S3FlatDataProvider) %> <%= show_table(@provider, :as => :data_provider, :header => "Cloud Storage Configuration", :edit_condition => true) do |t| %> <% t.edit_cell(:cloud_storage_client_identifier, :header => 'Client Identifier', :show_width => 2) do |f| %> <%= f.text_field :cloud_storage_client_identifier, :size => 40, :autocomplete => 'off' %> @@ -167,7 +179,9 @@ <%= text_field_tag "data_provider[cloud_storage_region]", @provider.cloud_storage_region, :size => 80 %> <% end %> <% end %> + <% end %> + <% if @provider.is_a?(DataladDataProvider) %> <%= show_table(@provider, :as => :data_provider, :header => "Datalad Configuration", :edit_condition => true) do |t| %> <% t.edit_cell(:datalad_repository_url, :header => 'Datalad Repository URL', :show_width => 2) do |f| %> <%= f.text_field :datalad_repository_url %> @@ -259,22 +273,21 @@

-<% if (check_role(:admin_user) || @provider.user_id == current_user.id) && (@provider.is_a?(SshDataProvider) || @provider.is_a?(SmartDataProviderInterface)) %> - -

- -

- - - - -
Public SSH Key for this CBRAIN Portal
This key should be installed on this Data Provider's host machine to allow remote access.
<%= pretty_ssh_key(RemoteResource.current_resource.get_ssh_public_key || 'Unknown! Talk to sysadmin!') %>
-
+<% if has_owner_access %> + <% if is_userkey_dp %> + <%= render :partial => 'show_user_key' %> + <% elsif needs_ssh_config %> +
+ + + + +
Public SSH Key for this CBRAIN Portal
This key should be installed on this Data Provider's host machine to allow remote access.
<%= pretty_ssh_key(RemoteResource.current_resource.get_ssh_public_key || 'Unknown! Talk to sysadmin!') %>
+
+ <% end %> -<% end %> +

-<% if @provider.has_owner_access?(current_user) %> -

<%= render :partial => "layouts/log_report", :locals => { :log => @provider.getlog, :title => "Data Provider Log" } %> <% end %> diff --git a/BrainPortal/app/views/disk_quotas/_disk_quotas_table.html.erb b/BrainPortal/app/views/disk_quotas/_disk_quotas_table.html.erb index c73eaa726..940692d83 100644 --- a/BrainPortal/app/views/disk_quotas/_disk_quotas_table.html.erb +++ b/BrainPortal/app/views/disk_quotas/_disk_quotas_table.html.erb @@ -57,7 +57,7 @@ :sortable => true, :filters => default_filters_for(@base_scope, User) ) do |dq| - if dq.user_id == 0 + if dq.is_for_dp? html_colorize("(Default for all users)", 'orange') else link_to_user_if_accessible(dq.user) @@ -71,20 +71,23 @@ t.column("Max Size", :max_bytes, :sortable => true, - ) { |dq| colored_pretty_size(dq.max_bytes) } + ) { |dq| pretty_quota_max_bytes(dq) } t.column("Max Files", :max_files, :sortable => true, - ) { |dq| dq.max_files.to_s } + ) { |dq| pretty_quota_max_files(dq) } + # This column is a bit misleading: it shows the CURRENT USER's resources for all + # quota records that are DP-wide, and the AFFECTED USER'S resources for the user-specific quotas. t.column("My Usage") do |dq| what = dq.exceeded?(dq.user_id == 0 ? current_user.id : dq.user_id) + what = nil if dq.cursize.zero? && dq.curfiles.zero? # happens for dq with -1,-1 if what.nil? html_colorize("OK","green") + - " (#{colored_pretty_size(dq.cursize)}, #{dq.curfiles} files)".html_safe + " (#{colored_pretty_size(dq.cursize)} and #{number_with_commas(dq.curfiles)} files)".html_safe else html_colorize("Exceeded: #{what.to_s.humanize}","red") + - " (#{colored_pretty_size(dq.cursize)}, #{dq.curfiles} files)".html_safe + " (#{colored_pretty_size(dq.cursize)} and #{number_with_commas(dq.curfiles)} files)".html_safe end end @@ -92,7 +95,7 @@ link_to 'Table', report_path( :table_name => 'userfiles.combined_file_rep', - :user_id => (dq.user_id.zero? ? "" : dq.user_id), + :user_id => (dq.is_for_user? ? dq.user_id : ""), :data_provider_id => dq.data_provider_id, :row_type => :user_id , :col_type => :type, diff --git a/BrainPortal/app/views/disk_quotas/index.html.erb b/BrainPortal/app/views/disk_quotas/index.html.erb index 492d8fdb5..f80724bae 100644 --- a/BrainPortal/app/views/disk_quotas/index.html.erb +++ b/BrainPortal/app/views/disk_quotas/index.html.erb @@ -22,11 +22,12 @@ # -%> -<% title 'Disk Quotas' %> +<% title 'Disk Quotas Configurations' %> <% if current_user.has_role? :admin_user %>

- <%= link_to "New Quota Entry", new_disk_quota_path(), :class => :button %> + <%= link_to "Exceeded Quotas Report", report_disk_quotas_path(), :class => :button %> + <%= link_to "New Quota Entry", new_disk_quota_path(), :class => :button %>
<% end %> diff --git a/BrainPortal/app/views/disk_quotas/report.html.erb b/BrainPortal/app/views/disk_quotas/report.html.erb new file mode 100644 index 000000000..04f34612c --- /dev/null +++ b/BrainPortal/app/views/disk_quotas/report.html.erb @@ -0,0 +1,86 @@ + +<%- +# +# CBRAIN Project +# +# Copyright (C) 2008-2023 +# The Royal Institution for the Advancement of Learning +# McGill University +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +# +-%> + +<% title 'Exceeded Quotas' %> + +
+ <%= link_to "Quota Records Table", disk_quotas_path(), :class => :button %> + <%= link_to "New Quota Entry", new_disk_quota_path(), :class => :button %> +

+

+ + + + + + + + + + + + + + +<% @user_id_and_quota.each do |user_id,quota| %> + <% + # the following next statement should never get triggered, unless + # at some point I enhance the controller code to show 'nearly exceeded' quotas + # and then we should remove it. + %> + <% situation = quota.exceeded?(user_id) %> + <% next unless situation.present? %> + <% user_class = quota.is_for_user? ? 'class="disk_quota_user_quota_highlight"'.html_safe : "" %> + <% dp_class = quota.is_for_dp? ? 'class="disk_quota_dp_quota_highlight"'.html_safe : "" %> + <% bytes_class = situation.to_s =~ /bytes/ ? 'class="disk_quota_exceed_bytes"'.html_safe : "" %> + <% files_class = situation.to_s =~ /files/ ? 'class="disk_quota_exceed_files"'.html_safe : "" %> + + + + + + + + + + + +<% end %> + +
UserDataProviderSizeSize quotaNumber of filesNumber of files quotaSituationDetailsQuota record
><%= link_to_user_if_accessible(user_id) %>><%= link_to_data_provider_if_accessible(quota.data_provider_id) %>><%= colored_pretty_size(quota.cursize) %><%= pretty_quota_max_bytes(quota) %>><%= number_with_commas(quota.curfiles) %><%= pretty_quota_max_files(quota) %><%= situation.to_s.humanize %><%= + link_to 'Table', + report_path( + :table_name => 'userfiles.combined_file_rep', + :user_id => user_id, + :data_provider_id => quota.data_provider_id, + :row_type => :user_id , + :col_type => :type, + :generate => "ok" + ), :class => "action_link" + %> + + <% label = quota.is_for_dp? ? "(DP Quota)" : "(User Quota)" %> + <%= link_to("Show/Edit #{label}", disk_quota_path(quota), :class => "action_link") %> +
+ diff --git a/BrainPortal/app/views/disk_quotas/show.html.erb b/BrainPortal/app/views/disk_quotas/show.html.erb index d462ba6d2..fcb218ac2 100644 --- a/BrainPortal/app/views/disk_quotas/show.html.erb +++ b/BrainPortal/app/views/disk_quotas/show.html.erb @@ -49,33 +49,41 @@ <% t.cell("User") do %> <% if @disk_quota.new_record? %> - <%= user_select("disk_quota[user_id]", { :selector => (@disk_quota.user_id.presence || ""), :include_blank => '(Default For All Users)' }) %> + <%= user_select("disk_quota[user_id]", { :selector => @disk_quota.user_id, :include_blank => '(Default For All Users)' }) %> <% else %> - <%= @disk_quota.user_id.zero? ? + <%= @disk_quota.is_for_dp? ? html_colorize("(Default for all users)", 'orange') : link_to_user_if_accessible(@disk_quota.user) %> <% end %> <% end %> - <% t.edit_cell(:max_bytes, :content => colored_pretty_size(@disk_quota.max_bytes), :header => "Max Disk Space") do |f| %> + <% t.edit_cell(:max_bytes, :header => "Max Disk Space", :content => pretty_quota_max_bytes(@disk_quota)) do |f| %> <%= f.text_field :max_bytes, :size => 12 %>
Sizes are in bytes; when entering a new value, you can use a unit as a suffix, such as in 2.3 kb and 10 G. + A value of -1 means no files allowed at all.
<% end %> <% t.cell("Data Provider") do %> <% if @disk_quota.new_record? %> - <%= data_provider_select("disk_quota[data_provider_id]", { :selector => (@disk_quota.data_provider_id.presence || ""), :include_blank => '(Select a DataProvider)' }) %> + <%= data_provider_select("disk_quota[data_provider_id]", { :selector => @disk_quota.data_provider_id, :include_blank => '(Select a DataProvider)' }) %> <% else %> <%= link_to_data_provider_if_accessible(@disk_quota.data_provider) %> <% end %> <% end %> - <% t.edit_cell(:max_files, :header => "Max Num Files") do |f| %> + <% t.edit_cell(:max_files, :header => "Max Number Of Files", :content => pretty_quota_max_files(@disk_quota)) do |f| %> <%= f.text_field :max_files, :size => 12 %> +
+ A value of -1 means no files allowed at all. +
<% end %> <% end %> + +

+<%= render :partial => "layouts/log_report", :locals => { :log => @disk_quota.getlog, :title => 'Disk Quota Record Log' } %> + diff --git a/BrainPortal/app/views/groups/_groups_table.html.erb b/BrainPortal/app/views/groups/_groups_table.html.erb index 6ee54aac1..5b52e0f33 100644 --- a/BrainPortal/app/views/groups/_groups_table.html.erb +++ b/BrainPortal/app/views/groups/_groups_table.html.erb @@ -22,9 +22,26 @@ # -%> +<% button_view = @scope.custom[:button].present? %> +

- <%= link_to "Create Project", new_group_path, :class => 'button' %> - <%= overlay_ajax_link "Help", "/doc/groups/groups_info.html", :class => "button" %> + <%= link_to "Create Project", new_group_path, :class => 'button' %> + + <%= + scope_custom_link( + "Switch to #{button_view ? 'List' : 'Button'} View", + @scope, { 'button' => !button_view }, { :link => { :class => 'button' } } + ) + %> + + <%= + scope_custom_link( + "#{@scope.custom[:small_buttons] ? 'Large' : 'Small'} buttons", + @scope, { 'small_buttons' => !@scope.custom[:small_buttons] }, { :link => { :class => 'button' } } + ) if button_view + %> + + <%= overlay_ajax_link "Help", "/doc/groups/groups_info.html", :class => "button" %>
<%= @@ -34,28 +51,10 @@ }) %> -<% button_view = @scope.custom[:button] %> - <% end %> + <% t.edit_cell("Public", :content => check_box_tag(nil ,nil, @group.public?, :disabled => true)) do |f| %> + <%= f.check_box :public %> +
+ If checked, a public project makes all its files visible to all the users. Be careful + with this option! +
+ <% end %> + <% if current_user.has_role?(:admin_user) && @group.is_a?(WorkGroup) %> <% t.edit_cell("Invisible", :content => check_box_tag(nil ,nil, @group.invisible?, :disabled => true)) do |f| %> diff --git a/BrainPortal/app/views/layouts/_section_account.html.erb b/BrainPortal/app/views/layouts/_section_account.html.erb index 62d0f1ec5..5d8fd1b2f 100644 --- a/BrainPortal/app/views/layouts/_section_account.html.erb +++ b/BrainPortal/app/views/layouts/_section_account.html.erb @@ -55,6 +55,7 @@ <%= link_to 'Tools', tools_path %>
<%= link_to 'Tool Versions', tool_configs_path %>
<%= link_to 'Usage', resource_usage_index_path %>
+ <%= link_to 'Full list of tools and datasets', available_path %>
<% end %> <% end %> <% help_url = RemoteResource.current_resource.help_url %> diff --git a/BrainPortal/app/views/layouts/_section_menu.html.erb b/BrainPortal/app/views/layouts/_section_menu.html.erb index 785c734c1..df3a64f76 100644 --- a/BrainPortal/app/views/layouts/_section_menu.html.erb +++ b/BrainPortal/app/views/layouts/_section_menu.html.erb @@ -42,12 +42,13 @@ <%= hover_dropdown(link_to(current_project.try(:name) || "All", current_project ? group_path(current_project) : groups_path), :dropdown_class => "project_select_dropdown") do %>
Quick Project Switcher
- <% current_user.groups.where(:type => "WorkGroup", :invisible => false).order(:name).limit(20).all.each do |g| %> + <% current_user.groups.where(:type => "WorkGroup", :invisible => false, :creator_id => current_user.id).order(:name).limit(20).all.each do |g| %> <%= link_to h(crop_text_to(95, g.name)), {:controller => :groups, :action => :switch, :id => g.id}, {:method => :post, :class => "button"} %> <% end %>
+ <%= link_to "#{current_user.own_group.name} (default private project)", {:controller => :groups, :action => :switch, :id => current_user.own_group.id.to_s}, {:method => :post, :class => "button"} %> <%= link_to "All (no specific project: see all files and tasks)", {:controller => :groups, :action => :switch, :id => "all"}, {:method => :post, :class => "button"} %> <%= link_to "(Full project list)", groups_path, :class => "button" %> <% end %> diff --git a/BrainPortal/app/views/neurohub_portal/welcome.html.erb b/BrainPortal/app/views/neurohub_portal/welcome.html.erb index f5a3a3a5a..450829638 100644 --- a/BrainPortal/app/views/neurohub_portal/welcome.html.erb +++ b/BrainPortal/app/views/neurohub_portal/welcome.html.erb @@ -60,9 +60,10 @@ <% @dashboard_messages.each do |message| %>
-

<%= message.header %> - <%= message.created_at.strftime("%B %e, %Y") %>

+

<%= message.header %>

+ (Posted: <%= message.created_at.strftime("%B %e, %Y") %>)
<%= (message.description.presence || "").html_safe %>
diff --git a/BrainPortal/app/views/portal/_available_datasets_table.html.erb b/BrainPortal/app/views/portal/_available_datasets_table.html.erb index c261d472b..bf9e800db 100644 --- a/BrainPortal/app/views/portal/_available_datasets_table.html.erb +++ b/BrainPortal/app/views/portal/_available_datasets_table.html.erb @@ -24,16 +24,12 @@ - - - - -<% @groups.each do |group| %> +<% groups.each do |group| %> <% name = group.name description = (group.description.presence || "").strip diff --git a/BrainPortal/app/views/portal/_available_tools_table.html.erb b/BrainPortal/app/views/portal/_available_tools_table.html.erb index 84b6deaea..05d7adf97 100644 --- a/BrainPortal/app/views/portal/_available_tools_table.html.erb +++ b/BrainPortal/app/views/portal/_available_tools_table.html.erb @@ -24,26 +24,23 @@
Datasets
Name and description Availability
- - - - + -<% @tools.each do |tool| %> +<% tools.each do |tool| %> <% name = tool.name description = (tool.description.presence || "").strip description = "" if description.downcase == name.strip.downcase + tags = tool.get_all_tags versions = tool.tool_configs .to_a .select { |tc| tc.bourreau_id.present? } .select { |tc| tc.bourreau_id > 0 } - .select { |tc| tc.bourreau.try(:online) } .map(&:version_name) .map(&:presence) .compact @@ -58,7 +55,8 @@ - + + <% end %> diff --git a/BrainPortal/app/views/portal/available.html.erb b/BrainPortal/app/views/portal/available.html.erb index 47bd8d3cc..ef97708ed 100644 --- a/BrainPortal/app/views/portal/available.html.erb +++ b/BrainPortal/app/views/portal/available.html.erb @@ -30,13 +30,18 @@ Not all of them are available to all users.

-

- <%= render :partial => 'available_tools_table' %> -
+<% open_tools = @tools.select { |tool| (tool.group_id == @everyone_gid) && tool.tool_configs.where(:group_id => @everyone_gid).exists? } %> +<% restrict_tools = @tools - open_tools %> -
+<%= build_tabs do |tb| %> + <%= tb.tab("Tools") do %> + <%= render :partial => 'available_tools_table', :locals => { :tools => open_tools } %> + <%= render :partial => 'available_tools_table', :locals => { :tools => restrict_tools } %> + <% end %> -
- <%= render :partial => 'available_datasets_table' %> -
+ <%= tb.tab("Datasets") do %> + <%= render :partial => 'available_datasets_table', :locals => { :groups => @groups.select(&:public?) } %> + <%= render :partial => 'available_datasets_table', :locals => { :groups => @groups.reject(&:public?) } %> + <% end %> +<% end %> diff --git a/BrainPortal/app/views/portal/report.html.erb b/BrainPortal/app/views/portal/report.html.erb index e4439c6b4..c54719112 100644 --- a/BrainPortal/app/views/portal/report.html.erb +++ b/BrainPortal/app/views/portal/report.html.erb @@ -297,7 +297,15 @@ in a tabular layout. Proceed as follow: <% @table_row_values.each do |row_key| %> <% total_of_row = Array.new(vector_size,0) %> - <% row_sort_value = row_key.present? ? row_model ? row_model.find(row_key).name : row_key : "(None)" %> + <% + row_sort_value = "" + if row_key.present? + row_sort_value = row_key + if row_model + row_sort_value = row_model.where(:id => row_key).first.try(:name) || "#{row_model.name}-#{row_key}" + end + end + %> <% @table_col_values.each do |col_key| %> <% diff --git a/BrainPortal/app/views/service/detailed_stats.html.erb b/BrainPortal/app/views/portal/stats.html.erb similarity index 100% rename from BrainPortal/app/views/service/detailed_stats.html.erb rename to BrainPortal/app/views/portal/stats.html.erb diff --git a/BrainPortal/app/views/portal/welcome.html.erb b/BrainPortal/app/views/portal/welcome.html.erb index a79a38183..5a0a64a3a 100644 --- a/BrainPortal/app/views/portal/welcome.html.erb +++ b/BrainPortal/app/views/portal/welcome.html.erb @@ -30,7 +30,8 @@

CBRAIN News

<% @dashboard_messages.each do |message| %> -

<%= message.header %> - <%= message.created_at.strftime("%B %e, %Y") %>

+

<%= message.header %>

+ Posted: <%= message.created_at.strftime("%B %e, %Y") %>
<%= message.description.html_safe %> <% end %>
diff --git a/BrainPortal/app/views/service/stats.html.erb b/BrainPortal/app/views/service/stats.html.erb deleted file mode 100644 index 9d61fb511..000000000 --- a/BrainPortal/app/views/service/stats.html.erb +++ /dev/null @@ -1,57 +0,0 @@ - -<%- -# -# CBRAIN Project -# -# Copyright (C) 2008-2012 -# The Royal Institution for the Advancement of Learning -# McGill University -# -# This program is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation, either version 3 of the License, or -# (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with this program. If not, see . -# --%> - -<% title 'Service Stats' %> - -

CBRAIN Web Service Stats

- -
-
Tools
Name and description VersionsTags Availability
<%= overlay_description((name + "\n" + description).strip) %> <%= versions %><%= access %><%= tags.join(", ") %><%= access %>
<%= row_key.nil? ? "(None)" : row_proc.call(row_key) %>
- - - - - - - - - - <% @summary_stats.keys.sort.each do |client| %> - <% counts = @summary_stats[client] %> - <% next unless counts.is_a?(Array) && counts.size == 2 %> - - - - - <% end %> -
Totals by client type
Client TypeRequests
<%= client %><%= counts[0] + counts[1] %>
-
- -

- - Counters last reset: <%= @last_reset %> - -

- - For a more detailed report, see the <%= link_to "Detailed Service Stats", :action => :detailed_stats %> page. diff --git a/BrainPortal/app/views/tasks/edit.html.erb b/BrainPortal/app/views/tasks/edit.html.erb index 3240b7955..7e34ecc80 100644 --- a/BrainPortal/app/views/tasks/edit.html.erb +++ b/BrainPortal/app/views/tasks/edit.html.erb @@ -54,7 +54,7 @@

-<%= submit_tag "Save modified parameters for this task", :class => "button" %> +<%= submit_tag "Save modified parameters for this task", :class => "button", :disabled => @task.errors[:unsavable].present? %>
<% end %> diff --git a/BrainPortal/app/views/tasks/new.html.erb b/BrainPortal/app/views/tasks/new.html.erb index 4a1d7af76..8e33a5017 100644 --- a/BrainPortal/app/views/tasks/new.html.erb +++ b/BrainPortal/app/views/tasks/new.html.erb @@ -53,7 +53,7 @@ <% unless @task.class.properties[:no_submit_button] %>

- <%= submit_tag "Start #{@task.pretty_name}", :class => "button" %> + <%= submit_tag "Start #{@task.pretty_name}", :class => "button", :disabled => @task.errors[:unsavable].present? %>
<% end %> diff --git a/BrainPortal/app/views/tasks/show.html.erb b/BrainPortal/app/views/tasks/show.html.erb index 1f216818e..e08d691ac 100644 --- a/BrainPortal/app/views/tasks/show.html.erb +++ b/BrainPortal/app/views/tasks/show.html.erb @@ -150,7 +150,7 @@ <% if @task.zenodo_doi.starts_with?( ZenodoHelper::ZenodoSandboxDOIPrefix ) %> Published: <%= link_to_deposit(@task.zenodo_deposit_id) %> <% else %> - Published: <%= link_to_doi(@task.zenodo_doi) %> + Published: <%= link_to_zenodo_doi(@task.zenodo_doi) %> <% end %> <% elsif @task.zenodo_deposit_id.present? %> In progress: <%= link_to_deposit(@task.zenodo_deposit_id) %> diff --git a/BrainPortal/app/views/tool_configs/_by_resource.erb b/BrainPortal/app/views/tool_configs/_by_resource.erb index 174b780fb..fad1f0d52 100644 --- a/BrainPortal/app/views/tool_configs/_by_resource.erb +++ b/BrainPortal/app/views/tool_configs/_by_resource.erb @@ -56,9 +56,9 @@ no_version_summary = "" if versus_without_tcs.present? if for_tool - no_version_summary << html_colorize("No versions configured for these tools: ") - else no_version_summary << html_colorize("No versions configured for these servers: ") + else + no_version_summary << html_colorize("No versions configured for these tools: ") end versus_without_tcs.each do |vs| diff --git a/BrainPortal/app/views/tool_configs/_form_fields.html.erb b/BrainPortal/app/views/tool_configs/_form_fields.html.erb index 24a3abb41..fb166cb6a 100644 --- a/BrainPortal/app/views/tool_configs/_form_fields.html.erb +++ b/BrainPortal/app/views/tool_configs/_form_fields.html.erb @@ -210,7 +210,7 @@ for now.

<% end %> - + <% t.edit_cell :containerhub_image_name, :content => link_to_userfile_if_accessible(@tool_config.container_image), :header => "ID of the container image" do |f| %> <%= f.text_field :container_image_userfile_id %>
@@ -227,8 +227,9 @@ A specification can be either a full path (e.g. file:/a/b/data.squashfs), a path with a pattern (e.g. file:/a/b/data*.squashfs), - a registered file identified by ID (e.g. userfile:123) - or a SquashFS Data Provider identified by its ID or name (e.g. dp:123, dp:DpNameHere). + a registered file identified by ID (e.g. userfile:123), + a SquashFS Data Provider identified by its ID or name (e.g. dp:123, dp:DpNameHere) + or an ext3 capture overlay basename (e.g. ext3capture:basename=SIZE where size is 12G or 12M). In the case of a Data Provider, the overlays will be the files that the provider uses. Each overlay specification should be on a separate line. You can add comments, indicated with hash symbol #. @@ -244,6 +245,12 @@
<% end %> + <% t.boolean_edit_cell('tool_config[singularity_use_short_workdir]', + (@tool_config.singularity_use_short_workdir ? "1" : "0"), + "1", "0", + :header => "Use short workdirs inside Singularity") + %> + <% end %> diff --git a/BrainPortal/app/views/tool_configs/_tool_configs_table.html.erb b/BrainPortal/app/views/tool_configs/_tool_configs_table.html.erb index 14af8073a..d7eee7f01 100644 --- a/BrainPortal/app/views/tool_configs/_tool_configs_table.html.erb +++ b/BrainPortal/app/views/tool_configs/_tool_configs_table.html.erb @@ -60,11 +60,6 @@ <% t.pagination - t.column("Execution Server", :bourreau, - :sortable => true, - :filters => default_filters_for(@base_scope, Bourreau) - ) { |tc| tc.bourreau ? link_to_bourreau_if_accessible(tc.bourreau) : html_colorize("(All servers)",'orange')} - t.column("Tool Name", :tool, :sortable => true, :filters => default_filters_for(@base_scope, Tool) @@ -76,6 +71,12 @@ end end + t.column("Execution Server", :bourreau, + :sortable => true, + :filters => default_filters_for(@base_scope, Bourreau) + ) { |tc| tc.bourreau ? link_to_bourreau_if_accessible(tc.bourreau) : html_colorize("(All servers)",'orange')} + + t.column("Tool Project", 'tools.group_id', #:sortable => true, #:filters => default_filters_for(@base_scope, Group) diff --git a/BrainPortal/app/views/tool_configs/show.html.erb b/BrainPortal/app/views/tool_configs/show.html.erb index cd6774997..6b570a903 100644 --- a/BrainPortal/app/views/tool_configs/show.html.erb +++ b/BrainPortal/app/views/tool_configs/show.html.erb @@ -68,9 +68,10 @@ 

-<%= @bourreau_glob_config.to_bash_prologue if @bourreau_glob_config %>
-<%= @tool_glob_config.to_bash_prologue     if @tool_glob_config     %>
-<%= @tool_local_config.to_bash_prologue    if @tool_local_config    %>
+
+<%= @bourreau_glob_config.to_bash_prologue @tool_local_config&.use_singularity? if @bourreau_glob_config %>
+<%= @tool_glob_config.to_bash_prologue     @tool_local_config&.use_singularity? if @tool_glob_config     %>
+<%= @tool_local_config.to_bash_prologue    @tool_local_config&.use_singularity? if @tool_local_config    %>
 ##########################################
 #### [Wrapped commands would be here] ####
 ##########################################
diff --git a/BrainPortal/app/views/userfiles/_default_qc_panel.html.erb b/BrainPortal/app/views/userfiles/_default_qc_panel.html.erb
index cc68d01fd..20af26df6 100644
--- a/BrainPortal/app/views/userfiles/_default_qc_panel.html.erb
+++ b/BrainPortal/app/views/userfiles/_default_qc_panel.html.erb
@@ -23,13 +23,24 @@
 -%>
 
 <% if ! @userfile.is_locally_synced? %>
-  This file must be synced locally to view QC data.
+  
+    This file must be synced locally to view QC data.
+  
 <% else %>
-  <% if @userfile.is_a?(ImageFile) %>
-    <%= image_tag url_for(:action  => :content, :id => @userfile.id) %>

+  <% div_id_to_replace = "sub_viewer_#{@userfile.id}" %>
+  <% link = data_link(@userfile.name, @userfile, div_id_to_replace) %>
+  <% if link =~ /data-url=/ %>
+    

+      <%= link %>
+    

+    
   <% else %>
     
-    This file does not seem to contain any QC data, or no template is available to QC this file type.
+      This file does not seem to contain any QC data, or no template is available to QC this file type.
     
   <% end %>
 <% end %>
diff --git a/BrainPortal/app/views/userfiles/_quality_control_panel.html.erb b/BrainPortal/app/views/userfiles/_quality_control_panel.html.erb
index f7c436546..dee09e12e 100644
--- a/BrainPortal/app/views/userfiles/_quality_control_panel.html.erb
+++ b/BrainPortal/app/views/userfiles/_quality_control_panel.html.erb
@@ -36,10 +36,12 @@
     Navigation: file <%= @current_index + 1 %> out of <%= @filelist.size %>
     <%= link_to_userfile_if_accessible(@userfile, current_user, :html_options => { :target => '_blank' }) %>
     

-    <% if @current_index > 0 %>
+    <% not_first_file = @current_index != 0 %>
+    <% not_last_file  = @current_index < @filelist.size - 1 %>
+    <% if  not_first_file %>
       <%= submit_button "Previous File", :name => :previous %>
     <% end %>
-    <% if @current_index < @filelist.size - 1 %>
+    <% if not_last_file %>
       <%= submit_button "Next File", :name => :next %>
     <% end %>
   
@@ -66,7 +68,9 @@
 
 

 
-<%= submit_tag "Update (and go to next file)", :name => :update %>
+<% update_message  = "Update" %>
+<% update_message += " (and go to next file)" if not_last_file %>
+<%= submit_tag "#{update_message}", :name => :update, :data => {:current_file_id => @userfile.id } %>
 
 

 
diff --git a/BrainPortal/app/views/userfiles/show.html.erb b/BrainPortal/app/views/userfiles/show.html.erb
index fe3e43b73..ac315b56e 100644
--- a/BrainPortal/app/views/userfiles/show.html.erb
+++ b/BrainPortal/app/views/userfiles/show.html.erb
@@ -152,7 +152,7 @@
         <% if @userfile.zenodo_doi.starts_with?( ZenodoHelper::ZenodoSandboxDOIPrefix ) %>
           Published: <%= link_to_deposit(@userfile.zenodo_deposit_id) %>
         <% else %>
-          Published: <%= link_to_doi(@userfile.zenodo_doi) %>
+          Published: <%= link_to_zenodo_doi(@userfile.zenodo_doi) %>
         <% end %>
       <% elsif @userfile.zenodo_deposit_id.present? %>
           In progress: <%= link_to_deposit(@userfile.zenodo_deposit_id) %>
@@ -204,26 +204,27 @@
     Content
 
     <% if @userfile.archived? %>
+
       <%= html_colorize("This #{@userfile.pretty_type} has been archived.", 'red') %>

       Content viewers are disabled until the file is unarchived.
-    <% else %>
-      <% if ! @userfile.can_be_accessed_by?(current_user, :read) %>
+
+    <% elsif ! @userfile.can_be_accessed_by?(current_user, :read) %>
 
         (This file cannot be viewed by you; I wonder how you got here.)
 
-      <% elsif @userfile.data_provider.meta[:no_viewers] %>
+    <% elsif @userfile.data_provider.meta[:no_viewers] %>
 
         (This file cannot be viewed as it is stored on Data Provider
         <%= link_to_data_provider_if_accessible(@userfile.data_provider) %>
         which is marked as non-viewable)
 
-      <% elsif @userfile.data_provider.not_syncable? %>
+    <% elsif @userfile.data_provider.not_syncable? %>
 
         (This file cannot be viewed as it is stored on Data Provider
         <%= link_to_data_provider_if_accessible(@userfile.data_provider) %>
         which is configured to not allow synchronization at all)
 
-      <% elsif @sync_status == "Corrupted" %>
+    <% elsif @sync_status == "Corrupted" %>
 
         
           (The content of this file seems to be corrupted. This might be the result
@@ -232,26 +233,20 @@
           by a task, consider restarting the task's Post Processing stage.)
         
 
-      <% elsif ! @userfile.data_provider.rr_allowed_syncing? %>
+    <% elsif ! @userfile.data_provider.rr_allowed_syncing? %>
 
         (This file cannot be viewed as it is stored on Data Provider
         <%= link_to_data_provider_if_accessible(@userfile.data_provider) %>
         which is configured to not allow synchronization to this Portal)
 
-      <% elsif (! @userfile.is_locally_synced?) && (! @userfile.data_provider.online?) %>
+    <% elsif (! @userfile.is_locally_synced?) && (! @userfile.data_provider.online?) %>
 
         (This data is not currently synchronized and its Data Provider
         <%= link_to_data_provider_if_accessible(@userfile.data_provider) %>
         is offline, so its content is not viewable for the moment)
 
-      <% elsif @userfile.is_locally_synced? && @userfile.viewers_with_applied_conditions.blank? %>
-
-        (The contents of this file cannot be viewed: no viewer code available at this moment
-        for files of type '<%= @userfile.pretty_type %>')
-
-      <% else %>
+    <% elsif ! @userfile.is_locally_synced? %>
 
-        <% if ! @userfile.is_locally_synced? %>
           <% if @sync_status =~ /^To/ %>
             (This data file is currently being synchronized. Wait a few seconds for this to complete)
           <% else %>
@@ -260,8 +255,13 @@
             to start the synchronization process.
             This may allow you to view displayable content<% if @userfile.is_a?(FileCollection) %> and extract files from this collection<% end %>).
           <% end %>
-          

-        <% end %>
+
+    <% elsif @userfile.viewers_with_applied_conditions.blank? %>
+
+        (The contents of this file cannot be viewed: no viewer code available at this moment
+        for files of type '<%= @userfile.pretty_type %>')
+
+    <% else %>
 
         <% if @userfile.viewers_with_applied_conditions.size > 1 %>
             Change view:
@@ -293,8 +293,9 @@
             <% end %>
           
         
-      <% end %>
+
     <% end %>
+
   
 
 
diff --git a/BrainPortal/cbrain_plugins/cbrain-plugins-base/boutiques_descriptors/new_multi_boutiques_demo.json b/BrainPortal/cbrain_plugins/cbrain-plugins-base/boutiques_descriptors/new_multi_boutiques_demo.json
index acc8e1269..c2d2ec4ef 100644
--- a/BrainPortal/cbrain_plugins/cbrain-plugins-base/boutiques_descriptors/new_multi_boutiques_demo.json
+++ b/BrainPortal/cbrain_plugins/cbrain-plugins-base/boutiques_descriptors/new_multi_boutiques_demo.json
@@ -133,7 +133,7 @@
               "du_report_out": "TextFile"
             },
             "BoutiquesOutputFilenameRenamer": {
-              "my_output_name": "sinput1"
+              "du_report_out": [ "sinput1", "my_output_name" ]
             }
         }
     }
diff --git a/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/bash_scriptor/bourreau/bash_scriptor.rb b/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/bash_scriptor/bourreau/bash_scriptor.rb
index 5745079f0..4ae3f5457 100644
--- a/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/bash_scriptor/bourreau/bash_scriptor.rb
+++ b/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/bash_scriptor/bourreau/bash_scriptor.rb
@@ -57,6 +57,7 @@ def setup #:nodoc:
   def cluster_commands #:nodoc:
     params       = self.params
     file_ids     = params[:interface_userfile_ids] || []
+    File.unlink(self.stdout_cluster_filename) rescue nil # needed in case of retries
 
     raw_text     = params[:bash_script]
     raw_text.tr!("\r","") # text areas have CRs in line terminators, yuk!
diff --git a/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/boutiques_descriptor_maker_handler/portal/boutiques_descriptor_maker_handler.rb b/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/boutiques_descriptor_maker_handler/portal/boutiques_descriptor_maker_handler.rb
index 86fffe623..3ab1847ce 100644
--- a/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/boutiques_descriptor_maker_handler/portal/boutiques_descriptor_maker_handler.rb
+++ b/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/boutiques_descriptor_maker_handler/portal/boutiques_descriptor_maker_handler.rb
@@ -56,6 +56,7 @@ def descriptor_for_form
       self.errors.add(:base, "Your descriptor has syntax errors")
       desc_user_posted = self.descriptor_when_json_error
     end
+    desc_user_posted.delete(:groups) if desc_user_posted.groups.blank?
     added_input = self.boutiques_descriptor.input_by_id('_bdm_json_descriptor').dup
     desc_user_posted.inputs.unshift(added_input)
     desc_user_posted
@@ -76,6 +77,7 @@ def before_form
   # there is nothing to launch.
   def after_form
     desc = descriptor_for_form
+
     if self.errors.empty?
       self.bosh_validation_messages = generate_validation_messages(desc)
       if self.bosh_validation_messages.to_s.strip != "OK"
@@ -84,6 +86,16 @@ def after_form
         self.bosh_command_preview = generate_command_preview(desc, self.invoke_params)
       end
     end
+
+    if self.errors.empty? && (params[:_bdm_reorder] == 'on' || params[:_bdm_pad] == 'on')
+      btq    = descriptor_from_posted_form
+      btq    = btq.pretty_ordered    if params[:_bdm_reorder] == 'on'
+      btq.delete(:groups) if btq.groups.blank?
+      json   = btq.super_pretty_json if params[:_bdm_pad]     == 'on'
+      json ||= JSON.pretty_generate(btq)
+      self.invoke_params[:_bdm_json_descriptor] = json
+    end
+
     if self.errors.empty?
       # We must add at least one error to prevent CBRAIN from attempting to launch something.
       self.errors.add(:base, <<-ALL_OK
@@ -93,6 +105,7 @@ def after_form
          ALL_OK
       )
     end
+
     ""
   end
 
@@ -116,6 +129,20 @@ def descriptor_from_posted_form #:nodoc:
     text = descriptor_text_from_posted_form
     return nil unless text
     desc = BoutiquesSupport::BoutiquesDescriptor.new_from_string(text) rescue nil
+
+    # Check for something bosh doesn't verify: input IDs mentioned in groups
+    # that do not exist
+    zap_it = false
+    (desc&.groups || []).each do |group|
+      members = group.members || []
+      badid = members.detect { |inputid| (desc.input_by_id(inputid) rescue nil).nil? }
+      if badid
+        self.errors.add(:base, "The group '#{group.name}' has a member input id '#{badid}' which doesn't exist")
+        zap_it = true
+      end
+    end
+    desc = nil if zap_it
+
     desc
   end
 
@@ -131,7 +158,7 @@ def generate_validation_messages(desc) #:nodoc:
   rescue => ex
     return "Bosh validation failed: #{ex.class} #{ex.message}"
   ensure
-    File.unlink tmpfile
+    File.unlink(tmpfile) rescue nil
   end
 
   # Invokes bosh to generate a command preview.
diff --git a/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/boutiques_descriptor_maker_handler/views/_boutiques_preview.html.erb b/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/boutiques_descriptor_maker_handler/views/_boutiques_preview.html.erb
index 3776dff98..92844ed13 100644
--- a/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/boutiques_descriptor_maker_handler/views/_boutiques_preview.html.erb
+++ b/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/boutiques_descriptor_maker_handler/views/_boutiques_preview.html.erb
@@ -26,6 +26,8 @@
   

       
+      ()
+      ()
       
   

diff --git a/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/boutiques_task/views/_edit_help.html.erb b/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/boutiques_task/views/_edit_help.html.erb
index 0d3ee1746..c2b6649ee 100644
--- a/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/boutiques_task/views/_edit_help.html.erb
+++ b/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/boutiques_task/views/_edit_help.html.erb
@@ -59,6 +59,11 @@
   

 <% end %>
 
+<% if @descriptor.author.present? %>
+  Tool Author: <%= @descriptor.author %>
+  

+<% end %>
+
 <% if @descriptor.tool_doi.present? %>
   Tool DOI: <%= link_to @descriptor.tool_doi, @descriptor.tool_doi, :target => '_blank', :class => 'action_link' %>
   

@@ -70,7 +75,7 @@
 <% end %>
 
 <% if @descriptor.descriptor_url.present? %>
-  Boutiques Descriptor:: <%= link_to @descriptor.descriptor_url, @descriptor.descriptor_url, :target => '_blank', :class => 'action_link' %>
+  Boutiques Descriptor: <%= link_to @descriptor.descriptor_url, @descriptor.descriptor_url, :target => '_blank', :class => 'action_link' %>
   

 <% end %>
 
diff --git a/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/boutiques_task/views/_show_params.html.erb b/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/boutiques_task/views/_show_params.html.erb
index 5b2daa58a..845e9ebc6 100644
--- a/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/boutiques_task/views/_show_params.html.erb
+++ b/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/boutiques_task/views/_show_params.html.erb
@@ -63,7 +63,11 @@
       
         <%= param.name %>
         
-          <%= format_param.(@task.invoke_params[param.id]) %>
+          <% if param.type == 'Flag' %>
+            <%= red_if(@task.invoke_params[param.id].to_s =~ /^1$|^true$/, "No", "Yes", { :color1 => 'red', :color2 => 'green' }) %>
+          <% else %>
+            <%= format_param.(@task.invoke_params[param.id]) %>
+          <% end %>
         
       
     <%- end -%>
diff --git a/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/diagnostics/bourreau/diagnostics.rb b/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/diagnostics/bourreau/diagnostics.rb
index b1e7a2289..46cdf29c7 100644
--- a/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/diagnostics/bourreau/diagnostics.rb
+++ b/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/diagnostics/bourreau/diagnostics.rb
@@ -168,11 +168,11 @@ def cluster_commands #:nodoc:
       echo ""
 
       echo "==== Host Info ===="
-      uname -a
-      uptime
+      uname -a 2>/dev/null
+      uptime   2>/dev/null
       echo ""
 
-      if test -n "$(type lsb_release)" ; then
+      if test -n "$(type -p lsb_release)" ; then
         echo "==== LSB Release ===="
         lsb_release -a
         echo ""
@@ -185,8 +185,8 @@ def cluster_commands #:nodoc:
       fi
 
       if test -e /proc/cpuinfo ; then
-        echo "==== Last CPU Info ===="
-        cat /proc/cpuinfo | perl -ne '@x=grep(/./,<>);unshift(@y,pop(@x)) while @x > 0 && $y[0] !~ /^processor/; END { print @y }'
+        echo "==== Compacted CPU Info ===="
+        cat /proc/cpuinfo | sort | uniq | grep -v -E 'apicid|^processor|core id'
         echo ""
       fi
 
@@ -206,6 +206,10 @@ def cluster_commands #:nodoc:
       ls -la
       echo ""
 
+      echo "==== Listing Content of Work Directory With Dereferencing ===="
+      ls -laL
+      echo ""
+
     _DIAGNOSTIC_COMMANDS_
 
     file_ids.each do |id|
diff --git a/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/apptainer_image/apptainer_image.rb b/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/apptainer_image/apptainer_image.rb
new file mode 100644
index 000000000..8e77a7eb6
--- /dev/null
+++ b/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/apptainer_image/apptainer_image.rb
@@ -0,0 +1,59 @@
+
+#
+# CBRAIN Project
+#
+# Copyright (C) 2008-2023
+# The Royal Institution for the Advancement of Learning
+# McGill University
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see .
+#
+
+# This model represents a single file containing an Apptainer container image.
+class ApptainerImage < FilesystemImage
+
+  Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
+
+  has_viewer :name => 'Image Info', :partial  => :info, :if => :is_viewable?
+
+  def self.file_name_pattern #:nodoc:
+    /\.s?img\z|\.sif\z/i
+  end
+
+  def is_viewable? #:nodoc:
+    if ! self.has_apptainer_support?
+      return [ "The local portal doesn't support inspecting Apptainer images." ]
+    elsif ! self.is_locally_synced?
+      return [ "Apptainer image file not yet synchronized" ]
+    else
+      true
+    end
+  end
+
+  def has_apptainer_support? #:nodoc:
+    self.class.has_apptainer_support?
+  end
+
+  # Detects if the system has the 'apptainer' command.
+  # Caches the result in the class so it won't need to
+  # be detected again after the first time, for the life
+  # of the current process.
+  def self.has_apptainer_support? #:nodoc:
+    return @_has_apptainer_support if ! @_has_apptainer_support.nil?
+    out = IO.popen("bash -c 'type -p apptainer'","r") { |f| f.read }
+    @_has_apptainer_support = out.present?
+  end
+
+end
+
diff --git a/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/apptainer_image/views/_info.html.erb b/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/apptainer_image/views/_info.html.erb
new file mode 100644
index 000000000..f3c3b07f5
--- /dev/null
+++ b/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/apptainer_image/views/_info.html.erb
@@ -0,0 +1,47 @@
+
+<%
+#
+# CBRAIN Project
+#
+# Copyright (C) 2008-2023
+# The Royal Institution for the Advancement of Learning
+# McGill University
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see .
+#
+%>
+
+<% path = @userfile.cache_full_path.to_s.bash_escape %>
+<% cat  = lambda { |com| IO.popen(com,"r") { |fh| fh.read } } %>
+
+
Image Inspect

+
+
<%= cat.("apptainer inspect #{path}") %>

+
+
SIF Header

+
+
<%= cat.("apptainer sif header #{path}") %>

+
+
SIF List

+
+
<%= text = cat.("apptainer sif list #{path}") %>

+
+
SIF Items

+
+<% text.split(/\n/).map { |line| line[/^(\d+)/] }.compact.each do |id| %>
+
+  
<%= cat.("apptainer sif info #{id} #{path}") %>

+
+<% end %>
+
diff --git a/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/cbrain_file_list/cbrain_file_list.rb b/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/cbrain_file_list/cbrain_file_list.rb
index 62139f5d7..aebfca32d 100644
--- a/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/cbrain_file_list/cbrain_file_list.rb
+++ b/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/cbrain_file_list/cbrain_file_list.rb
@@ -96,7 +96,7 @@ def load_from_content(csv_file_content)
   # as extracted by cached_csv_array(). IDs will be numeric, or for
   # missing rows, will contain nils. IDs can be zero.
   #
-  #  [ 12, 0, 45, nil nil, 433 ]
+  #  [ 12, 0, 45, nil, nil, 433 ]
   #
   # Note that this method caches internally its result. To clear the
   # cache (if the userfile's content has changed for instance) call
@@ -241,15 +241,14 @@ def flush_internal_caches
   # for the array of +userfiles+. nil entries are allowed in +userfiles+
   # and will be properly encoded as missing rows with ID set to 0.
   def self.create_csv_file_from_userfiles(userfiles)
-    userfile_model_hash = Userfile.columns_hash
     text_rows           = []
     assoc_cache         = {}
     userfiles.each do |userfile|
       row = []
       if (userfile.nil?)
-        row = [0] + Array.new(ATTRIBUTES_LIST.size - 1, "")
+        row = [0] + Array.new(self::ATTRIBUTES_LIST.size - 1, "")
       else
-        ATTRIBUTES_LIST.each do |att|
+        self::ATTRIBUTES_LIST.each do |att|
           val = userfile.send(att)  # attribute value in mode; can be an id of an assoc
           if att =~ /_id$/ # try to look up names in other models
             assoc_cache[[att,val]] ||= ( userfile.send(att.to_s.sub(/_id$/,"")).try(att == :user_id ? :login : :name) || "-")
@@ -268,4 +267,33 @@ def self.create_csv_file_from_userfiles(userfiles)
     csv_file
   end
 
+  # This is like CbrainFileList.create!() but you must
+  # also provide :userfiles among the attributes; these
+  # userfiles will be stored as the content of the created
+  # CbrainFileList.
+  def self.create_with_userfiles!(attributes)
+    userfiles = attributes[:userfiles] || cb_error("Need some userfiles for CbrainFileList")
+    attlist   = attributes.reject { |k,v| k.to_s == 'userfiles' }
+    cbfile    = self.create!(attlist)
+    cbfile.set_userfiles(userfiles)
+    cbfile
+  end
+
+  # Replace the content of the CbrainFileList with a new
+  # CbrainFileList representing +userfiles+. The content
+  # of the CSV will be immediately uploaded to the provider.
+  def set_userfiles(userfiles)
+    flush_internal_caches()
+    csv = self.class.create_csv_file_from_userfiles(userfiles)
+    self.cache_writehandle { |fh| fh.write csv }
+    self
+  end
+
+  private
+
+  # Can be redefine in sub class
+  def self.userfile_model_hash
+    Userfile.columns_hash
+  end
+
 end
diff --git a/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/cbrain_file_list/views/_cb_file_list.html.erb b/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/cbrain_file_list/views/_cb_file_list.html.erb
index fe73edb0b..cdfa2695b 100644
--- a/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/cbrain_file_list/views/_cb_file_list.html.erb
+++ b/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/cbrain_file_list/views/_cb_file_list.html.erb
@@ -90,7 +90,7 @@
             <% val = cvs_row[idx] %>
             
               <% if att == :id %>
-                <% cur_file = Userfile.find_all_accessible_by_user(current_user).where(:id => val).first %>
+                <% cur_file = Userfile.find_all_accessible_by_user(current_user, :access_requested => :read).where(:id => val).first %>
                 <%= val %> : <%= link_to_userfile_if_accessible(cur_file) %>
               <% else %>
                 <%= val.nil? ? "-" : val %>
diff --git a/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/extended_cbrain_file_list/extended_cbrain_file_list.rb b/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/extended_cbrain_file_list/extended_cbrain_file_list.rb
new file mode 100644
index 000000000..f23587b18
--- /dev/null
+++ b/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/extended_cbrain_file_list/extended_cbrain_file_list.rb
@@ -0,0 +1,131 @@
+
+#
+# CBRAIN Project
+#
+# Copyright (C) 2008-2012
+# The Royal Institution for the Advancement of Learning
+# McGill University
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see .
+#
+
+# This class extand the attributes_list array used by the
+# CbrainFileList by adding an extra key that correspond
+# to the last column of the CSV file.
+#
+# Example of file content:
+#
+#   232123,"myfile.txt",425,"TextFile","MainStoreProvider","jsmith","mygroup","{extra_param_1: value_1}"
+#   112233,"plan.pdf",3894532,"SingleFile","SomeDP","jsmith","secretproject", "{extra_param_2: value_2}"
+#   0,,,,,,,
+#   933,"hello.txt",3433434,"TextFile","SomeDP","jsmith","mygroup","{extra_param_3: value_3}"
+#
+class ExtendedCbrainFileList < CbrainFileList
+
+  Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
+
+  # Structure of the CSV file; only the ID is used when this object is used as input to something else.
+  # When displayed in a web page, the associations to other models are shown by name.
+  ATTRIBUTES_LIST = superclass::ATTRIBUTES_LIST + [ :json_params ]
+
+  def self.pretty_type #:nodoc:
+    "Extended CBRAIN List of files"
+  end
+
+  # Returns an hash extract from the last column of the Extended CBCsv file
+  # as extracted by cached_csv_array(). Value will be a hash (can be empty)
+  #
+  #  [ {key_param_1_task_1: value_for_param_1_task_1, key_param_2_task_1: value_for_param_2_task_1},
+  #    {key_param_1_task_1: value_for_param_1_task_1},
+  #    {},
+  #    {},
+  #    {key_param_1_task_5: value_for_param_1_task_5, key_param_2_task_5: value_for_param_2_task_5}
+  #  ]
+  #
+  # Note that this method caches internally its result. To clear the
+  # cache (if the userfile's content has changed for instance) call
+  # the method flush_internal_caches().
+  #
+  def ordered_params()
+    json_params_idx = ATTRIBUTES_LIST.index(:json_params)
+    @extra_params ||= cached_csv_array.map do |row|
+      JSON.parse(row[json_params_idx])
+    end
+
+    @extra_params
+  end
+
+  # Many methods of this class cache their result internally
+  # to avoid reduplicating costly work. If the content of
+  # the CSV file change, calling flush_internal_caches() will
+  # clean these caches so they return new, accurate results.
+  def flush_internal_caches
+    super
+    @extra_params            = nil
+  end
+
+  # ["a/b/c", "a/d/e", "x/y/z", "x/w/a"]
+  #   return {"a" => ["a/b/c", "a/d/f"]
+  #           "x" => ["x/y/z", "x/w/a"]
+  #          }
+  def self.roots_to_fullpaths(relpaths)
+    # Special situation when a file with a path
+    # is specified instead of just a basename.
+    relpaths.inject({}) do |results,relpath|
+      filenames =  Pathname.new(relpath).each_filename.to_a
+      # E.g: root == sub-123
+      parent_dir = filenames.first
+      res = results[parent_dir] ||= []
+      res << relpath if filenames.size != 1
+      results
+    end
+  end
+
+  # Add json_params reader method to userfile object
+  def self.extend_userfile_json_params_reader(userfile,json_params_value)
+    userfile.define_singleton_method(:json_params) {
+      json_params_value
+    }
+  end
+
+  # Extend each userfile with json_params_reader
+  def self.extended_userfiles_by_name(userfiles,id_to_values)
+    userfiles.to_a.each do |userfile|
+      extend_userfile_json_params_reader(userfile,id_to_values[userfile.name])
+    end
+    userfiles
+  end
+
+  # Extended Userfile.columns_hash with json_params key
+  def self.userfile_model_hash
+    extended_userfile_model_hash = Userfile.columns_hash.dup
+    extended_userfile_model_hash["json_params"].define_singleton_method(:type) { :hash }
+    extended_userfile_model_hash
+  end
+
+  # add json_params reader method to userfile object
+  def self.extend_userfile_json_params_reader(userfile,json_params_value)
+    userfile.define_singleton_method(:json_params) {
+      json_params_value
+    }
+  end
+
+  # userfile_name => {Id: values}
+  def self.extended_userfiles_by_name(userfiles,id_to_values)
+    userfiles.to_a.each do |userfile|
+      extend_userfile_json_params_reader(userfile,id_to_values[userfile.name])
+    end
+    userfiles
+  end
+end
diff --git a/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/squashfs_file/squashfs_file.rb b/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/squashfs_file/squashfs_file.rb
new file mode 100644
index 000000000..ffb344be2
--- /dev/null
+++ b/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/squashfs_file/squashfs_file.rb
@@ -0,0 +1,62 @@
+
+#
+# CBRAIN Project
+#
+# Copyright (C) 2008-2023
+# The Royal Institution for the Advancement of Learning
+# McGill University
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see .
+#
+
+# Model for filesystem files in SquashFS format.
+class SquashfsFile < SingleFile
+
+  Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
+
+  has_viewer :name => 'SquashFS Filesystem', :partial => :squashfs_file, :if => :is_viewable?
+
+  def self.file_name_pattern #:nodoc:
+    /\.(sqs|squashfs|sqfs|sfs)\z/i
+  end
+
+  def self.pretty_type #:nodoc:
+    "SquashFS Filesystem File"
+  end
+
+  def is_viewable? #:nodoc:
+    if ! self.has_unsquashfs_support?
+      return [ "The local portal doesn't support inspecting SquashFS images." ]
+    elsif ! self.is_locally_synced?
+      return [ "The SquashFS image file is not yet synchronized" ]
+    else
+      true
+    end
+  end
+
+  def has_unsquashfs_support? #:nodoc:
+    self.class.has_unsquashfs_support?
+  end
+
+  # Detects if the system has the 'unsquashfs' command.
+  # Caches the result in the class so it won't need to
+  # be detected again after the first time, for the life
+  # of the current process.
+  def self.has_unsquashfs_support? #:nodoc:
+    return @_has_unsquashfs_support if ! @_has_unsquashfs_support.nil?
+    out = IO.popen("bash -c 'type -p unsquashfs'","r") { |f| f.read }
+    @_has_unsquashfs_support = out.present?
+  end
+
+end
diff --git a/BrainPortal/app/views/service/support.html.erb b/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/squashfs_file/views/_squashfs_file.html.erb
similarity index 64%
rename from BrainPortal/app/views/service/support.html.erb
rename to BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/squashfs_file/views/_squashfs_file.html.erb
index ded686517..fccb6e610 100644
--- a/BrainPortal/app/views/service/support.html.erb
+++ b/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/squashfs_file/views/_squashfs_file.html.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
 #
@@ -22,15 +22,15 @@
 #
 -%>
 
-<% title 'Service Support' %>
+<% path = @userfile.cache_full_path.to_s.bash_escape %>
+<% cat  = lambda { |com| IO.popen(com,"r") { |fh| fh.read } } %>
+<% max_list = 300 %>
 
-  
CBRAIN Basic Support

-  

-    <% if @support[:helpUrl].present? %>
-      
Help URL:
<%= link_to 'Support', @support[:helpUrl] %> (<%= @support[:helpUrl] %>)

-    <% end %>
-    
Email
<%= mail_to(@support[:supportEmail]) %>

-    
Information
<%= link_to 'About Us', @support[:aboutUs] %>

-  

+
SquashFS Superblock Information

 
+
<%= cat.("unsquashfs -p 1 -s #{path}") %>

+
+
SquashFS File List (first <%= max_list %> entries only)

+
+
<%= cat.("unsquashfs -p 1 -lls #{path} | head -#{max_list}") %>

 
diff --git a/BrainPortal/config/console_rc/lib/interactive_bourreau_control.rb b/BrainPortal/config/console_rc/lib/interactive_bourreau_control.rb
index ada09bed3..d791343b0 100644
--- a/BrainPortal/config/console_rc/lib/interactive_bourreau_control.rb
+++ b/BrainPortal/config/console_rc/lib/interactive_bourreau_control.rb
@@ -20,6 +20,8 @@
 # along with this program.  If not, see .
 #
 
+require 'reline'   # Readline.get_screen_size fails me
+
 # We need some sort of constant to refer to the console's
 # context, which has access to all the pretty helpers etc.
 ConsoleCtx = self # also in pretty_view.rb in the same directory
@@ -56,7 +58,7 @@ def initialize(bourreaux_list = Bourreau.order(:id).all, term_width = nil)
     @bourreaux = bourreaux_list
     @width     = term_width
     if term_width.blank? || term_width.to_i < 1
-      _,numcols = Readline.get_screen_size rescue [25,120]
+      _,numcols = Reline.get_screen_size rescue [25,120]
       @width          = numcols
     end
     @selected = {}
@@ -113,7 +115,7 @@ def interactive_control(initial_command = nil)
       OPERATIONS
 
       userinput     = initial_command.presence
-      userinput   ||= Readline.readline("Do something (h for help): ",false)
+      userinput   ||= Reline.readline("Do something (h for help): ",false)
       userinput     = "Q" if userinput.nil?
       inputkeywords = userinput.downcase.split(/\W+/).map(&:presence).compact
 
@@ -124,7 +126,7 @@ def interactive_control(initial_command = nil)
       end
       puts ""
       if dowait && initial_command.blank?
-        Readline.readline("Press RETURN to continue: ",false)
+        Reline.readline("Press RETURN to continue: ",false)
         puts ""
       end
       initial_command = nil
@@ -320,7 +322,12 @@ def process_user_letter(letter) #:nodoc:
           uptime   &&= ConsoleCtx.send(:pretty_elapsed, uptime, :num_components => 2)
           uptime   &&= "up for #{uptime}"
           uptime   ||= "DOWN"
-          printf "%#{max_size}s rev %-9.9s %s, %d/%d workers\n", bou.name, gitrev, uptime, numworkers, expworkers
+          color_on   = color_off = nil
+          color_on   = "\e[31m" if uptime == 'DOWN'          # RED    for down bourreaux
+          color_on ||= "\e[33m" if numworkers != expworkers  # YELLOW for missing workers
+          color_on ||= "\e[32m"                              # GREEN  when everything ok
+          color_off  = "\e[0m"  if color_on
+          printf "#{color_on}%#{max_size}s rev %-9.9s %s, %d/%d workers#{color_off}\n", bou.name, gitrev, uptime, numworkers, expworkers
         end
       end
       return true
@@ -352,7 +359,7 @@ def process_user_letter(letter) #:nodoc:
       puts " * @r@ will be substituted by the Bourreau's RAILS root path"
       puts " * @d@ will be substituted by the Bourreau's DP cache dir path"
       puts " * @g@ will be substituted by the Bourreau's gridshare dir path"
-      comm = Readline.readline("Bash command: ")
+      comm = Reline.readline("Bash command: ")
       bash_command_on_bourreaux(comm)
       return true
     end
diff --git a/BrainPortal/config/console_rc/lib/reports.rb b/BrainPortal/config/console_rc/lib/reports.rb
index 97dccd0d5..1e674fd12 100644
--- a/BrainPortal/config/console_rc/lib/reports.rb
+++ b/BrainPortal/config/console_rc/lib/reports.rb
@@ -54,6 +54,11 @@ def acttasks(tasks = CbrainTask.active.all)
       result
     end
 
+    # Remove column c_types if it's empty everywhere
+    if list1.all? { |struct| struct[:c_types].blank? }
+      list1.each  { |struct| struct.delete(:c_types) }
+    end
+
     # Remove duplicates from list1 and count them
     seen={}
     list2 = list1.select { |r| seen[r] ||= 0 ; seen[r] += 1 ; seen[r] == 1 }
diff --git a/BrainPortal/config/initializers/cbrain.rb b/BrainPortal/config/initializers/cbrain.rb
index 8a7391f74..478881eaa 100644
--- a/BrainPortal/config/initializers/cbrain.rb
+++ b/BrainPortal/config/initializers/cbrain.rb
@@ -95,6 +95,9 @@ def self.spawn_with_active_records(destination = nil, taskname = 'Internal Backg
     reader,writer = IO.pipe  # The stream that we use to send the subchild's pid to the parent
     childpid = Kernel.fork do
 
+      # Need to properly tell MySQL/MariaDB that we're disconnecting
+      ApplicationRecord.connection.disconnect! rescue nil
+
       # Child code starts here
       reader.close # Not needed in the child!
 
@@ -198,6 +201,9 @@ def self.spawn_fully_independent(taskname = 'Independent Background Task')
     reader,writer = IO.pipe  # The stream that we use to send the subchild's pid to the parent
     childpid = Kernel.fork do
 
+      # Need to properly tell MySQL/MariaDB that we're disconnecting
+      ApplicationRecord.connection.disconnect! rescue nil
+
       # Child code starts here
       reader.close # Not needed in the child!
 
diff --git a/BrainPortal/config/initializers/cors.rb b/BrainPortal/config/initializers/cors.rb
new file mode 100644
index 000000000..4420121d9
--- /dev/null
+++ b/BrainPortal/config/initializers/cors.rb
@@ -0,0 +1,12 @@
+
+Rails.application.config.middleware.insert_before 0, Rack::Cors do
+  allow do
+    # This is a dummy configuration.
+    # Adjust as needed.
+    origins 'https://example.com:8888'
+    resource '/doesnotexist',
+      :headers => :any,
+      :methods => [:get]
+  end
+end
+
diff --git a/BrainPortal/config/initializers/validation_portal.rb b/BrainPortal/config/initializers/validation_portal.rb
index 1df6e1d5b..8244286fc 100644
--- a/BrainPortal/config/initializers/validation_portal.rb
+++ b/BrainPortal/config/initializers/validation_portal.rb
@@ -83,8 +83,8 @@
   #
   # Rake Exceptions By First Argument
   #
-  skip_validations_for = [ /^db:/, /^cbrain:plugins/, /^cbrain:test/, /^route/, /^assets/, /^cbrain:nagios/ ]
-  first_arg   = ARGV.detect { |x| x =~ /^[\w:]+$/i } # first thing that looks like abc:def:ghi
+  skip_validations_for = [ /^db:/, /^cbrain:plugins/, /^cbrain:test/, /^route/, /^assets/, /^cbrain:nagios/, /^cbrain:boutiques:rewrite/ ]
+  first_arg   = ARGV.detect { |x| x =~ /^[\w:]+/i } # first thing that looks like abc:def:ghi
   first_arg ||= '(none)'
   if skip_validations_for.any? { |p| first_arg =~ p }
     #------------------------------------------------------------------------------
diff --git a/BrainPortal/config/routes.rb b/BrainPortal/config/routes.rb
index 9b0605940..1a283d135 100644
--- a/BrainPortal/config/routes.rb
+++ b/BrainPortal/config/routes.rb
@@ -2,7 +2,7 @@
 #
 # CBRAIN Project
 #
-# Copyright (C) 2008-2012
+# Copyright (C) 2008-2023
 # The Royal Institution for the Advancement of Learning
 # McGill University
 #
@@ -41,7 +41,11 @@
   resources :custom_filters,  :except => [ :index ]
   resources :tags,            :except => [ :new, :edit ]
   resources :access_profiles, :except => [ :edit ]
-  resources :disk_quotas,     :only   => [ :new, :index, :show, :create, :destroy, :update ]
+  resources :disk_quotas,     :only   => [ :new, :index, :show, :create, :destroy, :update ] do
+    collection do
+      get 'report'
+    end
+  end
 
   # Standard CRUD resources, with extra actions
 
@@ -111,10 +115,13 @@
       get  'report'
       post 'report'
       post 'repair'
+      post 'check_personal'
     end
     collection do
       get  'dp_access'
       get  'dp_transfers'
+      get  'new_personal'
+      post 'create_personal'
     end
   end
 
@@ -195,6 +202,7 @@
   get   '/about_us'               => 'portal#about_us'
   get   '/available'              => 'portal#available'
   get   '/search'                 => 'portal#search'
+  get   '/stats'                  => 'portal#stats'
   get   '/login'                  => 'sessions#new'
   get   '/logout'                 => 'sessions#destroy'
   get   '/session_status'         => 'sessions#show'
@@ -258,26 +266,6 @@
 
 
 
-  ####################################################################################
-  # Service; most of these actions are only needed
-  # for the CANARIE monitoring system, and are therefore
-  # shipped disabled by default, because it's not needed
-  # anywhere else.
-  ####################################################################################
-  #get   '/platform/info',           :controller => :service, :action => :info
-  #get   '/platform/stats',          :controller => :service, :action => :stats
-  #get   '/platform/detailed_stats', :controller => :service, :action => :detailed_stats
-  #get   '/platform/doc',            :controller => :service, :action => :doc
-  #get   '/platform/releasenotes',   :controller => :service, :action => :releasenotes
-  #get   '/platform/support',        :controller => :service, :action => :support
-  #get   '/platform/source',         :controller => :service, :action => :source
-  #get   '/platform/tryme',          :controller => :service, :action => :tryme
-  #get   '/platform/licence',        :controller => :service, :action => :licence
-  #get   '/platform/provenance',     :controller => :service, :action => :provenance
-  #get   '/platform/factsheet',      :controller => :service, :action => :factsheet
-
-
-
   ####################################################################################
   # NeuroHub routes
   ####################################################################################
diff --git a/BrainPortal/data_dumps/README.md b/BrainPortal/data_dumps/README.md
index 50bebafd8..09bde1c62 100644
--- a/BrainPortal/data_dumps/README.md
+++ b/BrainPortal/data_dumps/README.md
@@ -24,5 +24,33 @@ resources that no longer exist.
 The `reload` task requires a timestamp in argument
 (e.g. `2021-12-31T120856`).
 
+### Standard regular maintenance
+
+On a system with a large amount of activity, a regular cleanup
+of the ResourceUsage table is necessary. The process is performed
+in two steps:
+
+First dump all resource usage objects that refer to objects
+no longer existing in the database, and remove them from
+the database:
+
+```
+  RAILS_ENV=something rake cbrain:resource_usage:dump[DESTROY_ALL,no]
+```
+
+Second, re-insert monthly summaries of all removed records so that
+total historical usage by users is maintained:
+
+```
+  RAILS_ENV=something rake cbrain:resource_usage:monthly[All]
+```
+
+Note that this last step will re-create all monthly summaries
+cumulatively using the info in all previous YAML dumps. This
+rake task can safely be run multiple times, it will not duplicate
+summary information.
+
+### See also
+
 See the file [BrainPortal/lib/tasks/resource_usage_serialization.rake](https://github.com/aces/cbrain/blob/master/BrainPortal/lib/tasks/resource_usage_serialization.rake)
 for more information about the rake tasks.
diff --git a/BrainPortal/db/migrate/20221007094232_remove_old_remote_ressources_attributes.rb b/BrainPortal/db/migrate/20221007094232_remove_old_remote_ressources_attributes.rb
new file mode 100644
index 000000000..53c5d7fae
--- /dev/null
+++ b/BrainPortal/db/migrate/20221007094232_remove_old_remote_ressources_attributes.rb
@@ -0,0 +1,7 @@
+class RemoveOldRemoteRessourcesAttributes < ActiveRecord::Migration[5.0]
+  def change
+    remove_column :remote_resources, :nh_email_delivery_options, :text,    :after => :nh_system_from_email
+    remove_column :remote_resources, :tunnel_mysql_port,         :integer
+    remove_column :remote_resources, :tunnel_actres_port,        :integer
+  end
+end
diff --git a/BrainPortal/db/migrate/20230304184206_add_short_task_workdir_to_tool_configs.rb b/BrainPortal/db/migrate/20230304184206_add_short_task_workdir_to_tool_configs.rb
new file mode 100644
index 000000000..d8a023571
--- /dev/null
+++ b/BrainPortal/db/migrate/20230304184206_add_short_task_workdir_to_tool_configs.rb
@@ -0,0 +1,28 @@
+
+#
+# CBRAIN Project
+#
+# Copyright (C) 2008-2023
+# The Royal Institution for the Advancement of Learning
+# McGill University
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see .
+#
+
+class AddShortTaskWorkdirToToolConfigs < ActiveRecord::Migration[5.0]
+  def change
+    add_column :tool_configs, :singularity_use_short_workdir, :boolean,
+      :default => false, :null => false, :after => :singularity_overlays_specs
+  end
+end
diff --git a/BrainPortal/db/migrate/20230418205141_add_unique_sync_status_index.rb b/BrainPortal/db/migrate/20230418205141_add_unique_sync_status_index.rb
new file mode 100644
index 000000000..3b4c59691
--- /dev/null
+++ b/BrainPortal/db/migrate/20230418205141_add_unique_sync_status_index.rb
@@ -0,0 +1,10 @@
+class AddUniqueSyncStatusIndex < ActiveRecord::Migration[5.0]
+  def up
+    remove_index :sync_status, [ :userfile_id, :remote_resource_id ]
+    add_index    :sync_status, [ :userfile_id, :remote_resource_id ], :unique => true
+  end
+
+  def down
+    remove_index :sync_status, [ :userfile_id, :remote_resource_id ]
+  end
+end
diff --git a/BrainPortal/db/schema.rb b/BrainPortal/db/schema.rb
index 3ce3e9c33..bdb3f4dc2 100644
--- a/BrainPortal/db/schema.rb
+++ b/BrainPortal/db/schema.rb
@@ -10,7 +10,7 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema.define(version: 20220913183448) do
+ActiveRecord::Schema.define(version: 20230418205141) do
 
   create_table "access_profiles", force: :cascade, options: "ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci" do |t|
     t.string   "name",        null: false
@@ -263,8 +263,6 @@
     t.string   "ssh_control_host"
     t.integer  "ssh_control_port"
     t.string   "ssh_control_rails_dir"
-    t.integer  "tunnel_mysql_port"
-    t.integer  "tunnel_actres_port"
     t.string   "cache_md5"
     t.boolean  "portal_locked",                             default: false, null: false
     t.integer  "cache_trust_expire",                        default: 0
@@ -290,7 +288,6 @@
     t.text     "email_delivery_options",      limit: 65535
     t.string   "nh_support_email"
     t.string   "nh_system_from_email"
-    t.text     "nh_email_delivery_options",   limit: 65535
     t.string   "external_status_page_url"
     t.string   "docker_executable_name"
     t.string   "singularity_executable_name"
@@ -411,7 +408,7 @@
     t.datetime "accessed_at"
     t.datetime "synced_at"
     t.index ["remote_resource_id"], name: "index_sync_status_on_remote_resource_id", using: :btree
-    t.index ["userfile_id", "remote_resource_id"], name: "index_sync_status_on_userfile_id_and_remote_resource_id", using: :btree
+    t.index ["userfile_id", "remote_resource_id"], name: "index_sync_status_on_userfile_id_and_remote_resource_id", unique: true, using: :btree
     t.index ["userfile_id"], name: "index_sync_status_on_userfile_id", using: :btree
   end
 
@@ -441,12 +438,12 @@
 
   create_table "tool_configs", force: :cascade, options: "ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci" do |t|
     t.string   "version_name"
-    t.text     "description",                 limit: 65535
+    t.text     "description",                   limit: 65535
     t.integer  "tool_id"
     t.integer  "bourreau_id"
-    t.text     "env_array",                   limit: 65535
-    t.text     "script_prologue",             limit: 65535
-    t.text     "script_epilogue",             limit: 65535
+    t.text     "env_array",                     limit: 65535
+    t.text     "script_prologue",               limit: 65535
+    t.text     "script_epilogue",               limit: 65535
     t.datetime "created_at"
     t.datetime "updated_at"
     t.integer  "group_id"
@@ -463,9 +460,10 @@
     t.string   "containerhub_image_name"
     t.string   "container_engine"
     t.string   "container_index_location"
-    t.text     "singularity_overlays_specs",  limit: 65535
+    t.text     "singularity_overlays_specs",    limit: 65535
+    t.boolean  "singularity_use_short_workdir",               default: false, null: false
     t.string   "container_exec_args"
-    t.boolean  "inputs_readonly",                           default: false
+    t.boolean  "inputs_readonly",                             default: false
     t.string   "boutiques_descriptor_path"
     t.index ["bourreau_id"], name: "index_tool_configs_on_bourreau_id", using: :btree
     t.index ["tool_id"], name: "index_tool_configs_on_tool_id", using: :btree
diff --git a/BrainPortal/lib/boutiques_boot_integrator.rb b/BrainPortal/lib/boutiques_boot_integrator.rb
index fcd3fe1de..6b3dd9b49 100644
--- a/BrainPortal/lib/boutiques_boot_integrator.rb
+++ b/BrainPortal/lib/boutiques_boot_integrator.rb
@@ -95,7 +95,7 @@ def self.link_from_json_file(path)
   # This method scans a directory for JSON boutiques descriptors and
   # loads them all.
   def self.link_all(dir = CBRAIN::BoutiquesDescriptorsPlugins_Dir)
-    jsons=Dir.glob(Pathname.new(dir) + "*.json")
+    jsons=Dir.glob(Pathname.new(dir) + "*.json").sort
     jsons.each do |json|
       self.link_from_json_file(json)
     end
diff --git a/BrainPortal/lib/boutiques_collection_basenames_list_maker.rb b/BrainPortal/lib/boutiques_collection_basenames_list_maker.rb
new file mode 100644
index 000000000..81e140e79
--- /dev/null
+++ b/BrainPortal/lib/boutiques_collection_basenames_list_maker.rb
@@ -0,0 +1,98 @@
+
+#
+# CBRAIN Project
+#
+# Copyright (C) 2008-2023
+# The Royal Institution for the Advancement of Learning
+# McGill University
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see .
+#
+
+# This module will extract pattern based on a regex
+# specified in the descriptor by:
+#
+#   "cbrain:integrator_modules": {
+#     "BoutiquesCollectionBasenamesListMaker": [ "input_id", "FileCollection", "A regex to extract prefix from the file name" ]
+#   }
+#
+# It is possible to specify a FileCollection type in order to know on which
+# input file to apply the regex.
+#
+# The extracted names will populate the input with value-choices
+# according to what was extracted.
+#
+# Then one task will be created for each choice.
+#
+# *Note*: The usage of this module is not usable with a Cbcsv file.
+# If it will be used with a Cbcsv file, the Cbcsv file will be the input file
+# and one task will be created by sample.
+#
+# Should be usable with ExtendedCbcsv file though.
+#
+module BoutiquesCollectionBasenamesListMaker
+
+    # Note: to access the revision info of the module,
+    # you need to access the constant directly, the
+    # object method revision_info() won't work.
+    Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
+
+    # If more than one choice is detected in the FileCollection,
+    # the input_id option will be populated with prefix
+    # extracted based on pattern specified by the regex in the descriptor.
+    def descriptor_for_form #:nodoc:
+        descriptor             = super.dup()
+        input_id, type, regex_string,  = descriptor.custom_module_info('BoutiquesCollectionBasenamesListMaker')
+
+        # Get the userfile_ids from the params
+        # Return immediately if there is no exactly one file.
+        userfile_ids = params["interface_userfile_ids"] || []
+        type_class   = type.constantize
+        userfiles    =  Userfile.find(userfile_ids).select{|x| x.is_a?(type_class)}
+        return descriptor if userfiles.count != 1
+
+        # Fill the input with the list of prefix
+        regex      = Regexp.new(regex_string)
+        userfile   = userfiles.first
+        file_names = userfile.provider_collection_index(:top, :regular).map(&:name)
+        file_names.map! {|x| Pathname.new(x).basename.to_s }
+        input      = descriptor.input_by_id(input_id)
+
+        input["value-choices"] =  file_names.map do |f_n|
+                                    f_n.match(regex) && Regexp.last_match[1]
+                                  end.compact.uniq
+
+        descriptor
+    end
+
+    # One task will be created by value of
+    # the input specified in the descriptor.
+    def final_task_list #:nodoc:
+      descriptor     = self.descriptor_for_final_task_list
+      input_id, _, _ = descriptor.custom_module_info('BoutiquesCollectionBasenamesListMaker')
+
+      params_values = self.invoke_params[input_id]
+      return super if params_values.blank? || params_values.size == 1
+
+      # Create one task for each value
+      params_values.map do |value|
+        task = self.dup
+        task.description    = task.description || ""
+        task.description   += "\n\nRun with value: #{value}, for input #{input_id}."
+        task.invoke_params[input_id] = [value]
+        task
+      end
+
+    end
+  end
diff --git a/BrainPortal/lib/boutiques_ext3_capturer.rb b/BrainPortal/lib/boutiques_ext3_capturer.rb
new file mode 100644
index 000000000..9b9bf15fa
--- /dev/null
+++ b/BrainPortal/lib/boutiques_ext3_capturer.rb
@@ -0,0 +1,65 @@
+
+#
+# CBRAIN Project
+#
+# Copyright (C) 2008-2023
+# The Royal Institution for the Advancement of Learning
+# McGill University
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see .
+#
+
+# This module adds automatic setting up of mounted
+# ext3 filesystem as subdirectories of a task, provided
+# the tool works in Singularity/Apptainer.
+# It is the exact equivalent of adding an ext3 overlay
+# configuration entry in the task's tool config.
+#
+# To include the module automatically at boot time
+# in a task integrated by Boutiques, add a new entry
+# in the 'custom' section of the descriptor, like this:
+#
+#   "custom": {
+#       "cbrain:integrator_modules": {
+#           "BoutiquesExt3Capturer": {
+#             "work":   "50g",
+#             "tmpdir": "20m"
+#           }
+#       }
+#   }
+#
+module BoutiquesExt3Capturer
+
+  # Note: to access the revision info of the module,
+  # you need to access the constant directly, the
+  # object method revision_info() won't work.
+  Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
+
+  # Override the default behavior by adding new entries directly
+  # from the descriptor.
+  def ext3capture_basenames
+    # Get standard list as described in tool config
+    initial_list = super.dup # [ [ basename, size], [basename, size], ... ]
+
+    # Get values in descriptor, as a hash
+    descriptor = self.descriptor_for_cluster_commands
+    ext3_specs = descriptor.custom_module_info('BoutiquesExt3Capturer')
+
+    # Append our own entries; note that duplications of basenames
+    # will mean only the first entry is used!
+    initial_list + ext3_specs.to_a  # the .to_a transforms the hash into an array of pairs.
+  end
+
+end
+
diff --git a/BrainPortal/lib/boutiques_forced_output_browse_path.rb b/BrainPortal/lib/boutiques_forced_output_browse_path.rb
index 383d2b675..e86f7980c 100644
--- a/BrainPortal/lib/boutiques_forced_output_browse_path.rb
+++ b/BrainPortal/lib/boutiques_forced_output_browse_path.rb
@@ -75,8 +75,25 @@ def name_and_type_for_output_file(output, pathname)
     config      = descriptor.custom_module_info('BoutiquesForcedOutputBrowsePath')
     browse_path = config[output.id]  # "a/b/c"
     return [ name, type ] if browse_path.blank? # no configured browse_path for this output
+    browse_path = apply_value_keys(browse_path) # replaces [XYZ] strings with values from params
     combined    = (Pathname.new(browse_path) + name).to_s # "a/b/c/name"
     [ combined, type ]
   end
 
+  # Returns a modified version of browse_path where the
+  # substrings [XYZ] are replaced by the value-keys of
+  # the invoke structure.
+  def apply_value_keys(browse_path)
+    descriptor = self.descriptor_for_save_results
+
+    # Prepare the substitution hash
+    substitutions_by_token  = descriptor.build_substitutions_by_tokens_hash(
+                                JSON.parse(File.read(self.invoke_json_basename))
+                              )
+
+    new_browse_path = descriptor.apply_substitutions(browse_path, substitutions_by_token)
+
+    new_browse_path
+  end
+
 end
diff --git a/BrainPortal/lib/boutiques_input_value_fixer.rb b/BrainPortal/lib/boutiques_input_value_fixer.rb
new file mode 100644
index 000000000..dee765ea2
--- /dev/null
+++ b/BrainPortal/lib/boutiques_input_value_fixer.rb
@@ -0,0 +1,157 @@
+
+#
+# CBRAIN Project
+#
+# Copyright (C) 2008-2024
+# The Royal Institution for the Advancement of Learning
+# McGill University
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see .
+#
+
+# This module allows one to fix some of input parameters to specific constand values
+# The fixed input(s) would no longer be shown to the user in the form.
+# The optional inputs assigned null value will be removed 
+# (do not use with mandatory input parameters)
+#
+# In the descriptor, the spec would look like:
+#
+#   "custom": {
+#       "cbrain:integrator_modules": {
+#           "BoutiquesInputValueFixer": {
+#               "n_cpus": 1,
+#               "mem": "4G",
+#               "optional_custom_query": null,
+#               "level": "group"
+#           }
+#       }
+#   }
+#
+# Our main use case is resource related parameter which seldom participate
+# in dependencies and constraints.
+# Therefore we remove parameters from the form in a straightforward fashion
+# and do not address indirect or transitive dependencies. For instance,
+# if say i1-requires->i2-requires->i3 while i2 is deleted, dependency
+# of i3 on i1 no longer be reflected in web form UI dynamically
+module BoutiquesInputValueFixer
+
+  # Note: to access the revision info of the module,
+  # you need to access the constant directly, the
+  # object method revision_info() won't work.
+  Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
+
+
+  # the hash of input parameter values to be fixed or, if value is null, to be omited  
+  def fixed_values
+    self.boutiques_descriptor.custom_module_info('BoutiquesInputValueFixer')
+  end
+
+  # deletes fixed inputs listed in the custom 'integrator_modules'
+  def descriptor_without_fixed_inputs(descriptor)
+    # input parameters are marked by null values will be excluded from the command line
+    # other will be given fixed values during execution; neither should appear in web form UI
+
+    fixed_input_ids = fixed_values.keys
+    descriptor_dup  = descriptor.dup
+    fully_removed   = fixed_input_ids.select do |i_id|  # this variables are flagged to be removed rather than assigned value
+                                                   # in the spec, so they will be treated slightly different
+      input = descriptor_dup.input_by_id(i_id)
+      value = fixed_values[i_id]
+      value.nil? || (input.type == 'Flag') &&  (value.presence.to_s.strip =~ /0|null|false/i || value.blank?)
+    end
+
+    # generally speaking, boutiques input groups can have three different constraints,
+    # here we address 1) mutually exclusive constraint, which is the only one present in GUI javascript (the rest are evaluated
+    # after submission of the form), 2) 'one is required' constraint that affect the initial rendering of the form
+    # ( though IMHO red stars or other indicators to draw user attention should eventually implemented )
+
+    descriptor_dup.groups.each do |g| # filter groups, relax restriction to ensure that form can still be submitted
+      members = g.members - fixed_input_ids
+
+      # some actions at least some group members are actually assigned vals rather than deleted
+      if (fixed_input_ids & g.members - fully_removed).present? #
+        # since one input parameter is already selected permanently (fixed),
+        # we can drop one_is_required constraint
+        g.one_is_required = false  # as result group's checkbox is unselected in form rendering
+
+        # as one of mutually exclusive parameters is selected by setting a fixed value
+        # the rest of group should be disabled, no remaining
+        # Whenever deleting all remaining parameters of the group is preferred to disabling
+        # boutiques author/admin can modify the list of fixed values accordingly
+        block_inputs(descriptor_dup, members) if g.mutually_exclusive
+        g.mutually_exclusive = false  # will make form's javascript smaller/faster
+
+        # all-or-none constraint is seldom used, does not affect form itself,
+        # and only validated after the form submission
+        # and generally presents less pitfalls
+        # Therefore, at the moment, 'all or none' constraint is not addressed here
+
+      end
+      g.members = members
+    end
+
+    # remove empty groups
+    descriptor_dup.groups = descriptor_dup.groups.select {|g| g.members.present? }
+
+    # delete fixed inputs
+    descriptor_dup.inputs = descriptor_dup.inputs.select { |i| ! fixed_values.key?(i.id) } # filter out fixed inputs
+
+    # straight-forward delete of fixed inputs from dependencies.
+    # Indirect and transitive dependencies may be lost for UI
+    # but will be validated after form submission
+    descriptor_dup.inputs.each do |i|
+      i.requires_inputs = i.requires_inputs - fixed_input_ids if i.requires_inputs.present?
+      i.disables_inputs = i.disables_inputs - fixed_input_ids if i.disables_inputs.present?
+      i.value_requires.each { |v, a| i.value_requires[v] -= fixed_input_ids } if i.value_requires.present?
+      i.value_disables.each { |v, a| i.value_disables[v] -= fixed_input_ids } if i.value_disables.present?
+    end
+
+    descriptor_dup
+  end
+
+  # this blocks an input parameter by 'self-disabling', rather than explicitly deleting it
+  # it is a bit unorthodox yet expected to be used seldom
+  def block_inputs(descriptor, input_ids)
+    input_ids.each do |input_id|
+      input = descriptor.input_by_id(input_id) rescue next
+      input.disables_inputs ||= []
+      input.disables_inputs |= [input_id]
+      input.name += " ( unavailable )"
+    end
+  end
+
+  # adjust descriptor to allow check the number of supplied files
+  def descriptor_for_before_form
+    descriptor_without_fixed_inputs(super)
+  end
+
+  # prevent from showing/submitting fixed inputs in the form
+  def descriptor_for_form
+    descriptor_without_fixed_inputs(super)
+  end
+
+  # show all the params
+  def descriptor_for_show_params
+    self.invoke_params.merge!(fixed_values) # shows 'fixed' parameters, user would not be able to edit them
+    super    # standard values
+  end
+
+  # validation step - the original boutiques with combined invocation, for the greatest accuracy
+  # note, error messages might involve fixed variables
+  def after_form
+    self.invoke_params.merge!(fixed_values.compact) # put back fixed values into invocation, if needed
+    super    # Performs standard processing
+  end
+
+end
diff --git a/BrainPortal/lib/boutiques_output_cache_cleaner.rb b/BrainPortal/lib/boutiques_output_cache_cleaner.rb
index 0e1311e82..24f2dacf1 100644
--- a/BrainPortal/lib/boutiques_output_cache_cleaner.rb
+++ b/BrainPortal/lib/boutiques_output_cache_cleaner.rb
@@ -57,12 +57,16 @@ def descriptor_with_special_input(descriptor)
     new_input = BoutiquesSupport::Input.new(
       "name"          => "Enable Output Cache Cleaning",
       "id"            => "cbrain_enable_output_cache_cleaner",
-      "description"   => "If set, the cached content of produced outputs are erased when the task completes successfuly.",
+      "description"   => <<-DESC,
+        If set, the cached content of produced outputs are erased when the task completes successfully.
+        This does not affect the actual outputs of the task, only their cached content on the execution server.
+        Turn off this option only if you need a copy of the outputs on the server, e.g. for further processing.
+      DESC
       "type"          => "Flag",
       "optional"      => false,
       "default-value" => true,
     )
-    descriptor.inputs <<= new_input
+    descriptor.inputs << new_input
 
     # Add new group with that input
     groups       = descriptor.groups || []
@@ -76,7 +80,7 @@ def descriptor_with_special_input(descriptor)
       )
       groups << cb_mod_group
     end
-    cb_mod_group.members <<= new_input.id
+    cb_mod_group.members << new_input.id
 
     descriptor.groups = groups
     descriptor
diff --git a/BrainPortal/lib/boutiques_post_processing_cleaner.rb b/BrainPortal/lib/boutiques_post_processing_cleaner.rb
index a0f75272e..fd1f630b2 100644
--- a/BrainPortal/lib/boutiques_post_processing_cleaner.rb
+++ b/BrainPortal/lib/boutiques_post_processing_cleaner.rb
@@ -37,10 +37,17 @@
 #             "work",
 #             "*.tmp",
 #             "[OUTFILE_NAME].*.work"
-#           [
+#           ]
 #       }
 #   }
 #
+# This module will also erase EXT3 capture filesystems created by CBRAIN
+# if the basename of the filesystem, as configured in the ToolConfig, matches
+# one of the entries in this module's configuration. So in the code above,
+# the content of the file ".capt_work.ext3" would also be erased if a capture
+# filesystem was configured for "work". Patterns are not supported for
+# this feature.
+#
 module BoutiquesPostProcessingCleaner
 
   # Note: to access the revision info of the module,
@@ -81,6 +88,15 @@ def save_results
       end
     end
 
+    # Also erase ext3 catpure files IF they match one of the patterns
+    ext3capture_basenames.each do |basename, _|
+      next unless patterns.include?(basename) # must be exact match, e.g. 'work' == 'work'
+      fs_name = ".capt_#{basename}.ext3"      # e.g. .capt_work.ext3, see also in cluster_task.rb
+      next unless File.file?(fs_name)
+      self.addlog("Cleaning up EXT3 capture filesystem '#{fs_name}' in work directory")
+      File.delete(fs_name) rescue nil
+    end
+
     true
   end
 
diff --git a/BrainPortal/lib/boutiques_save_std_out_std_err.rb b/BrainPortal/lib/boutiques_save_std_out_std_err.rb
new file mode 100644
index 000000000..83933ba68
--- /dev/null
+++ b/BrainPortal/lib/boutiques_save_std_out_std_err.rb
@@ -0,0 +1,152 @@
+
+#
+# CBRAIN Project
+#
+# Copyright (C) 2008-2023
+# The Royal Institution for the Advancement of Learning
+# McGill University
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see .
+#
+
+# This module allow to save the stdout and stderr files of a Boutiques task
+#
+# To use this module, you need to add the following lines in the descriptor:
+#   "cbrain:integrator_modules": {
+#     "BoutiquesSaveStdOutStdErr": {
+#       "stdout_output_dir": "",
+#       "stderr_output_dir": "path/to/dir"
+#     }
+#   }
+#
+# In case of a MultilevelSshDataProvider the "path/to/dir" will be use to save the output.
+# In case of a no MultilevelSshDataProvider the "path/to/dir" will be ignored.
+#
+# The value of the key "stdout_output_dir" and "stderr_output_dir" can be set to an empty string,
+# in this situation the files will be saved directly in the root folder of the DataProvider.
+#
+# The output files will be saved as a LogFile with the name: -.std(out|err)
+#
+module BoutiquesSaveStdOutStdErr
+
+  # Note: to access the revision info of the module,
+  # you need to access the constant directly, the
+  # object method revision_info() won't work.
+  Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
+
+  # This method overrides the one in BoutiquesClusterTask.
+  # Save the stdout and stderr files of the task as output files.
+  # The files will be saved as a child of the first input file.
+  def save_results
+    # Get the folder where to save the log files from the descriptor
+    descriptor  = self.descriptor_for_save_results
+    module_info = descriptor.custom_module_info('BoutiquesSaveStdOutStdErr')
+
+    # Get parent file to set stderr and stdout as children of first input file
+    main_input_id = descriptor.file_inputs.first.id
+    file_id       = self.invoke_params[main_input_id]
+    parent_file   = Userfile.find(file_id)
+
+    # Save stdout
+    science_stdout_basename = science_stdout_basename(self.run_number)
+    save_stdout_basename    = (Pathname.new(module_info["stdout_output_dir"]) +
+                              "#{self.pretty_type}-#{self.bname_tid_dashed}.stdout").to_s
+    stdout_file             = save_log_file(science_stdout_basename, save_stdout_basename, parent_file)
+    self.params["_cbrain_output_cbrain_stdout"] = [stdout_file.id] if stdout_file
+
+    # Save stderr
+    science_stderr_basename = science_stderr_basename(self.run_number)
+    save_stderr_basename    = (Pathname.new(module_info["stderr_output_dir"]) +
+                              "#{self.pretty_type}-#{self.bname_tid_dashed}.stderr").to_s
+    stderr_file             = save_log_file(science_stderr_basename, save_stderr_basename, parent_file)
+    self.params["_cbrain_output_cbrain_stderr"] = [stderr_file.id] if stderr_file
+
+    self.save
+
+    super
+  end
+
+  # Add the stdout and stderr files to the descriptor
+  # for the show page of the task.
+  def descriptor_for_show_params  #:nodoc:
+    descriptor = super.dup
+
+    stdout_file = BoutiquesSupport::OutputFile.new({
+      "id"   => "cbrain_stdout",
+      "name" => "Standard output",
+      "description" => "Standard output of the tool",
+      "optional" => true
+    })
+
+    stderr_file = BoutiquesSupport::OutputFile.new({
+      "id"   => "cbrain_stderr",
+      "name" => "Standard error",
+      "description" => "Standard error of the tool",
+      "optional" => true
+    })
+
+    descriptor["output-files"] << stdout_file if !descriptor.output_files.any? { |f| f.id == "cbrain_stdout" }
+    descriptor["output-files"] << stderr_file if !descriptor.output_files.any? { |f| f.id == "cbrain_stderr" }
+
+    descriptor
+  end
+
+  private
+
+  # Returns a Userfile object, prepared with a browse_path if necessary.
+  # To do that it can override the attlist to add a browse_path and then
+  # call the standard safe_userfile_find_or_new() method.
+  def safe_logfile_find_or_new(klass, attlist)
+    name = attlist[:name]
+    return safe_userfile_find_or_new(klass, attlist) if ! (name.include? "/") # if there is no relative path, just do normal stuff
+
+    # Find all the info we need
+    attlist = attlist.dup
+    dp_id   = attlist[:data_provider_id] || self.results_data_provider_id
+    dp      = DataProvider.find(dp_id)
+    pn      = Pathname.new(name)  # "a/b/c/hello.txt"
+
+    # Make adjustements to name and browse_path
+    attlist[:name] = pn.basename.to_s  # "hello.txt"
+    if dp.has_browse_path_capabilities?
+      attlist[:browse_path] = pn.dirname.to_s   # "a/b/c"
+      self.addlog "BoutiquesSaveStdErrOut: result DataProvider browse_path for Stderr and Stdout will be '#{pn.dirname}'"
+    else
+      attlist[:browse_path] = nil # ignore the browse_path
+      self.addlog "BoutiquesSaveStdErrOut: result DataProvider doesn't have multi-level capabilities, ignoring forced browse_path for Stderr and Stdout '#{pn.dirname}'."
+    end
+
+    # Invoke the standard code
+    return safe_userfile_find_or_new(klass, attlist)
+  end
+
+  # Save the log with original_file_path to filename as
+  # a child of parent_file on the results data provider.
+  def save_log_file(original_file_path, filename, parent_file) #:nodoc:
+    self.addlog("Saving log file #{filename}")
+    file = safe_logfile_find_or_new(LogFile, :name => filename)
+
+    if ! file.save
+      self.addlog("Could not save back log file #{filename}")
+      return nil
+    end
+
+    file.cache_copy_from_local_file(original_file_path)
+    file.move_to_child_of(parent_file)
+    self.addlog("Saved log file #{filename}")
+
+    file
+  end
+end
+
diff --git a/BrainPortal/lib/boutiques_support.rb b/BrainPortal/lib/boutiques_support.rb
index 670634031..2b51c5426 100644
--- a/BrainPortal/lib/boutiques_support.rb
+++ b/BrainPortal/lib/boutiques_support.rb
@@ -60,6 +60,13 @@ def self.validate(json)
     Group          = Class.new(RestrictedHash) { allowed_keys group_prop_names  }
     ContainerImage = Class.new(RestrictedHash) { allowed_keys cont_prop_names   }
 
+    # Adds a comparison operator to these subobjects so that
+    # they can be sorted.
+    # See also Hash.resorted in the CBRAIN core extensions.
+    [ Input, OutputFile, Group ].each do |klass|
+      klass.send(:define_method, :'<=>') { |other| self.id <=> other.id }
+    end
+
     def initialize(hash={})
       super(hash)
       # The following re-assignment transforms hashed into subobjects (like OutputFile etc)
@@ -68,7 +75,7 @@ def initialize(hash={})
       self.output_files      = self.output_files    || []
       self.groups            = self.groups          || []
       self.custom            = self.custom          || {}
-      self.container_image &&= self.container_image # we need to to remain nil if already nil
+      self.container_image &&= self.container_image # we need it to remain nil if already nil
       self
     end
 
@@ -203,6 +210,7 @@ def build_substitutions_by_tokens_hash(invoke_structure)
       self.inputs.map do |input|
         next nil if input.value_key.blank?
         value = invoke_structure[input.id]
+        value = input.default_value if value.nil?
         next nil if value.nil?
         [ input.value_key, value ]
       end.compact.to_h
@@ -227,6 +235,172 @@ def apply_substitutions(string, substitutions_by_tokens, to_strip=[])
       newstring
     end
 
+    PRETTY_ORDER_TOP = %w(
+      name
+      tool-version
+      author
+      description
+      url
+      descriptor-url
+      online-platform-urls
+      doi
+      tool-doi
+      shell
+      command-line
+      schema-version
+      container-image
+      inputs
+      groups
+      output-files
+      error-codes
+      suggested-resources
+      tags
+      tests
+      custom
+    )
+    PRETTY_ORDER_INPUT = %w(
+      id
+      name
+      description
+      type
+      optional
+      integer
+      minimum
+      exclusive-minimum
+      maximum
+      exclusive-maximum
+      list
+      list-separator
+      min-list-entries
+      max-list-entries
+      default-value
+      command-line-flag
+      command-line-flag-separator
+      value-key
+      value-choices
+      value-disables
+      disables-inputs
+      requires-inputs
+    )
+    PRETTY_ORDER_OUTPUT = %w(
+      id
+      name
+      description
+      optional
+      list
+      command-line-flag
+      value-key
+      path-template
+      path-template-stripped-extensions
+    )
+    PRETTY_ORDER_GROUP = %w(
+      id
+      name
+      description
+      all-or-none
+      one-is-required
+      members
+    )
+
+    # Returns a dup() of the current descriptor, but with
+    # the fields re-ordered so as to create a 'pretty'
+    # layout when printed out (as JSON, YAML etc).
+    #
+    # The order puts things like the name, description, command
+    # version number etc near the top, then then inputs, the
+    # groups, the outputs, and the custom sections.
+    def pretty_ordered
+      ordered  = Hash.new # we use a plain hash to hold the newly ordered elems.
+      selfcopy = self.dup
+      PRETTY_ORDER_TOP.each { |k| ordered[k] = selfcopy.delete(k).dup if selfcopy.has_key?(k) }
+      selfcopy.each { |k,v| puts "Top miss: #{k}" ; ordered[k] = v.dup }
+      final = self.class.new(ordered)
+
+      # Order fields in each input
+      final.inputs = final.inputs.map do |input|
+        ordered  = Hash.new
+        selfcopy = input.dup
+        PRETTY_ORDER_INPUT.each { |k| ordered[k] = selfcopy.delete(k).dup if selfcopy.has_key?(k) }
+        selfcopy.each { |k,v| puts "Inp miss: #{k}" ; ordered[k] = v.dup }
+        input.class.new(ordered)
+      end
+
+      # Order fields in each output-file
+      final.output_files = final.output_files.map do |output|
+        ordered  = Hash.new
+        selfcopy = output.dup
+        PRETTY_ORDER_OUTPUT.each { |k| ordered[k] = selfcopy.delete(k).dup if selfcopy.has_key?(k) }
+        selfcopy.each { |k,v| puts "Out miss: #{k}" ; ordered[k] = v.dup }
+        output.class.new(ordered)
+      end
+
+      # Order fields in each group
+      final.groups = final.groups.map do |group|
+        ordered  = Hash.new
+        selfcopy = group.dup
+        PRETTY_ORDER_GROUP.each { |k| ordered[k] = selfcopy.delete(k).dup if selfcopy.has_key?(k) }
+        selfcopy.each { |k,v| puts "Group miss: #{k}" ; ordered[k] = v.dup }
+        group.class.new(ordered)
+      end
+
+      final
+    end
+
+    # Returns a JSON text version of the descriptor but with
+    # the fields aligned with pretty whitespaces, e.g.
+    # instead of
+    #
+    #   "name": "megatool",
+    #   "tool-version": "3.14.15926",
+    #   "url": "https://example.com",
+    #
+    # we get
+    #
+    #   "name":         "megatool",
+    #   "tool-version": "3.14.15926",
+    #   "url":          "https://example.com",
+    def super_pretty_json
+
+      # Internally, the alignment is made by padding property names with '|'
+      # and then stripping them out of the normal JSON generated.
+      pad_keys = ->(hash,length) do
+        hash.transform_keys! { |k| k.to_s.size >= length ? k : k + ('|' * (length-k.size) ) }
+      end
+      maxkeylength = ->(hash) { hash.keys.map(&:to_s).map(&:size).max }
+
+      # Returns a modified hash with keys all padded with '|'
+      max_pad_keys = ->(hash) do
+        copy = HashWithIndifferentAccess.new.merge(hash.dup)
+        max  = maxkeylength.(copy)
+        pad_keys.(copy,max)
+        copy
+      end
+
+      final  = HashWithIndifferentAccess.new.merge(self.dup)
+
+      final['inputs'].map!       { |input|  max_pad_keys.(input)  }
+      final['output-files'].map! { |output| max_pad_keys.(output) } if final['output-files'].present?
+      final['groups'].map!       { |group|  max_pad_keys.(group)  } if final['groups'].present?
+      final.delete('groups') if final['groups'].blank?
+
+      final['container-image'] &&= max_pad_keys.(final['container-image'])
+      final['custom']          &&= max_pad_keys.(final['custom'])
+
+      final = max_pad_keys.(final)
+
+      json_with_bars = JSON.pretty_generate(final)
+      new_json = json_with_bars
+        .gsub( /\|+": / ) do |bars|
+          spaces = bars.size - 3; '": ' + (' ' * spaces)
+        end
+
+      new_json
+    end
+
+    #------------------------------------------------------
+    # Aditional methods for the sub-objects of a descriptor
+    #------------------------------------------------------
+
     class Input
 
       # This method return the parameter name for the input.
diff --git a/BrainPortal/lib/boutiques_task_logs_copier.rb b/BrainPortal/lib/boutiques_task_logs_copier.rb
new file mode 100644
index 000000000..bc2504c35
--- /dev/null
+++ b/BrainPortal/lib/boutiques_task_logs_copier.rb
@@ -0,0 +1,187 @@
+
+#
+# CBRAIN Project
+#
+# Copyright (C) 2008-2023
+# The Royal Institution for the Advancement of Learning
+# McGill University
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see .
+#
+
+# This module implement a special step that is executed BEFORE the standard
+# post-processing code of CBRAIN is triggered. A Boutiques descriptor can
+# include it in the custom section like this:
+#
+#   "custom": {
+#     "cbrain:integrator_modules": {
+#       "BoutiquesTaskLogsCopier": {
+#          "stdout":     "local/path/[PARAM1]/ses*/basename[PARAM2]_{taskid}_stdout.log",
+#          "stderr":     "local/path/[PARAM1]/ses*/basename[PARAM2]_{taskid}_stderr.log",
+#          "runtime":    "blah/blah/runtime.kv",
+#          "descriptor": "blah/blah/descriptor.json",
+#          "invoke":     "blah/blah/params.json",
+#          "jobscript":  "blah/blah/cbrain_script.sh"
+#       }
+#     }
+#   }
+#
+# The module's behavior is to copy some CBRAIN-specific files (e.g. the STDOUT and STDERR
+# capture files of the task) and install them in some subdirectory that (normally)
+# will be saved as an output. It can also copy other useful configuration files,
+# as shown in the example above.
+#
+# The copy code will get triggered before CBRAIN runs its normal post-processing
+# code, so before it is aware whether or not the task completed successfully,
+# or failed.
+#
+# Configuration errors in the paths will raise a fatal exception. A missing
+# output directory path, however, will only generate a warning within
+# the task's processing logs.
+#
+# The pathnames patterns provided can include standard filesystem glob elements
+# and Boutiques value-key parameters. The module will try to make sure that
+# only one subdirecty path matches the parent location specified by the path, though
+# it will attempt the create the last component of the parent if necessary.
+#
+# Several examples of what is supported:
+#
+#   # Direct path:
+#   "abc/def/stdout.log"
+#
+#   # Paths with value-keys taken from Boutiques parameters:
+#   "[OUTPUT_DIR]/[INPUT_FILE].stdout"
+#   "work/[SUBJECT_ID]/logs/stdout_[SUBJECT_ID].log"
+#
+#   # Path with a value-key AND a glob to find a subdirectory ses-N :
+#   "work/[SUBJECT_ID]/ses-*/logs/stdout_[SUBJECT_ID].log"
+#
+# When tring to find the final path for the copied file, the parent dir
+# is initially globbed(), and if a single directory is returned,
+# it will be used. If none are found, the parent of THAT
+# is checked and if it exists, the missing last component directory
+# will be created. E.g. for the last example above, if
+# "work/sub-1234/ses-2" exists but "work/sub-1234/ses-2/logs" doesn't
+# exist, the "logs" subdirectory will be created.
+module BoutiquesTaskLogsCopier
+
+  # Note: to access the revision info of the module,
+  # you need to access the constant directly, the
+  # object method revision_info() won't work.
+  Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
+
+  # This method overrides the one in BoutiquesClusterTask.
+  # It will attempt to copy the stdout and stderr files
+  # that CBRAIN captured, and then invoke the normal
+  # post processing code.
+  def save_results
+
+    # Get the cleaning paths patterns from the descriptor
+    descriptor = self.descriptor_for_save_results
+    destpaths  = descriptor.custom_module_info('BoutiquesTaskLogsCopier')
+
+    # Copy STDOUT and STDERR, if possible
+    install_std_log_file(science_stdout_basename, destpaths[:stdout],     "stdout")
+    install_std_log_file(science_stderr_basename, destpaths[:stderr],     "stderr")
+
+    # Copy Boutiques configuration files
+    install_std_log_file(boutiques_json_basename, destpaths[:descriptor], "boutiques descriptor")
+    install_std_log_file(invoke_json_basename,    destpaths[:invoke],     "boutiques parameters")
+
+    # Copy Runtime info file
+    install_std_log_file(runtime_info_basename,   destpaths[:runtime],    "runtime info")
+
+    # Copy sbatch/qsub script
+    install_std_log_file(science_script_basename, destpaths[:jobscript],  "jobscript")
+
+    # Performs standard processing
+    super
+  end
+
+  # Try to install a file +stdlogfile+ into the destination path
+  # specified by +destpath+ . destpath can be a pattern
+  # with glob components and Boutiques parameter value-keys, and
+  # must be at least one level deep.
+  #
+  # See the examples at the top of the module.
+  def install_std_log_file(stdlogfile, destpath, typeinfo)
+
+    # If we have not configured a capture path, do nothing.
+    return if destpath.blank?
+
+    # If for some reason the task's work directory doesn't have
+    # the required file, ignore it too.
+    return if ! File.file?(stdlogfile)
+
+    descriptor = self.descriptor_for_save_results
+
+    # Prepare the substitution hash and apply it
+    substitutions_by_token  = descriptor.build_substitutions_by_tokens_hash(
+                                JSON.parse(File.read(self.invoke_json_basename))
+                              )
+    destpath   = descriptor.apply_substitutions(destpath, substitutions_by_token)
+    destpath   = Pathname.new(destpath).cleanpath
+
+    # Extract the prefix subdirectory paths (which can be globbed) and the basename
+    prefixglob = destpath.parent
+    basename   = destpath.basename
+
+    # Sanity checks. These errors should never happen because the paths
+    # and patterns are normally configured by the administrator, who
+    # should know better than to misconfigure the module or
+    # point at paths outside the task's work directory.
+    cb_error "Misconfigured module BoutiquesTaskLogsCopier for #{typeinfo} with absolute path pattern '#{destpath}'" if destpath.absolute?
+    if prefixglob.to_s.blank? || prefixglob.to_s == '.'
+      cb_error "Misconfigured module BoutiquesTaskLogsCopier without a prefix subdirectory for #{typeinfo} '#{destpath}'"
+    end
+
+    # Try to find one and only one directory where to install the file.
+    dirglobs = Pathname.glob(prefixglob)
+
+    # If we get a pattern that matches several places, we can't do anything.
+    if dirglobs.size > 1
+      self.addlog "Warning: too many intermediate subdirectories match pattern '#{prefixglob}'; #{typeinfo} file not saved."
+      return
+    end
+
+    # If we can't find a match at all, maybe we can find a match with just the
+    # parent directory and we can create the final component.
+    if dirglobs.empty?
+      parent_of_prefix_glob = prefixglob.parent
+      parent_of_prefix_dirs = Pathname.glob(parent_of_prefix_glob)
+      if parent_of_prefix_dirs.size != 1
+        self.addlog "Warning: cannot find intermediate subdirectories matching pattern '#{prefixglob}'; #{typeinfo} file not saved."
+        return
+      end
+      mkdir_path = (Pathname.new(parent_of_prefix_dirs.first) + prefixglob.basename).to_s
+      Dir.mkdir(mkdir_path)
+      dirglobs = [ mkdir_path ]
+    end
+
+    destdir = dirglobs.first
+    if ! path_is_in_workdir?(destdir)
+      self.addlog "Misconfigured module BoutiquesTaskLogsCopier: path pattern '#{destpath}' is outside of the task's workdirectory; #{typeinfo} file not saved."
+      return
+    end
+
+    self.addlog "Copying #{typeinfo} file to '#{destdir}/#{basename}'"
+    FileUtils.copy_file(stdlogfile, "#{destdir}/#{basename}")
+
+  end
+
+end
+
+
+
+
diff --git a/BrainPortal/lib/cbrain_extensions/hash_extensions/conversions.rb b/BrainPortal/lib/cbrain_extensions/hash_extensions/conversions.rb
index 93c7db853..0292f75ff 100644
--- a/BrainPortal/lib/cbrain_extensions/hash_extensions/conversions.rb
+++ b/BrainPortal/lib/cbrain_extensions/hash_extensions/conversions.rb
@@ -81,6 +81,25 @@ def to_api_xml(options = {})
         to_xml({ :dasherize => false, :root => root_tag }.merge(options))
       end
 
+      # Returns a dup of the hash, where the keys are sorted, and
+      # any values that are arrays are also sorted. Applies these
+      # rules recursively. Assumes that all keys and all array values
+      # are things that can be compared, otherwise this will crash.
+      def resorted
+        res = self.class.new
+        self.keys.sort.each do |key|
+          val = self[key]
+          if val.is_a?(Hash)
+            res[key] = val.resorted
+          elsif val.is_a?(Array)
+            res[key] = val.sort.map { |x| x.respond_to?(:resorted) ? x.resorted : x }
+          else
+            res[key] = val
+          end
+        end
+        res
+      end
+
     end
   end
 end
diff --git a/BrainPortal/lib/cbrain_task_generators/schema_task_generator.rb b/BrainPortal/lib/cbrain_task_generators/schema_task_generator.rb
index df9e80abc..48edeed38 100644
--- a/BrainPortal/lib/cbrain_task_generators/schema_task_generator.rb
+++ b/BrainPortal/lib/cbrain_task_generators/schema_task_generator.rb
@@ -261,9 +261,10 @@ def register(task)
                 container_engine.capitalize!
       return if container_engine == "Singularity" && !resource.singularity_present?
       return if container_engine == "Docker"      && (!resource.docker_present? && !resource.singularity_present?)
-      
+
       # If Docker engine isn't present use Singularity
       container_engine = "Singularity" if (container_engine == "Docker" && !resource.docker_present?)
+      container_index  = 'docker://'   if container_index == 'index.docker.io' # old convention
 
       ToolConfig.new(
         :tool_id                  => task.tool.id,
diff --git a/BrainPortal/app/views/service/info.html.erb b/BrainPortal/lib/data_provider_test_connection_error.rb
similarity index 57%
rename from BrainPortal/app/views/service/info.html.erb
rename to BrainPortal/lib/data_provider_test_connection_error.rb
index 545527fb5..7d2b8fefd 100644
--- a/BrainPortal/app/views/service/info.html.erb
+++ b/BrainPortal/lib/data_provider_test_connection_error.rb
@@ -1,9 +1,8 @@
 
-<%-
 #
 # CBRAIN Project
 #
-# Copyright (C) 2008-2012
+# Copyright (C) 2008-2023
 # The Royal Institution for the Advancement of Learning
 # McGill University
 #
@@ -20,18 +19,13 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see .
 #
--%>
 
-<% title 'Service Info' %>
+# This class provides an exception class for
+# representing a user key connection error.
+# At the moment it does not guaranty though that connection is good.
+class DataProviderTestConnectionError < CbrainError
+
+  Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
+
+end
 
-  
CBRAIN Web Service Information

-  
Basic Information

-  

-    
Name
<%= @info[:name] %>

-    
Version
<%= @info[:version] %>

-    
Synopsis
<%= @info[:synopsis] %>

-    
Release Time
<%= @info[:releaseTime] %>

-    
Research Subject
<%= @info[:researchSubject] %>

-    
Support Email
<%= @info[:supportEmail] %>

-    
Tags
<%= @info[:tags].join(", ") %>

-  

diff --git a/BrainPortal/lib/models_report.rb b/BrainPortal/lib/models_report.rb
index 66894aca9..533298c52 100644
--- a/BrainPortal/lib/models_report.rb
+++ b/BrainPortal/lib/models_report.rb
@@ -154,7 +154,7 @@ def self.search_for_token(token, user=current_user) #:nodoc:
     is_numeric  = token =~ /\A\d+\z/  || token == "-9998877" # ... because we'll find by ID
 
 
-    file_scope  = Userfile      .find_all_accessible_by_user(user) .order(:name)
+    file_scope  = Userfile      .find_all_accessible_by_user(user, :access_requested => :read).order(:name)
     task_scope  = CbrainTask    .find_all_accessible_by_user(user) .order(:id)
     rr_scope    = RemoteResource.find_all_accessible_by_user(user) .order(:name)
     dp_scope    = DataProvider  .find_all_accessible_by_user(user) .order(:name)
diff --git a/BrainPortal/lib/portal_sanity_checks.rb b/BrainPortal/lib/portal_sanity_checks.rb
index def73adf4..6d9f40179 100644
--- a/BrainPortal/lib/portal_sanity_checks.rb
+++ b/BrainPortal/lib/portal_sanity_checks.rb
@@ -373,5 +373,23 @@ def self.ensure_scratch_data_provider_exists #:nodoc:
     scratch.meta['no_viewers'] = 'on'  # files can't be viewed in interface
   end
 
+  def self.ensure_expired_messages_are_purged #:nodoc:
+
+    #-----------------------------------------------------------------------------
+    puts "C> Ensuring expired Messages are purged"
+    #-----------------------------------------------------------------------------
+
+    todel = Message.all.to_a
+      .select { |m| m.expiry.present? }
+      .select { |m| m.expiry < Time.now }
+    if todel.size > 0
+      puts "C> \t - There are #{todel.size} messages to delete."
+      todel.each { |m| m.destroy }
+    else
+      puts "C> \t - There are no messages to delete."
+    end
+
+  end
+
 end
 
diff --git a/BrainPortal/lib/portal_system_checks.rb b/BrainPortal/lib/portal_system_checks.rb
index f8ac0757c..6d3466baa 100644
--- a/BrainPortal/lib/portal_system_checks.rb
+++ b/BrainPortal/lib/portal_system_checks.rb
@@ -119,11 +119,11 @@ def self.z000_ensure_we_have_a_local_ssh_agent #:nodoc:
     puts "C> Making sure we have a CBRAIN key for the agent..."
     #----------------------------------------------------------------------------
 
-    cbrain_identity_file = "#{CBRAIN::Rails_UserHome}/.ssh/id_cbrain_portal"
+    cbrain_identity_file = "#{CBRAIN::Rails_UserHome}/.ssh/id_cbrain_ed25519"
     if ! File.exists?(cbrain_identity_file)
       puts "C> \t- Creating identity file '#{cbrain_identity_file}'."
       with_modified_env('SSH_ASKPASS' => '/bin/true', 'DISPLAY' => 'none:0.0') do
-        system("/bin/bash","-c","ssh-keygen -t rsa -f #{cbrain_identity_file.bash_escape} -C 'CBRAIN_Portal_Key' /dev/null 2>/dev/null")
+        system("/bin/bash","-c","ssh-keygen -t ed25519 -f #{cbrain_identity_file.bash_escape} -C 'CBRAIN_Portal_Key' /dev/null 2>/dev/null")
       end
     end
 
@@ -132,8 +132,8 @@ def self.z000_ensure_we_have_a_local_ssh_agent #:nodoc:
     else
       CBRAIN.with_unlocked_agent
       curkeys=agent.list_keys
-      if curkeys.size > 0
-        puts "C> \t- Identity already present in agent: #{curkeys[0]}"
+      if digest = curkeys.detect { |string| string.to_s =~ /\(ED25519\)/i } # = not ==
+        puts "C> \t- Identity already present in agent: #{digest}"
       else
         ok = with_modified_env('SSH_ASKPASS' => '/bin/true', 'DISPLAY' => 'none:0.0') do
           agent.add_key_file(cbrain_identity_file) rescue nil # will raise exception if anything wrong
@@ -146,6 +146,20 @@ def self.z000_ensure_we_have_a_local_ssh_agent #:nodoc:
         end
       end
     end
+
+    # Add old key if it exists.
+    old_identity_file = "#{CBRAIN::Rails_UserHome}/.ssh/id_cbrain_portal"
+    if File.exists?(old_identity_file)
+      ok_old = with_modified_env('SSH_ASKPASS' => '/bin/true', 'DISPLAY' => 'none:0.0') do
+        agent.add_key_file(old_identity_file) rescue nil
+      end
+      if ok_old
+        puts "C> \t- Added OLD identity to agent from file: '#{old_identity_file}'."
+      else
+        puts "C> \t- WARNING: cannot add OLD identity from file: '#{old_identity_file}'."
+      end
+    end
+
   end
 
 
diff --git a/BrainPortal/lib/ssh_key.rb b/BrainPortal/lib/ssh_key.rb
index 9f996d348..3024072ed 100644
--- a/BrainPortal/lib/ssh_key.rb
+++ b/BrainPortal/lib/ssh_key.rb
@@ -39,7 +39,7 @@ class SshKey
   CONFIG = { #:nodoc:
     :ssh_keys_dir     => (Rails.root rescue nil) ? "#{Rails.root.to_s}/user_keys" : "/not/yet/configured",
     :exec_ssh_keygen  => `bash -c "type -p ssh-keygen"`.strip,
-    :ssh_keygen_type  => "rsa",
+    :ssh_keygen_type  => "ed25519",
     :debug            => false,
   }
 
@@ -124,7 +124,7 @@ def validate_files!
     raise RuntimeError.new("Public file for SSH Key '#{@name}' does not exist.")  unless
       File.exists?(pub_path)  && File.size(pub_path)  > 50
     raise RuntimeError.new("Private file for SSH Key '#{@name}' does not exist.") unless
-      File.exists?(priv_path) && File.size(priv_path) > 1000
+      File.exists?(priv_path) && File.size(priv_path) > 300
     true
   end
 
@@ -211,7 +211,7 @@ def private_key_path
 
   # Returns the private key (in SSH format)
   def private_key(i_know_what_i_am_doing = false)
-    raise RuntimeError("Private key access denied") unless i_know_what_i_am_doing == 'I Know What I Am Doing'
+    raise RuntimeError.new("Private key access denied") unless i_know_what_i_am_doing == 'I Know What I Am Doing'
     File.read(private_key_path)
   end
 
diff --git a/BrainPortal/lib/tasks/boutiques_rewrite.rake b/BrainPortal/lib/tasks/boutiques_rewrite.rake
new file mode 100644
index 000000000..1013840d3
--- /dev/null
+++ b/BrainPortal/lib/tasks/boutiques_rewrite.rake
@@ -0,0 +1,98 @@
+
+#
+# CBRAIN Project
+#
+# Copyright (C) 2008-2023
+# The Royal Institution for the Advancement of Learning
+# McGill University
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see .
+#
+
+namespace :cbrain do
+  namespace :boutiques do
+    desc "Reads a Boutiques descriptor and writes it back with adjustments"
+
+    task :rewrite, [:action] => :environment do |t,args|
+
+      args.with_defaults(:action => 'reorder')
+      action = args.action
+      raise "This task's action must be 'reorder' (default), or 'pad' or 'pad+reorder'" unless
+        action.match /\A(reorder|pad|pad\+reorder)\z/
+
+      # There is no good way to provide standard command line
+      # args to a rake task, so I have to butcher ARGV myself.
+      args = ARGV.size > 1 ? ARGV[1..ARGV.size-1] : [] # remove 'rake'
+      while args.size > 0 && args[0] =~ /^cbrain:boutiques|^-/ # remove options and task name
+        args.shift
+      end
+
+      # Usage
+      if args.size != 1
+        puts <<-USAGE
+        Usage:
+          rake cbrain:boutiques:rewrite              boutiques.json
+          rake cbrain:boutiques:rewrite[reorder]     boutiques.json # default
+          rake cbrain:boutiques:rewrite[pad]         boutiques.json
+          rake cbrain:boutiques:rewrite[pad+reorder] boutiques.json
+
+        This task will read the content of 'boutiques.json' and
+        write back 'new_boutiques.json'.
+
+        The single option is a keyword that determines which rewriting
+        procedure to perform.
+
+        With 'reorder' (the default), the properties are reordered
+        in a pretty way.
+
+        With 'pad', the JSON produced will contain extra spaces to
+        align all the values together.
+
+        Unfortunately, because of the way rake tasks work, the
+        full path to 'boutiques.json' must be provided, or a
+        path relative to CBRAIN's BrainPortal directory.
+
+        USAGE
+        exit 1
+      end
+
+      filename = args.shift
+      pathname = Pathname.new(filename)
+      newfile  = pathname.dirname + "new_#{pathname.basename}"
+
+      puts "Reading file #{filename}..."
+      btq = BoutiquesSupport::BoutiquesDescriptor.new_from_file(filename)
+
+      if action =~ /reorder/
+        puts "Re-ordering..."
+        btq = btq.pretty_ordered
+        btq.delete('groups') if btq.groups.blank? # stupid btq spec say it must be completely absent
+        json = JSON.pretty_generate(btq)
+      end
+
+      if action =~ /pad/
+        puts "Padding values..."
+        btq.delete('groups') if btq.groups.blank? # stupid btq spec say it must be completely absent
+        json = btq.super_pretty_json
+      end
+
+      puts "Saving #{newfile}..."
+      File.open(newfile.to_s,"w") { |fh| fh.write json }
+
+      puts "Done."
+
+    end
+  end
+end
+
diff --git a/BrainPortal/lib/tasks/cbrain_nagios_checker.rake b/BrainPortal/lib/tasks/cbrain_nagios_checker.rake
index 55285a5b8..37a68833b 100644
--- a/BrainPortal/lib/tasks/cbrain_nagios_checker.rake
+++ b/BrainPortal/lib/tasks/cbrain_nagios_checker.rake
@@ -43,6 +43,7 @@ namespace :cbrain do
       task :dps => :environment do
 
         CbrainSystemChecks.check([:a002_ensure_Rails_can_find_itself])
+        PortalSystemChecks.check([:z000_ensure_we_have_a_local_ssh_agent])
 
         # Restores STDOUT and STDERR so that nagios
         # can capture our pretty message at the end.
diff --git a/BrainPortal/lib/tasks/resource_usage_serialization.rake b/BrainPortal/lib/tasks/resource_usage_serialization.rake
index 9f28673a2..8f29ec069 100644
--- a/BrainPortal/lib/tasks/resource_usage_serialization.rake
+++ b/BrainPortal/lib/tasks/resource_usage_serialization.rake
@@ -212,6 +212,9 @@ namespace :cbrain do
       # Main processing loop for all classes
       klass_names.each do |klass_name|
 
+        puts "\n-------------------------------------------------------"
+        puts "Reloading ResourceUsage records for class #{klass_name}"
+
         # Find all files for klass_name
         globpattern = Rails.root + "data_dumps" + "#{klass_name}.*.yaml*" # matches .gz too
         files       = Dir.glob(globpattern)
diff --git a/BrainPortal/lib/view_helpers.rb b/BrainPortal/lib/view_helpers.rb
index 9ad850b66..fbf791d1e 100644
--- a/BrainPortal/lib/view_helpers.rb
+++ b/BrainPortal/lib/view_helpers.rb
@@ -99,8 +99,6 @@ def pretty_elapsed(numseconds,options = {})
     ]
 
     components = components.select { |c| c[0] > 0 }
-    components.pop   while components.size > 0 && components[-1] == 0
-    components.shift while components.size > 0 && components[0]  == 0
 
     if options[:num_components]
       while components.size > options[:num_components]
diff --git a/BrainPortal/public/401.html b/BrainPortal/public/401.html
index 58e70975f..84d633712 100644
--- a/BrainPortal/public/401.html
+++ b/BrainPortal/public/401.html
@@ -3,63 +3,45 @@
 
   You are not authorized to view this page (401)
   
-  
 
 
 
   
+  
+  

   

-    

-      
You are not authorized to view this page.

-    

+    
You are not authorized to view this page.

     
Stop trying to be a hacker and get back to work.

   

 
diff --git a/BrainPortal/public/404.html b/BrainPortal/public/404.html
index ab1bceb20..a5bd42279 100644
--- a/BrainPortal/public/404.html
+++ b/BrainPortal/public/404.html
@@ -3,63 +3,45 @@
 
   The page you were looking for doesn't exist (404)
   
-  
 
 
 
   
+  
+  

   

-    

-      
The page you were looking for doesn't exist.

-    

+    
The page you were looking for doesn't exist.

     
You may have mistyped the address or the page may have moved.

   

 
diff --git a/BrainPortal/public/422.html b/BrainPortal/public/422.html
index 7e30a2f0b..3ac3de251 100644
--- a/BrainPortal/public/422.html
+++ b/BrainPortal/public/422.html
@@ -3,63 +3,45 @@
 
   The change you wanted was rejected (422)
   
-  
 
 
 
   
+  
+  

   

-    

-      
The change you wanted was rejected.

-    

+    
The change you wanted was rejected.

     
Maybe you tried to change something you didn't have access to.

   

 
diff --git a/BrainPortal/public/500.html b/BrainPortal/public/500.html
index a022b7da4..929fda37e 100644
--- a/BrainPortal/public/500.html
+++ b/BrainPortal/public/500.html
@@ -3,63 +3,45 @@
 
   We're sorry, but something went wrong (500)
   
-  
 
 
 
   
+  
+  

   

-    

-      
We're sorry, but something went wrong.

-    

+    
We're sorry, but something went wrong.

     
We've been notified about this issue and we'll take a look at it shortly.

   

 
diff --git a/BrainPortal/public/502.html b/BrainPortal/public/502.html
index 0d4d1417c..d9575c2b9 100644
--- a/BrainPortal/public/502.html
+++ b/BrainPortal/public/502.html
@@ -3,65 +3,48 @@
 
   We're sorry, this server is down for maintenance (502)
   
-  
 
 
 
   
+  
+  

   

-    

-      
We're sorry, this server is down for maintenance.

-    

-    
Please return in a few minutes.

-       Maintenance periods usually last between 5 and 30 minutes.

+    
We're sorry, this server is down for maintenance.

+    

+    Please return in a few minutes.
+    

+    Maintenance periods usually last between 5 and 30 minutes.
+    

   

 
 
diff --git a/BrainPortal/public/images/brainbrowser-loader.gif b/BrainPortal/public/images/brainbrowser-loader.gif
deleted file mode 100644
index cd6055863..000000000
Binary files a/BrainPortal/public/images/brainbrowser-loader.gif and /dev/null differ
diff --git a/BrainPortal/public/javascripts/cbrain.js b/BrainPortal/public/javascripts/cbrain.js
index d2df9e9d4..8dd335e87 100644
--- a/BrainPortal/public/javascripts/cbrain.js
+++ b/BrainPortal/public/javascripts/cbrain.js
@@ -117,7 +117,7 @@
 
     loaded_element.find("select").each(function(){
       var select = $(this);
-  
+
       var defined_width = (select.context.style.width);
       if ( defined_width !== '' ){
         select.chosen({ width: defined_width });
@@ -125,7 +125,7 @@
         select.chosen({ width: '25em' });
       }
     });
-		  
+
     /////////////////////////////////////////////////////////////////////
     //
     // UI Helper Methods see application_helper.rb for corresponding
@@ -631,8 +631,8 @@
       $(hidden_box).val( value );
     };
 
-    // Value of the header box is used to set 
-    // the checked status of child boxes 
+    // Value of the header box is used to set
+    // the checked status of child boxes
     var click_select_all = (header_box) => {
       var checkbox_class = header_box.data("checkbox-class");
 
@@ -649,27 +649,27 @@
     });
 
     // Define on click event for each child of a `select_all` element.
-    $(".select_all").each( (index,input) => { 
-      var checkbox_class = $(input).data("checkbox-class");
-
-      $(input).load(click_select_all($(input)));
-
-      var checkbox_class_elements = $('.' + checkbox_class);
-      checkbox_class_elements.each(function(index, element) {        
-        $(element).on("click", () => {
-          var number_of_checkbox = checkbox_class_elements.filter((i,e) => e.checked).length;
-          if (number_of_checkbox === 0) {
-            set_hidden_select_all($(input), "none");
-            input.checked = false; 
-          } else if (checkbox_class_elements.length === number_of_checkbox) {
-            set_hidden_select_all($(input), "all");
-            input.checked = true;
-          } else { 
-            set_hidden_select_all($(input), "some");
-            input.checked = false; 
-          }
+    $(".select_all").each( (index,input) => {
+      if ($(input).data("persistant-name")) {
+        var checkbox_class = $(input).data("checkbox-class");
+        $(input).load(click_select_all($(input)));
+        var checkbox_class_elements = $('.' + checkbox_class);
+        checkbox_class_elements.each(function(index, element) {
+          $(element).on("click", () => {
+            var number_of_checkbox = checkbox_class_elements.filter((i,e) => e.checked).length;
+            if (number_of_checkbox === 0) {
+              set_hidden_select_all($(input), "none");
+              input.checked = false;
+            } else if (checkbox_class_elements.length === number_of_checkbox) {
+              set_hidden_select_all($(input), "all");
+              input.checked = true;
+            } else {
+              set_hidden_select_all($(input), "some");
+              input.checked = false;
+            }
+          });
         });
-      });
+      };
     });
 
     $(document).delegate(".select_master", "change", function() {
diff --git a/BrainPortal/public/javascripts/dynamic-table.js b/BrainPortal/public/javascripts/dynamic-table.js
index 895db26a5..58f1c7dbf 100644
--- a/BrainPortal/public/javascripts/dynamic-table.js
+++ b/BrainPortal/public/javascripts/dynamic-table.js
@@ -167,6 +167,9 @@
 
     /* sorting, filtering and pagination requests */
     dyntbl
+      .delegate('.dt-fpop-find > input', 'keypress', function (event) {
+        if (event.key == "Enter") event.preventDefault();
+      })
       .undelegate('.dt-sort-btn, .dt-fpop-txt, .dt-pag-pages > a', 'click.dyn-tbl')
       .delegate(  '.dt-sort-btn, .dt-fpop-txt, .dt-pag-pages > a', 'click.dyn-tbl', function (event) {
         event.preventDefault();
diff --git a/BrainPortal/public/javascripts/userfiles.js b/BrainPortal/public/javascripts/userfiles.js
index 6a83c5d83..e22b4046f 100644
--- a/BrainPortal/public/javascripts/userfiles.js
+++ b/BrainPortal/public/javascripts/userfiles.js
@@ -33,7 +33,7 @@ function cbrain_userfile_launch_bar(tool_name, file_status_text, have_selection,
 
   $('#menu_bar').after(
     $('
')
-      .append($('Select some files to launch ' + tool_name + ''))
+      .append($('Select some files to launch ' + tool_name + ''))
       .append($('' + file_status_text + ''))
       .append($('').button({ disabled: !have_selection }))
   );
@@ -53,18 +53,60 @@ function cbrain_attach_userfile_checkboxes(userfile_checkboxes, tool_name, launc
   userfile_checkboxes
     .unbind('change.launch_task')
     .bind('change.launch_task', function () {
-      var checked = userfile_checkboxes.filter(':checked').length;
+      launch_task();
+    });
+}
 
-      /* Update the button in the dialog */
-      launch_button.val((checked ? "Launch " : "Prepare ") + tool_name);
+// Generate the launch_task div if prepare_tool_id present as a parameter
+function launch_task() {
+  var parameters          = window.location.search.split(/\?|&/);
+
+  // scan the query params in the URL, trying to find "prepare_tool_id=NNN"
+  var prepare_tool_id = undefined;
+  for (var i = 0; i < parameters.length; i++) {
+    var [name, id]     = parameters[i].split(/=/);
+    if (name === "prepare_tool_id") {
+      prepare_tool_id = id;
+      break;
+    }
+  }
+
+  var tool_name = $("#tool_name_to_launch").text();
+  if (tool_name === '') {
+    tool_name === undefined;
+  }
+
+  if (!prepare_tool_id && !tool_name) {
+    return;
+  }
+  // Fetch tool name according to `prepare_tool_id` or
+  // Fetch prepare_tool_id according to tool name.
+  for (let tool of document.getElementsByClassName("toolsLink")) {
+    var id   = tool.dataset.toolId;
+    var name = tool.childNodes[0].data;
+    if (prepare_tool_id && id === prepare_tool_id) {
+      tool_name = name;
+      break;
+    }
+    if (tool_name !== ''  && name === tool_name) {
+      prepare_tool_id = id;
+      break;
+    }
+  }
 
-      /* And the launch_bar, if it exists */
-      $('.launch_bar span.file_status')
-        .text(checked ? "Launch with " + checked + " file(s)" : "No files selected");
+  if (tool_name === undefined) {
+    return;
+  }
 
-      $('.launch_bar button')
-        .button(checked ? 'enable' : 'disable');
-    });
+  /* Do we have some files selected to launch the task on? */
+  var nb_selected_files = parseInt($('.psel-count').text());
+  var have_selection    = nb_selected_files > 0;
+
+  var file_status_text  = have_selection ? "Launch with " + nb_selected_files + " file(s)" : "No files selected";
+  var url               = "tasks/new?tool_id=" + prepare_tool_id;
+
+  // Generate the launch_bar div and attach action on the userfile_checkboxes
+  cbrain_userfile_launch_bar(tool_name, file_status_text, have_selection, url);
 }
 
 $(function() {
@@ -441,49 +483,6 @@ $(function() {
 
     /* Show/Hide dynamic actions/menu elements according to current selection */
     (function () {
-      // Generate the launch_task div if prepare_tool_id present as a parameter
-      function launch_task() {
-        var parameters          = window.location.search.split(/\?|&/);
-        var launch_button       = $(this).find('input.launch_tool');
-        var userfile_checkboxes = $("input[name='file_ids[]']");
-
-        // scan the query params in the URL, trying to find "prepare_tool_id=NNN"
-        var prepare_tool_id = undefined;
-        for (var i = 0; i < parameters.length; i++) {
-          var [name, id]     = parameters[i].split(/=/);
-          if (name === "prepare_tool_id") {
-            prepare_tool_id = id;
-            break;
-          }
-        }
-
-        if (!prepare_tool_id) {
-          return;
-        }
-
-        // Fetch tool name according to `prepare_tool_id`
-        var tool_name       = undefined;
-        for (let tool of document.getElementsByClassName("toolsLink")) {
-          var id   = tool.dataset.toolId;
-          var name = tool.childNodes[0].data;
-          if (id === prepare_tool_id) {
-            tool_name = name;
-            break;
-          }
-        }
-
-        /* Do we have some files selected to launch the task on? */
-        var nb_selected_files = parseInt($('.psel-count').text());
-        var have_selection    = nb_selected_files > 0;
-
-        var file_status_text  = have_selection ? "Launch with " + nb_selected_files + " file(s)" : "No files selected";
-        var url               = "tasks/new?tool_id=" + prepare_tool_id;
-
-        // Generate the launch_bar div and attach action on the userfile_checkboxes
-        cbrain_userfile_launch_bar(tool_name, file_status_text, have_selection, url);
-        cbrain_attach_userfile_checkboxes(userfile_checkboxes, tool_name, launch_button);
-      }
-
       function toggle(checked, persistent) {
         if (typeof checked === 'undefined')
           checked = $('input[name="file_ids[]"]:checked').length;
diff --git a/BrainPortal/spec/boutiques/boutiques_tester_spec.rb b/BrainPortal/spec/boutiques/boutiques_tester_spec.rb
index fe622f7a4..1eb4e96ac 100644
--- a/BrainPortal/spec/boutiques/boutiques_tester_spec.rb
+++ b/BrainPortal/spec/boutiques/boutiques_tester_spec.rb
@@ -50,6 +50,7 @@
   before(:all) do
     createInputFiles # Create required input files
     PWD = Dir.pwd # Save the starting dir form which the tests were launched
+    @admin = User.admin
   end
 
   before(:each) do
@@ -58,7 +59,7 @@
     # Build some of the cbrain environment
     @user, @group = FactoryBot.create(:user), FactoryBot.create(:group)
     @dp = FlatDirLocalDataProvider.new({
-      :online => true, :read_only => false, :remote_dir => '.', :name => "dp1", :user_id => @user.id, :group_id => @group.id
+      :online => true, :read_only => false, :remote_dir => '.', :name => "dp1", :user_id => @admin.id, :group_id => @group.id
     })
     @dp.save!
     # Lambda for constructing cbcsv files
diff --git a/BrainPortal/spec/controllers/userfiles_controller_spec.rb b/BrainPortal/spec/controllers/userfiles_controller_spec.rb
index 88c5b31df..687861b93 100644
--- a/BrainPortal/spec/controllers/userfiles_controller_spec.rb
+++ b/BrainPortal/spec/controllers/userfiles_controller_spec.rb
@@ -32,21 +32,19 @@ class << file; attr_reader :tempfile; end
 
 RSpec.describe UserfilesController, :type => :controller do
   let(:admin)                 { create(:admin_user, :login => "admin_user" ) }
+  let(:data_provider)         { create(:flat_dir_local_data_provider, :user => admin, :online => true, :group => EveryoneGroup.first, :read_only => false) }
   let(:site_manager)          { create(:site_manager) }
-  let(:dp_site_manager)       { create(:flat_dir_local_data_provider, :user => site_manager, :online => true, :read_only => false) }
   let(:user)                  { create(:normal_user, :site => site_manager.site) }
-  let(:dp_user)               { create(:flat_dir_local_data_provider, :user => user, :online => true, :read_only => false) }
   let(:admin_userfile)        { create(:single_file, :user => admin) }
   let(:admin_userfile_2)      { create(:single_file, :user => admin) }
-  let(:site_manager_userfile) { create(:single_file, :user => site_manager, :data_provider => dp_site_manager) }
+  let(:site_manager_userfile) { create(:single_file, :user => site_manager, :data_provider => data_provider) }
   let(:user_userfile)         { create(:single_file, :user => user, :data_provider => data_provider) }
   let(:child_userfile)        { create(:single_file, :user => admin, :parent_id => admin_userfile.id) }
-  let(:group_userfile)        { create(:single_file, :group_id => user.group_ids.last, :data_provider => dp_user) }
+  let(:group_userfile)        { create(:single_file, :group_id => user.group_ids.last, :data_provider => data_provider) }
   let(:public_group)          { create(:group, :public => true, :creator_id => admin.id )}
   let(:public_group_file)     { create(:single_file, :user=> user, :group_id => public_group.id, :data_provider => data_provider)}
   let(:mock_userfile)         { mock_model(TextFile, :id => 1).as_null_object }
   let(:mock_userfile2)        { mock_model(TextFile, :id => 2).as_null_object }
-  let(:data_provider)         { create(:flat_dir_local_data_provider, :user => user, :online => true, :read_only => false) }
   userfile = FactoryBot.attributes_for(:userfile)
 
   after(:all) do
diff --git a/BrainPortal/spec/factories/portal_factories.rb b/BrainPortal/spec/factories/portal_factories.rb
index 03c532c47..06f3512a3 100644
--- a/BrainPortal/spec/factories/portal_factories.rb
+++ b/BrainPortal/spec/factories/portal_factories.rb
@@ -121,7 +121,7 @@
     sequence(:name) { |n| "dataprovider_#{n}" }
     read_only       { true }
     type            { "FlatDirLocalDataProvider" }
-    association     :user, factory: :normal_user
+    association     :user, factory: :admin_user
     association     :group
   end
 
diff --git a/BrainPortal/spec/models/remote_resource_spec.rb b/BrainPortal/spec/models/remote_resource_spec.rb
index 4b4a04294..a127854cf 100644
--- a/BrainPortal/spec/models/remote_resource_spec.rb
+++ b/BrainPortal/spec/models/remote_resource_spec.rb
@@ -334,7 +334,6 @@
     end
     it "should return a 'localhost' url if ssh control and active resource tunnel info given" do
       allow(remote_resource).to receive(:has_ssh_control_info?).and_return(true)
-      allow(remote_resource).to receive(:tunnel_actres_port).and_return(true)
       expect(remote_resource.site).to match(/^http:\/\/localhost/)
     end
   end
diff --git a/BrainPortal/spec/models/tool_config_spec.rb b/BrainPortal/spec/models/tool_config_spec.rb
index 5ab14038a..731851f1f 100644
--- a/BrainPortal/spec/models/tool_config_spec.rb
+++ b/BrainPortal/spec/models/tool_config_spec.rb
@@ -32,7 +32,6 @@
     let(:no_b_tool_config)  { create(:tool_config, :bourreau => nil) }
     let(:no_t_tool_config)  { create(:tool_config, :tool => nil) }
 
-
     it "should allow admin user to access a tool config even if they don't belong to its group" do
       expect(tool_config.can_be_accessed_by?(user)).to be_truthy
     end
@@ -159,12 +158,14 @@
 
    context "fill HEADER" do
       it "should print 'Configuration: tool_config.id'" do
-        expect(tool_config.to_bash_prologue).to match(/Configuration\s?:\s+#\s+#{tool_config.id}/)
+        expect(tool_config.to_bash_prologue).to                    match(/Configuration\s?:\s+#\s+#{tool_config.id}/)
+        expect(tool_config.to_bash_prologue(singularity: true)).to match(/Configuration\s?:\s+#\s+#{tool_config.id}/)
       end
 
       it "should print 'Tool: ALL' if specific tool is not defined"  do
         tool_config.tool = nil
-        expect(tool_config.to_bash_prologue).to match(/Tool\s?:\s+ALL/)
+        expect(tool_config.to_bash_prologue).to                    match(/Tool\s?:\s+ALL/)
+        expect(tool_config.to_bash_prologue(singularity: true)).to match(/Tool\s?:\s+ALL/)
       end
 
       it "should print 'Tool: tool_config.tool.name' if specific tool is defined"  do
@@ -195,12 +196,14 @@
       it "should print 'Description: (NONE SUPPLIED)' if description is blank" do
         tool_config.description = nil
         tool_config.tool        = tool
-        expect(tool_config.to_bash_prologue).to match(/Description\s?:\s+\(NONE SUPPLIED\)/)
+        expect(tool_config.to_bash_prologue).to      match(/Description\s?:\s+\(NONE SUPPLIED\)/)
+        expect(tool_config.to_bash_prologue true).to match(/Description\s?:\s+\(NONE SUPPLIED\)/)
       end
 
       it "should print 'Description: tool_config.description' if description is blank" do
         tool_config.tool        = tool
-        expect(tool_config.to_bash_prologue).to match(/Description\s?:\n\#\-+\n\n\#\s+#{tool_config.description}/)
+        expect(tool_config.to_bash_prologue).to      match(/Description\s?:\n\#\-+\n\n\#\s+#{tool_config.description}/)
+        expect(tool_config.to_bash_prologue true).to match(/Description\s?:\n\#\-+\n\n\#\s+#{tool_config.description}/)
       end
     end
 
@@ -222,6 +225,22 @@
 
         expect(tool_config.to_bash_prologue).to match(/Environment variables\s?:\n\#\-+\n\n#{script}/)
       end
+      it "should not print 'Environment variables: export SINGULARITYENV_name1=\"value1\".... if config has no singularity" do
+        tool_config.env_array = [["name1", "value1"],["name2","value2"]]
+        expect(tool_config.to_bash_prologue).not_to match(/(SINGULARITYENV|APPTAINERENV)/)
+      end
+      it "should print 'export SINGULARITYENV_name1=\"value1\".... if env is not empty and config uses singularity" do
+        tool_config.env_array = [["name1", "value1"],["name2","value2"]]
+
+        script = ""
+        tool_config.env_array.each do |name_val|
+          name = "SINGULARITYENV_" + name_val[0].strip
+          val  = name_val[1]
+          script += "export #{name}=\\\"#{val}\\\"\\n"
+        end
+
+        expect(tool_config.to_bash_prologue true).to match(/#{script}/)
+      end
     end
 
     context "fill SCRIPT" do
diff --git a/BrainPortal/spec/modules/github_ci_spec.rb b/BrainPortal/spec/modules/github_ci_spec.rb
index 811df96df..7307515a8 100644
--- a/BrainPortal/spec/modules/github_ci_spec.rb
+++ b/BrainPortal/spec/modules/github_ci_spec.rb
@@ -23,7 +23,7 @@
 require 'rails_helper'
 
 # This test file is meant to test stuff that are particular to
-# being in a Travis CI testing environment.
+# being in a Github CI testing environment.
 describe "GithubCI" do
 
   describe "environment" do
diff --git a/BrainPortal/spec/modules/resource_access_spec.rb b/BrainPortal/spec/modules/resource_access_spec.rb
index c924b8feb..0d621374a 100644
--- a/BrainPortal/spec/modules/resource_access_spec.rb
+++ b/BrainPortal/spec/modules/resource_access_spec.rb
@@ -26,11 +26,10 @@
   let(:normal_user)    { create(:normal_user) }
   let(:site_manager)   { create(:site_manager) }
   let(:admin)          { create(:admin_user) }
-  let(:scratch_dp)     { ScratchDataProvider.main }
-  let(:free_resource)  { create(:ssh_data_provider) }
-  let(:group_resource) { create(:ssh_data_provider, :group => user.groups.last) }
-  let(:site_resource)  { create(:ssh_data_provider, :user => create(:normal_user, :site => user.site)) }
-  let(:owned_resource) { create(:ssh_data_provider, :user => user) }
+  let(:free_resource)  { create(:cbrain_task) }
+  let(:group_resource) { create(:cbrain_task, :group => user.groups.last) }
+  let(:site_resource)  { create(:cbrain_task, :user => create(:normal_user, :site => user.site)) }
+  let(:owned_resource) { create(:cbrain_task, :user => user) }
 
 
   describe "#can_be_accessed_by?" do
@@ -147,7 +146,7 @@
         site_resource
         owned_resource
         # BTW: fails if the rake task 'db:sanity:check' was not run
-        expect(DataProvider.find_all_accessible_by_user(admin).map(&:id)).to match_array([scratch_dp.id, free_resource.id, group_resource.id, site_resource.id, owned_resource.id])
+        expect(CbrainTask.find_all_accessible_by_user(admin).map(&:id)).to match_array([free_resource.id, group_resource.id, site_resource.id, owned_resource.id])
       end
     end
 
@@ -158,7 +157,7 @@
         group_resource
         site_resource
         owned_resource
-        expect(DataProvider.find_all_accessible_by_user(site_manager).map(&:id)).to match_array([group_resource.id, site_resource.id, owned_resource.id])
+        expect(CbrainTask.find_all_accessible_by_user(site_manager).map(&:id)).to match_array([group_resource.id, site_resource.id, owned_resource.id])
       end
     end
 
@@ -169,7 +168,7 @@
         group_resource
         site_resource
         owned_resource
-        expect(DataProvider.find_all_accessible_by_user(user).map(&:id)).to match_array([group_resource.id, owned_resource.id])
+        expect(CbrainTask.find_all_accessible_by_user(user).map(&:id)).to match_array([group_resource.id, owned_resource.id])
       end
     end
 
@@ -180,48 +179,48 @@
       let(:user) { admin }
 
       it "should find owned resources" do
-        expect(DataProvider.find_accessible_by_user(owned_resource.id, admin).id).to eq(owned_resource.id)
+        expect(CbrainTask.find_accessible_by_user(owned_resource.id, admin).id).to eq(owned_resource.id)
       end
       it "should find site-associated resources" do
-        expect(DataProvider.find_accessible_by_user(site_resource.id, admin).id).to eq(site_resource.id)
+        expect(CbrainTask.find_accessible_by_user(site_resource.id, admin).id).to eq(site_resource.id)
       end
       it "should find group-associated resources" do
-        expect(DataProvider.find_accessible_by_user(group_resource.id, admin).id).to eq(group_resource.id)
+        expect(CbrainTask.find_accessible_by_user(group_resource.id, admin).id).to eq(group_resource.id)
       end
       it "should find non-associated resources" do
-        expect(DataProvider.find_accessible_by_user(free_resource.id, admin).id).to eq(free_resource.id)
+        expect(CbrainTask.find_accessible_by_user(free_resource.id, admin).id).to eq(free_resource.id)
       end
     end
     describe "for site managers" do
       let(:user) { site_manager }
 
       it "should find owned resources" do
-        expect(DataProvider.find_accessible_by_user(owned_resource.id, site_manager).id).to eq(owned_resource.id)
+        expect(CbrainTask.find_accessible_by_user(owned_resource.id, site_manager).id).to eq(owned_resource.id)
       end
       it "should find site-associated resources" do
-        expect(DataProvider.find_accessible_by_user(site_resource.id, site_manager).id).to eq(site_resource.id)
+        expect(CbrainTask.find_accessible_by_user(site_resource.id, site_manager).id).to eq(site_resource.id)
       end
       it "should find group-associated resources" do
-        expect(DataProvider.find_accessible_by_user(group_resource.id, site_manager).id).to eq(group_resource.id)
+        expect(CbrainTask.find_accessible_by_user(group_resource.id, site_manager).id).to eq(group_resource.id)
       end
       it "should raise ActiveRecord::RecordNotFound when used to find non-associated resources" do
-        expect{DataProvider.find_accessible_by_user(free_resource.id, site_manager)}.to raise_error(ActiveRecord::RecordNotFound)
+        expect{CbrainTask.find_accessible_by_user(free_resource.id, site_manager)}.to raise_error(ActiveRecord::RecordNotFound)
       end
     end
     describe "for users" do
       let(:user) { normal_user }
 
       it "should find owned resources" do
-        expect(DataProvider.find_accessible_by_user(owned_resource.id, user).id).to eq(owned_resource.id)
+        expect(CbrainTask.find_accessible_by_user(owned_resource.id, user).id).to eq(owned_resource.id)
       end
       it "should rause ActiveRecord::RecordNotFound when used to find site-associated resources" do
-        expect{DataProvider.find_accessible_by_user(site_resource.id, user)}.to raise_error(ActiveRecord::RecordNotFound)
+        expect{CbrainTask.find_accessible_by_user(site_resource.id, user)}.to raise_error(ActiveRecord::RecordNotFound)
       end
       it "should find group-associated resources" do
-        expect(DataProvider.find_accessible_by_user(group_resource.id, user).id).to eq(group_resource.id)
+        expect(CbrainTask.find_accessible_by_user(group_resource.id, user).id).to eq(group_resource.id)
       end
       it "should rause ActiveRecord::RecordNotFound when used to find non-associated resources" do
-        expect{DataProvider.find_accessible_by_user(free_resource.id, user)}.to raise_error(ActiveRecord::RecordNotFound)
+        expect{CbrainTask.find_accessible_by_user(free_resource.id, user)}.to raise_error(ActiveRecord::RecordNotFound)
       end
     end
   end
diff --git a/Release-Notes.md b/Release-Notes.md
index 00e612e5c..dd046f5bb 100644
--- a/Release-Notes.md
+++ b/Release-Notes.md
@@ -1,6 +1,111 @@
 
 ## CBRAIN/NeuroHub Release Notes
 
+#### Version 6.3.0 Released 2023-01-26
+
+(Nearly a full year since the previous release! The diff is 19,773 lines long!)
+
+User support and user interface improvements:
+
+* The S3 DataProvider class has been extended to fully support the
+  browse_path feature, allowing files to be registered at arbitrary
+  depth within the object namespace tree of the S3 bucket.
+* The launch button in the file manager was improved so that external
+  sites can directly link to a prepared pair of dataset/tool. Used
+  by the CONP project, mostly.
+* We added the standard 'This site use a cookie' banner.
+* The globally visible list of available tools and datasets was
+  cleaned up and re-arranged in two tabs, each with two tables for
+  the public and restricted thingies.
+* Added a new userfile model in the base distribution: ZipArchive.
+* Special API hooks for the LORIS projects were adjusted; although
+  they can also be used by non LORIS actors, they're pretty specific.
+
+Admin and codebase improvements:
+
+* A new type of user called an 'AutomatedUser' has been added; it
+  is basically the same as a NormalUser, but the type can help admins
+  identify accounts that are meant to be accessed by automated
+  systems (API calls etc).
+* A DataUsage model was added to track and count how often files
+  are being downloaded, copied, used in processing, or viewed. Admins
+  can selectively enable this on a project by project basis, and
+  counts are aggregated on a user + month-by-month basis.
+* A DiskQuota model was added, it allows administrator to impose
+  limits on the number of files and their total sizes for any user
+  on any data provider.
+* The communication channels between the portal and the Bourreau
+  are now completely performed by setting up UNIX-domain sockets
+  on the Bourreau side. No longer do we open a network port on
+  localhost! The connections are established by proper -L and -R
+  SSH options, which now support such sockets.
+* A new rake task help developers and admins manage their CBRAIN
+  instances (cbrain:models:broken:*)
+* The boot mechanism for Bourreau was rewritten as plain bash shell
+  wrappers to allow a faster startup than then old Ruby bootstrapping
+  code. The Bourreau is still in Ruby, of course, but prepping it
+  up no longer requires a costly initial Ruby setup script.
+* Speaking of the boot system, Bourreaux servers now launch a
+  separate watchdog process (also a bash script) that will ping the
+  Bourreau every 20 minutes and force it to shutdown if the DB
+  connection (or any SSH tunnel) is shut down unexpectedly. This
+  keep the PID file from staying around for no reason.
+* We removed from the GitHub-hosted codebase the hardcoded cookie
+  secret keys; these were never really a security issue (given in
+  'production' mode the admin was supposed to create them), but for
+  convenience now any true production or developement CBRAIN system
+  will generate their own secret key deterministically (yet in a
+  non-guessable way).
+* Admins can force specific users to not only link their account
+  to a GlobusAuth provider, it can also be a specific provider chosen
+  by the admin. And once the linkage is done, the password method
+  is permanently disabled for such users.
+* We cleaned up a bunch of system attributes that are no longer
+  used (like port numbers for DB and ActiveResource connections to
+  Bourreaux, which are now always tunnelled through SSH)
+* Admins users have access to the new 'last' command in the console,
+  and the 'p' (ping) command in the ibc interface.
+* Support for Apptainer as the new Singularity engine.
+* Bourreaux can be configured to log to an external file some
+  information about each job submitted (user, jobid, name, user
+  Globus name, etc).
+* When configuring a ToolConfig, the admin no longer has to explicitely
+  duplicate the environment variables that the tool needs depending
+  on whether the tools runs in Singularity/Apptainer or not. Before,
+  the admins had to set both XYZ=a and SINGULARITYENV_XYZ=a, now
+  it's done automatically.
+* Admins can now visualize directly in the interface the Boutiques
+  descriptor associated with a particular ToolConfig, for a tool
+  configured with the new integrator.
+* We cleaned up (removed) most of the controller actions that were
+  required by the Canadian agency that initialy funded CBRAIN (CANARIE).
+  These were being monitored by them but they discontinued their
+  side.
+* Admins can create notification messages that will show up in the
+  dashboard of all users (e.g. notice for downtime etc)
+
+Boutiques improvements:
+
+* The (relatively) new Boutiques integrator has been extended with lots
+  of modules to let integrators customize the behavior of their tools:
+  * BoutiquesAllowedExitCodes
+  * BoutiquesFileNameMatcher
+  * BoutiquesForcedOutputBrowsePath
+  * BoutiquesInputCacheCleaner
+  * BoutiquesInputSubdirMaker
+  * BoutiquesOutputCacheCleaner
+  * BoutiquesOutputFilenameRenamer
+
+* Launching task arrays with a CbrainFileList now allows the user
+  to provide extra parameters specific to each row in the file list.
+  To do so, the file list should be an ExtendedCbrainFileList and
+  the last column should contain a serialized JSON structure that
+  can merge to the Boutiques parameters of the task.
+
+* A new tool BoutiquesDescriptorMaker is provided as part of the
+  base distribution. It allows a developer to test 'live' what a
+  Boutiques descriptor would look like in CBRAIN.
+
 #### Version 6.2.0 Released 2022-01-28
 
 (After eleven months, the `git diff` output is over 12,000 lines long!)
@@ -119,7 +224,7 @@ New CBRAIN features: (some of these apply to NeuroHub too)
   UserkeyFlatDirSshDataProvider class in NeuroHub.
 * These keys (full pair) can be pushed to a Bourreau so that
   the CBRAIN code running there can connect as the user. Users
-  have control over which bourreau to push their key pair to.
+  have control over which Bourreau to push their key pair to.
 * CBRAIN can generate a new API token and show it to the user
   in their 'my account' page.
 * When a user accepts an invitation to join a project, the
diff --git a/Travis/Dockerfile.travis b/Travis/Dockerfile.travis
deleted file mode 100644
index dcf1acdf7..000000000
--- a/Travis/Dockerfile.travis
+++ /dev/null
@@ -1,223 +0,0 @@
-
-############################################
-# This Dockerfile builds a docker image
-# suitable to boot a CBRAIN BrainPortal
-# where tests can be run. It is meant
-# to be run within a Travis Continuous
-# Integration virtual machine,
-# although invoking its entry point manually
-# from docker is also a possibility.
-#
-# Do not use the resulting docker container
-# as a CBRAIN installation, it won't work,
-# and you'll have no persistent data because
-# the SQL server is completely inside the
-# container fileystem.
-############################################
-
-# We use CentOS 7; CentOS 8 needs further adjustments, as it's new (Oct 2019)
-FROM centos:7
-
-
-
-#####################################
-# Package updates and installations #
-#####################################
-
-# Note: keep the package list alphabetically
-#       ordered to facilitate parsing
-
-RUN yum update -y
-RUN yum install -y epel-release
-RUN yum install -y \
-      autoconf \
-      automake \
-      make \
-      bzip2 \
-      bison \
-      gcc-c++ \
-      git \
-      glibc-devel \
-      glibc-headers \
-      gpg \
-      libffi-devel \
-      libmysqlclient-dev \
-      libsodium \
-      libtool \
-      libxml2 \
-      libxml2-devel \
-      libyaml-devel \
-      mariadb-devel \
-      mariadb-server \
-      openssl-devel \
-      patch \
-      readline-devel \
-      sqlite-devel \
-      zlib-devel \
-      which \
-      wget
-
-# The following UID and GID are chosen
-# to match what is usually the unprivileged user
-# that runs inside the Travis CI virtual machines,
-# but that should not make much difference.
-RUN groupadd -g 500        cbrain
-RUN useradd  -u 500 -g 500 cbrain
-
-# Environment variables for the MYSQL DB
-ENV MYSQL_ROOT_PASSWORD="my-secret-pw" MYSQL_USER="cb_user" MYSQL_DATABASE="cb_db_test" MYSQL_PASSWORD="cbpw12345"
-
-
-
-#############################################
-# MySQL server installation and configuration
-#############################################
-
-RUN mysql_install_db --force # we need --force so it ignores the fake hostname
-RUN mkdir -p /var/lib/mysql /var/run/mysqld
-RUN chown -R mysql:mysql /var/lib/mysql /var/run/mysqld && \
-    chmod 777 /var/run/mysqld
-RUN rm -f /var/lib/mysql/aria_log_control
-
-RUN mysqld_safe & sleep 3 && \
-    /usr/bin/mysqladmin -u root password "$MYSQL_ROOT_PASSWORD"
-
-RUN mysqld_safe & sleep 3 && \
-    /usr/bin/mysql -u root --password="$MYSQL_ROOT_PASSWORD" -e "create database $MYSQL_DATABASE;"
-
-RUN mysqld_safe & sleep 3 && \
-    /usr/bin/mysql -u root --password="$MYSQL_ROOT_PASSWORD" -e "grant all on $MYSQL_DATABASE.* to '$MYSQL_USER'@'localhost' identified by '$MYSQL_PASSWORD';"
-
-
-
-#############################
-# Ruby and rvm installation #
-#############################
-
-USER cbrain
-
-ENV RUBY_VERSION=2.6.3
-
-RUN cd $HOME && curl -sSL https://rvm.io/mpapis.asc | gpg2 --import -
-RUN cd $HOME && curl -sSL https://rvm.io/pkuczynski.asc | gpg2 --import -
-
-RUN cd $HOME && curl -sSL https://get.rvm.io | bash -s stable
-
-RUN cd $HOME && echo "source $HOME/.rvm/scripts/rvm" >> $HOME/.bashrc
-
-RUN bash --login -c 'rvm install $RUBY_VERSION --autolibs=read'
-
-RUN bash --login -c 'rvm --default $RUBY_VERSION'
-
-
-
-################################
-# Rails application bundling   #
-################################
-
-# These four statements is a way for the
-# people building the container to specify
-# variations on what base CBRAIN installation
-# to use.
-ARG CBRAIN_REPO=https://github.com/aces/cbrain.git
-ARG CBRAIN_BRANCH=dev
-ENV CBRAIN_REPO=$CBRAIN_REPO
-ENV CBRAIN_BRANCH=$CBRAIN_BRANCH
-
-# Edit manually the following line to have your docker installation
-# skip its cache of the previous container build, if necessary.
-# Just having a different commit number in the echo statement will do.
-# This can be necessary if you know that the code on the GitHub
-# repo has changed since that last build.
-RUN echo Force install using CBRAIN at commit c1e59cb4ac72a9ff66e76a42c607a269a043ee4d
-
-# Extract initial CBRAIN source (will be replaced at test time)
-# but having an initial installation speeds up bundling,
-# migrations, etc.
-# I would use --single-branch in the git clone command below, but
-# it seems not all git packages support it.
-RUN cd $HOME && \
-    git clone --branch "$CBRAIN_BRANCH" --depth 2 "$CBRAIN_REPO" cbrain_base
-
-# Install and configure the portal
-ENV RAILS_ENV=test
-
-RUN bash --login -c 'cd $HOME/cbrain_base/BrainPortal && gem install bundler'
-
-RUN bash --login -c 'cd $HOME/cbrain_base/BrainPortal && bundle install'
-
-RUN bash --login -c 'cd $HOME/cbrain_base/Bourreau && bundle install'
-
-RUN bash --login -c 'cd $HOME/cbrain_base/BrainPortal && cd $(bundle show sys-proctable) && rake install'
-
-COPY ./templates/database.yml.TEST     /home/cbrain/cbrain_base/BrainPortal/config/database.yml
-
-COPY ./templates/config_portal.rb.TEST /home/cbrain/cbrain_base/BrainPortal/config/initializers/config_portal.rb
-
-# Seed the DB
-USER root
-
-RUN  chown cbrain /home/cbrain/cbrain_base/BrainPortal/config/database.yml && \
-     chown cbrain /home/cbrain/cbrain_base/BrainPortal/config/initializers/config_portal.rb
-
-RUN su -c "bash --login -c 'cd \$HOME/cbrain_base/BrainPortal && rake cbrain:plugins:install:plugins'" cbrain
-
-RUN mysqld_safe & sleep 2 && \
-    su -c "bash --login -c 'cd \$HOME/cbrain_base/BrainPortal && rake db:schema:load'" cbrain
-
-RUN mysqld_safe & sleep 2 && \
-    su -c "bash --login -c 'cd \$HOME/cbrain_base/BrainPortal && rake db:seed'" cbrain
-
-RUN mysqld_safe & sleep 2 && \
-    su -c "bash --login -c 'cd \$HOME/cbrain_base/BrainPortal && rake db:seed:test:bourreau'" cbrain
-
-RUN mysqld_safe & sleep 2 && \
-    su -c "bash --login -c 'cd \$HOME/cbrain_base/BrainPortal && rake db:sanity:check'" cbrain
-
-
-
-########################################################
-# Cleanup files to make the image as small as possible #
-########################################################
-
-USER cbrain
-
-RUN bash --login -c 'rvm cleanup all'
-
-USER root
-
-RUN yum clean all
-
-# Not sure if next line won't interfere with future bundle updates...
-# but then it saves just a few dozen megabytes.
-RUN rm -rf /home/cbrain/.rvm/gems/ruby*/bundler/gems/*/.git
-
-
-
-#########################
-# Ports and entry point #
-#########################
-
-# This command will copy the code freshly extracted by travis
-# and perform the rest of the setup needed to run the tests
-# (migrate the DB, run rake tasks, run rspec); the path
-# /home/cbrain/cbrain_travis is a mounted volume from the
-# VM side.
-CMD [ "/home/cbrain/cbrain_travis/Travis/bootstrap.sh" ]
-
-###########
-# Volumes #
-###########
-#
-# Only one volume is needed, it is Travis CI's own
-# copy of the cbrain project to be tested.
-#
-# Note that this is distinct from
-#
-#   /home/cbrain/cbrain_base
-#
-# which is where we did the initial installation here
-# in this image, as a way to speed up the tests.
-
-VOLUME /home/cbrain/cbrain_travis
-
diff --git a/Travis/README.md b/Travis/README.md
deleted file mode 100644
index faa5451f0..000000000
--- a/Travis/README.md
+++ /dev/null
@@ -1,28 +0,0 @@
-
-# Continuous integration with [Travis CI](https://travis-ci.org/)
-
-This directory contain all the support files and scripts for testing CBRAIN within a Docker container running on a VM provided by Travis CI.
-
-The process works in two steps.
-
-* a docker container is prepared, once, and published on DockerHub or kept locally. This step is performed by the script `Travis/build_container.sh`.
-* when Travis detects a push on a CBRAIN repo that it tracks, it will invoke (through the `.travis.yml` file a the top of CBRAIN's repo) the script `Travis/travis_ci.sh`.
-
-This script `travis_ci.sh` will launch the container prepared in the first step.
-
-The container will run `bootstrap.sh`, which is the main docker entry point, and as root it performs these two operations:
-
-* first it simply starts the MySQL DB server
-* second it invokes, as user 'cbrain', the script `cb_run_tests.sh` which performs the setup necessary to run the test suites.
-
-## Trying it out locally
-
-The entire process can be tried locally without setting up all the Travis CI configuration, as long as Docker is available.
-
-```bash
-    cd Travis
-    bash build_container.sh -b hello/bye    # "hello/bye" can be any container name of your choice
-    cd ..
-    env CBRAIN_CI_IMAGE_NAME=hello/bye bash Travis/travis_ci.sh  # the container name can be given in argument too
-```
-
diff --git a/Travis/bootstrap.sh b/Travis/bootstrap.sh
deleted file mode 100755
index 5e7ed9859..000000000
--- a/Travis/bootstrap.sh
+++ /dev/null
@@ -1,43 +0,0 @@
-#!/bin/bash
-
-# This script is run as root as the entry point of
-# the CBRAIN docker container for running tests;
-# it basically just starts the DB server then
-# invokes cb_run_tests.sh as user 'cbrain'.
-
-set -e # exit as soon as any command fails
-
-if test "$UID" -ne 0 ; then
-  echo "This script is meant to be run as the entry point"
-  echo "to the docker container for running tests."
-  exit 2
-fi
-
-MAGENTA='\033[35m'
-NC='\033[0m'
-
-printf "${MAGENTA}Container bootstrap script starting at %s ${NC}\n" "$(date '+%F %T')"
-
-test_user="cbrain"            # normal user to run test suite
-test_script="cb_run_tests.sh" # the script for running the suite
-
-echo "Starting DB server as root"
-mysqld_safe &
-started=""
-for n in 1 2 3 4 5 ; do
-  echo "Waiting for DB server ($n/5)"
-  sleep 3
-  started=$(ps ax -o cmd | grep -v mysqld_safe | grep mysql | grep -v grep | head -1 | cut -d" " -f1 )
-  test -n "$started" && break
-done
-if test -z "$started" ; then
-  echo "Error: cannot start DB server?!?"
-  exit 2
-else
-  echo "DB server started."
-  echo ""
-fi
-
-echo "Running test script '$test_script' as user '$test_user'"
-su -c "bash --login -c /home/cbrain/cbrain_travis/Travis/$test_script" $test_user
-
diff --git a/Travis/build_container.sh b/Travis/build_container.sh
deleted file mode 100755
index e087e907e..000000000
--- a/Travis/build_container.sh
+++ /dev/null
@@ -1,96 +0,0 @@
-#!/bin/bash -e
-
-#
-# This bash script builds a docker image for testing CBRAIN.
-#
-
-# Default values for building the docker container.
-CBRAIN_REPO="https://github.com/aces/cbrain.git"
-CBRAIN_BRANCH="dev"
-IMAGE_NAME="mcin/cbrain_travis"
-
-function usage {
-  cat </dev/null
-  find . -print | sort | md5sum | cut -c1-32
-  popd >/dev/null
-}
-
-###############
-# Main script #
-###############
-
-# Install the code base to be tested
-cd $HOME
-
-test -e "$cb_test" && ls -la && die "Oh oh, some directory '$cb_test' is in the way..."
-cp -p -r "$cb_travis" "$cb_test" || die "Cannot copy the cbrain code base to '$cb_test'..."
-
-# Copy DB configuration file from the docker original install
-cp -p "$cb_base"/BrainPortal/config/database.yml \
-      "$cb_test"/BrainPortal/config/database.yml || die "Cannot copy DB configuration file"
-
-# Copy CBRAIN configuration file from the docker original install
-cp -p "$cb_base"/BrainPortal/config/initializers/config_portal.rb \
-      "$cb_test"/BrainPortal/config/initializers/config_portal.rb || die "Cannot copy CBRAIN configuration file"
-
-# Copy the symlinks for installed plugins
-rsync -a --ignore-existing \
-      "$cb_base"/BrainPortal/cbrain_plugins/installed-plugins/ \
-      "$cb_test"/BrainPortal/cbrain_plugins/installed-plugins
-
-# Make sure RVM is loaded
-source /home/cbrain/.bashrc
-export RAILS_ENV=test
-
-
-
-# ------------------------------
-# Report Version Numbers
-# ------------------------------
-echo ""
-printf "${YELLOW}Versions of CBRAIN code base installed:${NC}\n"
-
-cd $cb_base/BrainPortal || die "Cannot cd to base BrainPortal directory"
-printf "${BLUE}Container BASE CBRAIN:${NC} "
-git log --date=iso -n 1 --pretty="%h by %an at %ad, %s"
-
-cd $cb_test/BrainPortal || die "Cannot cd to test BrainPortal directory"
-printf "${BLUE}Travis CI TEST CBRAIN:${NC} "
-git log --date=iso -n 1 --pretty="%h by %an at %ad, %s"
-printf "${BLUE}Travis CI REV CBRAIN:${NC}  "; script/show_cbrain_rev -z
-
-echo ""
-
-
-
-# ------------------------------
-# Portal-Side Re-Initializations
-# ------------------------------
-
-# Go to the new code to test
-cd $cb_test/BrainPortal || die "Cannot cd to BrainPortal directory"
-
-# Prep all that needs to be prepared. With a bit of luck, bundle install
-# will be quite quick given that when building the docker image we already
-# ran it once in ~/cbrain_base.
-
-# Only bundle the gems if the Gemfile has changed
-if ! cmp -s "$cb_base/BrainPortal/Gemfile" \
-            "$cb_test/BrainPortal/Gemfile" ; then
-  printf "${YELLOW}Running Bundler on BrainPortal side.${NC}\n"
-  bundle install || die "Cannot bundle gems for the BrainPortal"
-else
-  printf "${BLUE}No need to run the Bundler on BrainPortal side, yippee!${NC}\n"
-  cp -p "$cb_base/BrainPortal/Gemfile.lock" \
-        "$cb_test/BrainPortal/Gemfile.lock"
-fi
-
-# Only install the plugins if the list of plugins files has changed.
-if test $(dir_list_cksum "$cb_base/BrainPortal/cbrain_plugins") != \
-        $(dir_list_cksum "$cb_test/BrainPortal/cbrain_plugins") ; then
-  printf "${YELLOW}Installing plugins symbolic links.${NC}\n"
-  rake "cbrain:plugins:install:plugins" || die "Cannot install cbrain:plugins" # works for Bourreau too
-else
-  printf "${BLUE}No need to install the plugins symbolic links, yippee!${NC}\n"
-fi
-
-
-
-# --------------------------------
-# Bourreau-Side Re-Initializations
-# --------------------------------
-
-# Go to the new code to test
-cd $cb_test/Bourreau || die "Cannot cd to Bourreau directory"
-
-# Only bundle the gems if the Gemfile has changed
-if ! cmp -s "$cb_base/Bourreau/Gemfile" \
-            "$cb_test/Bourreau/Gemfile" ; then
-  printf "${YELLOW}Running Bundler on Bourreau side.${NC}\n"
-  bundle install || die "Cannot bundle gems for the Bourreau"
-else
-  printf "${BLUE}No need to run the Bundler on Bourreau side, yippee!${NC}\n"
-  cp -p "$cb_base/Bourreau/Gemfile.lock" \
-        "$cb_test/Bourreau/Gemfile.lock"
-fi
-
-
-
-# ------------------------------
-# Bring the DB up to date
-# ------------------------------
-
-# Prep steps that necessitates the DB to be ready.
-cd $cb_test/BrainPortal || die "Cannot cd to BrainPortal directory"
-
-# Only migrate if the list of migration files have changed.
-if test $(dir_list_cksum "$cb_base/BrainPortal/db/migrate") != \
-        $(dir_list_cksum "$cb_test/BrainPortal/db/migrate") ; then
-  printf "${YELLOW}Running the database migrations.${NC}\n"
-  rake "db:migrate" || die "Cannot migrate the DB"
-else
-  printf "${BLUE}No need to migrate the DB, yippee!${NC}\n"
-fi
-
-# This cannot be avoided.
-printf "${YELLOW}Running the database sanity checks.${NC}\n"
-rake "db:sanity:check" || die "Cannot sanity check DB"
-
-
-
-# -------------------------------
-# Show TEST environment variables
-# -------------------------------
-# These environment variable allow the
-# user to skip over some test stages,
-# or make the API tests more verbose.
-printf "${BLUE}Environment variables for this test session:${NC}\n"
-echo   ""
-echo   "General control:"
-printf "${YELLOW}CBRAIN_SKIP_TEST_STAGES${NC}        = '${CBRAIN_SKIP_TEST_STAGES:=unset}'\n"
-printf "Possible values: \"RspecPortal,RspecBourreau,CurlAPI,GemAPI\"\n"
-echo   ""
-echo   "API test control:"
-printf "${YELLOW}CBRAIN_CURL_TEST_VERBOSE_LEVEL${NC} = '${CBRAIN_CURL_TEST_VERBOSE_LEVEL:=1}'\n"
-printf "${YELLOW}CBRAIN_CURL_TEST_FILTER${NC}        = '${CBRAIN_CURL_TEST_FILTER}'\n"
-printf "${YELLOW}CBRAIN_GEM_TEST_VERBOSE_LEVEL${NC}  = '${CBRAIN_GEM_TEST_VERBOSE_LEVEL:=1}'\n"
-printf "${YELLOW}CBRAIN_GEM_TEST_FILTER${NC}         = '${CBRAIN_GEM_TEST_FILTER}'\n"
-echo   ""
-
-
-
-# ------------------------------
-# Finally, run the tests!
-# ------------------------------
-# We save the failures of the main test commands in strings.
-# That way we run them all and report everything at the end.
-fail_portal=""
-fail_bourreau=""
-fail_api_curl=""
-fail_api_ruby=""
-
-
-
-# ------------------------------
-# Portal-Side Testing
-# ------------------------------
-cd $cb_test/BrainPortal || die "Cannot cd to BrainPortal directory"
-
-# Eventually, it would be nice if from a ENV variable set in Travis,
-# we could run only a subset of the tests.
-printf "${BLUE}Running rspec on BrainPortal side.${NC}\n"
-if echo "X$CBRAIN_SKIP_TEST_STAGES" | grep -q 'RspecPortal' >/dev/null ; then
-  printf "${YELLOW} -> Skipped by request from env CBRAIN_SKIP_TEST_STAGES${NC}\n"
-else
-  rspec spec || fail_portal="rspec on BrainPortal failed with return code $?"
-fi
-#CBRAIN_FAILTEST=1 rspec spec/modules/travis_ci_spec.rb || fail_portal="rspec on BrainPortal failed with return code $?"
-
-
-
-# ------------------------------
-# Bourreau-Side Testing
-# ------------------------------
-cd $cb_test/Bourreau || die "Cannot cd to Bourreau directory"
-
-# Eventually, it would be nice if from a ENV variable set in Travis,
-# we could run only a subset of the tests.
-# -> NOTE FIXME TODO : hardcoded 'spec/boutiques' for <-
-# -> the moment because no other test files work on Bourreau. <-
-printf "${BLUE}Running rspec on Bourreau side.${NC}\n"
-if echo "X$CBRAIN_SKIP_TEST_STAGES" | grep -q 'RspecBourreau' >/dev/null ; then
-  printf "${YELLOW} -> Skipped by request from env CBRAIN_SKIP_TEST_STAGES${NC}\n"
-else
-  rspec spec/boutiques || fail_bourreau="rspec on Bourreau failed with return code $?"
-fi
-
-
-
-# ------------------------------
-# Testing of API (curl)
-# ------------------------------
-printf "${BLUE}Running API tests with curl.${NC}\n"
-if echo "X$CBRAIN_SKIP_TEST_STAGES" | grep -q 'CurlAPI' >/dev/null ; then
-  printf "${YELLOW} -> Skipped by request from env CBRAIN_SKIP_TEST_STAGES${NC}\n"
-else
-  cd $cb_test/BrainPortal            || die "Cannot cd to BrainPortal directory"
-  rake "db:seed:test:api" >/dev/null || die "Cannot re-seed the DB for API testing"
-  rails server puma -p 3000 -d       || die "Cannot start local puma server?"
-  cd test_api                        || die "Cannot cd to test_api directory?"
-  sleep 5 # must wait a bit for puma to be ready
-  perl curl_req_tester.pl                 \
-    -h localhost                          \
-    -p 3000                               \
-    -s http                               \
-    -v"${CBRAIN_CURL_TEST_VERBOSE_LEVEL}" \
-    -R                                    \
-    ${CBRAIN_CURL_TEST_FILTER}            \
-    || fail_api_curl="API testing with CURL failed"
-  kill $(cat $cb_test/BrainPortal/tmp/pids/server.pid)
-fi
-
-
-
-# ------------------------------
-# Testing of API (Ruby Gem)
-# ------------------------------
-printf "${BLUE}Running API tests with Ruby CbrainClient gem.${NC}\n"
-if echo "X$CBRAIN_SKIP_TEST_STAGES" | grep -q 'GemAPI' >/dev/null ; then
-  printf "${YELLOW} -> Skipped by request from env CBRAIN_SKIP_TEST_STAGES${NC}\n"
-else
-  cd $cb_test/BrainPortal            || die "Cannot cd to BrainPortal directory"
-  rake "db:seed:test:api" >/dev/null || die "Cannot re-seed the DB for API testing"
-  rails server puma -p 3000 -d       || die "Cannot start local puma server?"
-  cd test_api                        || die "Cannot cd to test_api directory?"
-  sleep 5 # must wait a bit for puma to be ready
-  rake "cbrain:test:api:client"           \
-    -v "${CBRAIN_GEM_TEST_VERBOSE_LEVEL}" \
-    ${CBRAIN_GEM_TEST_FILTER}             \
-    || fail_api_ruby="API testing with Ruby CbrainClient failed"
-  kill $(cat $cb_test/BrainPortal/tmp/pids/server.pid)
-fi
-
-
-
-# ------------------------------
-# Return status of both rspec
-# ------------------------------
-test -z "$fail_portal$fail_bourreau$fail_api_curl$fail_api_ruby" && exit 0  # Pangloss
-echo ""
-printf "${YELLOW}**** Summary of command failures ****${NC}\n"
-test -n "$fail_portal"   && printf "${RED}$fail_portal${NC}\n"
-test -n "$fail_bourreau" && printf "${RED}$fail_bourreau${NC}\n"
-test -n "$fail_api_curl" && printf "${RED}$fail_api_curl${NC}\n"
-test -n "$fail_api_ruby" && printf "${RED}$fail_api_ruby${NC}\n"
-printf "${YELLOW}**** --------------------------- ****${NC}\n"
-echo ""
-exit 2
-
diff --git a/Travis/templates/config_portal.rb.TEST b/Travis/templates/config_portal.rb.TEST
deleted file mode 100644
index d27861229..000000000
--- a/Travis/templates/config_portal.rb.TEST
+++ /dev/null
@@ -1,13 +0,0 @@
-
-#
-# CBRAIN Project
-#
-# Configuration file for BrainPortal.
-# This is file is used within a docker
-# container for running the test suite.
-#
-
-class CBRAIN
-  CBRAIN_RAILS_APP_NAME = "CbrainPortalTravisTesting"
-end
-
diff --git a/Travis/templates/database.yml.TEST b/Travis/templates/database.yml.TEST
deleted file mode 100644
index 4e19a77f0..000000000
--- a/Travis/templates/database.yml.TEST
+++ /dev/null
@@ -1,16 +0,0 @@
-
-#
-# CBRAIN Project
-#
-# DB configuration file for BrainPortal.
-# This is file is used within a docker
-# container for running the test suite.
-#
-
-test:
-  adapter: mysql2
-  host: localhost
-  username: cb_user
-  database: cb_db_test
-  password: cbpw12345
-  encoding: utf8
diff --git a/Travis/travis_ci.sh b/Travis/travis_ci.sh
deleted file mode 100755
index b524ac98f..000000000
--- a/Travis/travis_ci.sh
+++ /dev/null
@@ -1,93 +0,0 @@
-#!/bin/bash
-
-###############################################################################
-#                                                                             #
-# This script is used by Travis CI (https://travis-ci.org/) to run the        #
-# CBRAIN test suite.                                                          #
-#                                                                             #
-# The script expects a testing docker container to already have been built    #
-# and made available from the local system. The name of that docker image is  #
-# expected in the environment variable $CBRAIN_CI_IMAGE_NAME, or given as a   #
-# first argument to the script.                                               #
-#                                                                             #
-# This script does the following:                                             #
-#   - Invoke the container which runs the test suite                          #
-#   - Wait for the container to finish, dumping its logs on the way           #
-#   - Returns the return code (and possibly diagnostics) of the suite.        #
-#                                                                             #
-###############################################################################
-
-# Terminal colors, using ANSI sequences.
-RED='\033[31m'
-GREEN='\033[32m'
-MAGENTA='\033[35m'
-NC='\033[0m'
-
-# Do we even have a Travis+Docker environment set up ?
-if test ! -d Travis ; then
-  printf "${RED}No 'Travis' subdirectory found.${NC}\n"
-  echo "Please invoke this program from the root of the CBRAIN project."
-  exit 2 # config error
-fi
-cbrain_travis="`pwd -P`" # Root of where the code to test is located.
-cd Travis || exit 2
-
-# Do we have a docker image name to run?
-CBRAIN_CI_IMAGE_NAME=${CBRAIN_CI_IMAGE_NAME:-$1} # can be given as argument
-if test "X$CBRAIN_CI_IMAGE_NAME" = "X" ; then
-  printf "${RED}No CBRAIN_CI_IMAGE_NAME environment variable supplied.${NC}\n"
-  exit 2 # config error
-fi
-
-# Count time
-SECONDS=0 # bash is great
-
-# Run the docker containers
-printf "${MAGENTA}Launching CBRAIN test container at %s ${NC}\n" "$(date '+%F %T')"
-
-# Note: to skip stages, set CBRAIN_SKIP_TEST_STAGES to
-# one or several of the keywords 'RspecPortal', 'RspecBourreau',
-# 'CurlAPI' or 'GemAPI', joined by commas or periods.
-docker_name="cb_travis" # pretty name of the process
-docker run -d \
-           --env CBRAIN_SKIP_TEST_STAGES        \
-           --env CBRAIN_CURL_TEST_VERBOSE_LEVEL \
-           --env CBRAIN_CURL_TEST_FILTER        \
-           --env CBRAIN_GEM_TEST_VERBOSE_LEVEL  \
-           --env CBRAIN_GEM_TEST_FILTER         \
-           -v "$cbrain_travis":/home/cbrain/cbrain_travis \
-           --name "$docker_name" \
-           ${CBRAIN_CI_IMAGE_NAME} | perl -ne 'print unless /^[0-9a-f]{64}\n$/'
-if [ $? -ne 0 ] ; then
-  printf "${RED}Docker Start Failed. So sorry.${NC}\n"
-  exit 10 # partial abomination
-fi
-
-# Print logs (always, by request).
-# Also Travis CI will abort the test if nothing is printed for too long.
-echo ""
-printf "${MAGENTA}==== Docker logs start here ====${NC}\n"
-docker logs ${docker_name} --follow
-printf "${MAGENTA}==== Docker logs end here ====${NC}\n"
-echo ""
-test_exit_code=$(docker wait ${docker_name})
-docker rm ${docker_name} >/dev/null || true
-printf "${MAGENTA}Docker container finished after $SECONDS seconds.${NC}\n"
-echo ""
-
-# Final Results
-if [ "X$test_exit_code" != "X0" ] ; then
-  printf "${RED}===================================================${NC}\n"
-  printf "${RED}Tests Failed${NC} - 'docker wait' exit code: $test_exit_code\n"
-  printf "${RED}===================================================${NC}\n"
-  exit 20 # total abomination
-fi
-
-# Yippee.
-printf "${GREEN}===================================================${NC}\n"
-printf "${GREEN}All tests Passed${NC}\n"
-printf "${GREEN}===================================================${NC}\n"
-
-# Important, eh, oh, not kidding here.
-exit 0
-
diff --git a/cbrain_file_revisions.csv b/cbrain_file_revisions.csv
index a53a15cbd..a9d46ac4f 100644
--- a/cbrain_file_revisions.csv
+++ b/cbrain_file_revisions.csv
@@ -1,10 +1,9 @@
-6.2.0 -#- 2022-01-28 14:28:08 -0500 -#- CBRAIN Team -#- __CBRAIN_TAG__
-fc85bf12a645af586c914e24ba1badd087377ac1 -#- 2022-01-28 11:50:17 -0500 -#- Pierre Rioux -#- __CBRAIN_HEAD__
+6.3.0 -#- 2023-01-26 14:22:35 -0500 -#- CBRAIN Team -#- __CBRAIN_TAG__
+966ca2b5fadee53078e654705ea6bd8340cb3d2b -#- 2023-01-26 14:09:50 -0500 -#- Pierre Rioux -#- __CBRAIN_HEAD__
 5b22b5d61971a45646ded4ff502025ce5a83eaa8 -#- 2019-07-04 14:12:52 -0400 -#- Shawn T. Brown -#- .github/CODE_OF_CONDUCT.md
-9dec9e0176b34764197d134ba1dc6f61499012f9 -#- 2021-02-12 13:05:13 -0500 -#- Pierre Rioux -#- .github/workflows/cbrain_ci.yaml
+69c1caadd61820cfedd9c44cf247ab6a4f7812ee -#- 2023-01-17 17:06:54 -0500 -#- Pierre Rioux -#- .github/workflows/cbrain_ci.yaml
 1b38ded2d16ee2b163149d0ae9bea35afdef47bd -#- 2021-01-21 10:06:59 -0500 -#- Pierre Rioux -#- .github/workflows/scripts/make_cbrain_app_name_rb.sh
 1b38ded2d16ee2b163149d0ae9bea35afdef47bd -#- 2021-01-21 10:06:59 -0500 -#- Pierre Rioux -#- .github/workflows/scripts/make_database_yml.sh
-1d321c6d4efcf45aea7898104ebd6b9378f69717 -#- 2021-01-21 10:47:46 -0500 -#- Pierre Rioux -#- .travis.yml.old
 81add9599705a5219617814a4fec5cb023004cf9 -#- 2017-12-07 19:19:03 -0500 -#- Pierre Rioux -#- Bourreau/.gitignore
 4ed47fcc8c35e42a8831de5d67bdf7a18a1e7d9d -#- 2016-12-02 17:53:51 -0500 -#- Pierre Rioux -#- Bourreau/.rspec
 58fc182e0053dd048659744080645af2eedae126 -#- 2020-03-10 16:42:40 -0400 -#- Pierre Rioux -#- Bourreau/Gemfile
@@ -30,8 +29,10 @@ e1908309c4ddae35b28c0170b696744b87833e6d -#- 2020-12-07 16:09:34 -0500 -#- Pierr
 d8351b666a97a4eefbb2768c8cc785d8cc968e46 -#- 2009-08-03 22:56:02 +0000 -#- prioux -#- Bourreau/app/models/active_record_log.rb
 9159ab6b65ee5f1cdc673bb8586e2c3d5ae3fb8a -#- 2012-04-16 18:30:37 -0400 -#- Tarek Sherif -#- Bourreau/app/models/admin_user.rb
 04c513d423b42a856c4493f105465b16bef3feeb -#- 2018-02-01 16:21:32 -0500 -#- Pierre Rioux -#- Bourreau/app/models/application_record.rb
+dc14b6bc410b3a77a20e409815c9cd93e55cd2c7 -#- 2022-06-21 12:47:44 -0400 -#- Pierre Rioux -#- Bourreau/app/models/automated_user.rb
 0765162a23b328e9f2cdea637f8bdaba242cb370 -#- 2009-07-08 15:24:14 +0000 -#- prioux -#- Bourreau/app/models/bourreau.rb
-b43298eb375d0754efac4a77e425610238fe8ea3 -#- 2019-09-10 14:53:58 -0400 -#- Pierre Rioux -#- Bourreau/app/models/bourreau_worker.rb
+8d67b48924a8f2dde0ce4ac5160b091007023e37 -#- 2022-06-28 13:13:44 -0400 -#- Pierre Rioux -#- Bourreau/app/models/bourreau_worker.rb
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 4ae88132ae49c202d5363fe1648d1f4861c81920 -#- 2015-04-29 16:40:11 -0400 -#- Natacha Beck -#- BrainPortal/spec/models/brain_portal_spec.rb
 b0c034565dc45e84f9a61175d82c49c103a33e0a -#- 2017-12-07 19:19:05 -0500 -#- Pierre Rioux -#- BrainPortal/spec/models/cbrain_session_spec.rb
 233bedc7abd20df4500e4edf039f105f4a14f567 -#- 2016-06-20 14:47:22 -0400 -#- Andrew Doyle -#- BrainPortal/spec/models/cbrain_task_spec.rb
@@ -1339,7 +1389,7 @@ b0c034565dc45e84f9a61175d82c49c103a33e0a -#- 2017-12-07 19:19:05 -0500 -#- Pierr
 53a10b65e54e72386777a9effb0370ebf9ad2c86 -#- 2017-12-07 19:19:01 -0500 -#- Natacha Beck -#- BrainPortal/spec/models/en_cbrain_local_data_provider_spec.rb
 4ae88132ae49c202d5363fe1648d1f4861c81920 -#- 2015-04-29 16:40:11 -0400 -#- Natacha Beck -#- BrainPortal/spec/models/en_cbrain_smart_data_provider_spec.rb
 64be7b629b38b421828ec9175374b52f5c1980b0 -#- 2020-03-10 18:35:39 -0400 -#- Pierre Rioux -#- BrainPortal/spec/models/en_cbrain_ssh_data_provider_spec.rb
-7cfa5c2a0fd77b5c386ad0b212f422527d83f0e1 -#- 2020-04-11 12:34:41 -0400 -#- Pierre Rioux -#- BrainPortal/spec/models/file_collection_spec.rb
+a0e192db0583bac2ce5942558ffaefeb085243c4 -#- 2022-03-18 11:33:10 -0400 -#- Natacha Beck -#- BrainPortal/spec/models/file_collection_spec.rb
 7cfa5c2a0fd77b5c386ad0b212f422527d83f0e1 -#- 2020-04-11 12:34:41 -0400 -#- Pierre Rioux -#- BrainPortal/spec/models/file_info_spec.rb
 925b9ec5790a125abf7c53eaf10f7de4fd42c02f -#- 2017-12-07 19:18:42 -0500 -#- Natacha Beck -#- BrainPortal/spec/models/flat_dir_local_data_provider_spec.rb
 af4c4ee7161b371b63740a95926c30adf08e7c69 -#- 2020-03-04 13:30:14 -0500 -#- Natacha Beck -#- BrainPortal/spec/models/group_spec.rb
@@ -1348,7 +1398,7 @@ af4c4ee7161b371b63740a95926c30adf08e7c69 -#- 2020-03-04 13:30:14 -0500 -#- Natac
 a18d0ebf4c40f6030dd233f2810ee2da9cf4b104 -#- 2018-11-06 18:33:45 -0500 -#- Pierre Rioux -#- BrainPortal/spec/models/params_errors_spec.rb
 a946d8ac3d0e19768e08b4137be79a6daa041560 -#- 2021-08-05 18:30:49 -0400 -#- Pierre Rioux -#- BrainPortal/spec/models/portal_task_spec.rb
 2abdc9daec787bc883f6d261432afeb9f7f3a5b2 -#- 2021-08-22 19:55:28 -0400 -#- Pierre Rioux -#- BrainPortal/spec/models/remote_resource_info_spec.rb
-ad7428f4d166daf281e6714c1fe28ffb554362fd -#- 2019-10-08 12:08:40 -0400 -#- Natacha Beck -#- BrainPortal/spec/models/remote_resource_spec.rb
+ea973f14d98d8bfe5af9f9b8a658a7371b7d7e9e -#- 2022-10-14 10:36:32 -0400 -#- Natacha Beck -#- BrainPortal/spec/models/remote_resource_spec.rb
 785d73ae1ecbc13e4afbde38d457d1ce4debf71d -#- 2021-08-02 16:52:22 -0400 -#- Pierre Rioux -#- BrainPortal/spec/models/restricted_hash_spec.rb
 4ae88132ae49c202d5363fe1648d1f4861c81920 -#- 2015-04-29 16:40:11 -0400 -#- Natacha Beck -#- BrainPortal/spec/models/single_file_spec.rb
 4ae88132ae49c202d5363fe1648d1f4861c81920 -#- 2015-04-29 16:40:11 -0400 -#- Natacha Beck -#- BrainPortal/spec/models/site_spec.rb
@@ -1356,7 +1406,7 @@ ad7428f4d166daf281e6714c1fe28ffb554362fd -#- 2019-10-08 12:08:40 -0400 -#- Natac
 4ae88132ae49c202d5363fe1648d1f4861c81920 -#- 2015-04-29 16:40:11 -0400 -#- Natacha Beck -#- BrainPortal/spec/models/system_group_spec.rb
 da3c5b4347357824167d4ebc3519aecc112fc297 -#- 2019-06-12 11:27:46 -0400 -#- Pierre Rioux -#- BrainPortal/spec/models/tag_spec.rb
 d7a8f5649874a35aae0d95641869d553d0b3f8d7 -#- 2019-05-14 12:40:03 -0400 -#- Pierre Rioux -#- BrainPortal/spec/models/task_custom_filter_spec.rb
-f81239b0450627d83286b438d1fcb3ae5af1a598 -#- 2016-08-18 11:19:43 -0400 -#- Pierre Rioux -#- BrainPortal/spec/models/tool_config_spec.rb
+f176c35d273d4df414595aedb30ce7af9370c92c -#- 2023-01-12 17:15:09 -0500 -#- Serge -#- BrainPortal/spec/models/tool_config_spec.rb
 da3c5b4347357824167d4ebc3519aecc112fc297 -#- 2019-06-12 11:27:46 -0400 -#- Pierre Rioux -#- BrainPortal/spec/models/tool_spec.rb
 7f9644d1f4b6a900b7c594fd3091c3eb248c5a73 -#- 2020-04-09 12:33:28 -0400 -#- Pierre Rioux -#- BrainPortal/spec/models/user_spec.rb
 d7a8f5649874a35aae0d95641869d553d0b3f8d7 -#- 2019-05-14 12:40:03 -0400 -#- Pierre Rioux -#- BrainPortal/spec/models/userfile_custom_filter_spec.rb
@@ -1368,7 +1418,7 @@ af4c4ee7161b371b63740a95926c30adf08e7c69 -#- 2020-03-04 13:30:14 -0500 -#- Natac
 53a10b65e54e72386777a9effb0370ebf9ad2c86 -#- 2017-12-07 19:19:01 -0500 -#- Natacha Beck -#- BrainPortal/spec/modules/act_rec_meta_data_spec.rb
 4ae88132ae49c202d5363fe1648d1f4861c81920 -#- 2015-04-29 16:40:11 -0400 -#- Natacha Beck -#- BrainPortal/spec/modules/cbrain_deep_clone_spec.rb
 233bedc7abd20df4500e4edf039f105f4a14f567 -#- 2016-06-20 14:47:22 -0400 -#- Andrew Doyle -#- BrainPortal/spec/modules/core_models_spec.rb
-d7a41d6bec9ffe35217c213c50dc85b80fa26717 -#- 2021-02-12 12:27:08 -0500 -#- Pierre Rioux -#- BrainPortal/spec/modules/github_ci_spec.rb
+5a499240b042520db2f8068d4f1ca71d2ba559a2 -#- 2022-10-03 15:16:27 -0400 -#- Natacha Beck -#- BrainPortal/spec/modules/github_ci_spec.rb
 dc2eaf46e933770354e47c8eb49ead6b6a14ae81 -#- 2019-05-17 15:12:30 -0400 -#- Pierre Rioux -#- BrainPortal/spec/modules/resource_access_spec.rb
 233bedc7abd20df4500e4edf039f105f4a14f567 -#- 2016-06-20 14:47:22 -0400 -#- Andrew Doyle -#- BrainPortal/spec/modules/ssh_agent_spec.rb
 53a10b65e54e72386777a9effb0370ebf9ad2c86 -#- 2017-12-07 19:19:01 -0500 -#- Natacha Beck -#- BrainPortal/spec/modules/view_scopes_spec.rb
@@ -1625,16 +1675,8 @@ c184bd8f84d7984c04b7581a61a6b3abc8f8c5bd -#- 2017-08-23 14:26:13 -0400 -#- Pierr
 df3e2af099c3247e5b7c350de3afc8f99b0253d8 -#- 2012-01-25 13:10:16 -0500 -#- Pierre Rioux -#- LICENSE.txt
 495db4c873eeb3294c04187047ce1c3a1ffc6a0e -#- 2020-09-23 11:54:45 -0400 -#- MontrealSergiy -#- NEUROHUB_README.md
 1b38ded2d16ee2b163149d0ae9bea35afdef47bd -#- 2021-01-21 10:06:59 -0500 -#- Pierre Rioux -#- README.md
-2bb36b003cc7ae98fe9d7017d399c7270ac27025 -#- 2021-02-26 15:51:43 -0500 -#- Pierre Rioux -#- Release-Notes.md
-2ad7e18a2361df9fa2fc5a880cae6f32205775a8 -#- 2020-03-10 17:33:32 -0400 -#- Pierre Rioux -#- Travis/Dockerfile.travis
-daa19ab96f0a6463c004742a8d4b0f42b3b3fe05 -#- 2017-04-11 14:32:59 -0400 -#- Pierre Rioux -#- Travis/README.md
-c4e436410858283f3ed06eaf65a52d1935253175 -#- 2019-06-12 12:49:49 -0400 -#- Pierre Rioux -#- Travis/bootstrap.sh
-aab7619bf65c941f03c5f944779bf31554b80f2f -#- 2016-11-26 19:35:28 -0500 -#- Pierre Rioux -#- Travis/build_container.sh
-0c218fa79ac0b288d421141c2c86554e74721639 -#- 2020-04-22 10:46:06 -0400 -#- Pierre Rioux -#- Travis/cb_run_tests.sh
-aab7619bf65c941f03c5f944779bf31554b80f2f -#- 2016-11-26 19:35:28 -0500 -#- Pierre Rioux -#- Travis/templates/config_portal.rb.TEST
-aab7619bf65c941f03c5f944779bf31554b80f2f -#- 2016-11-26 19:35:28 -0500 -#- Pierre Rioux -#- Travis/templates/database.yml.TEST
-22d7196f7fdaf23c990a450599f360d957308c34 -#- 2019-09-03 14:36:24 -0400 -#- Pierre Rioux -#- Travis/travis_ci.sh
-2e9aaa24b00460d88f774be8016d3a6477e7faad -#- 2021-02-26 10:20:23 -0500 -#- Pierre Rioux -#- cbrain_file_revisions.csv
+c2aec28d58e19e80e8fcc36ce5087aa40fd7d020 -#- 2022-01-28 14:33:02 -0500 -#- Pierre Rioux -#- Release-Notes.md
+c2aec28d58e19e80e8fcc36ce5087aa40fd7d020 -#- 2022-01-28 14:33:02 -0500 -#- Pierre Rioux -#- cbrain_file_revisions.csv
 6eff5f304c4f97b994d8b6f72992ceaba9516b3b -#- 2021-08-02 16:36:36 -0400 -#- Pierre Rioux -#- license_header.txt
 a7e0e34d6dbe195cdc06d7bd183bb56f164436db -#- 2016-08-14 14:37:17 -0400 -#- Pierre Rioux -#- script/README.md
 2bb36b003cc7ae98fe9d7017d399c7270ac27025 -#- 2021-02-26 15:51:43 -0500 -#- Pierre Rioux -#- script/gen_local_rev_csv.sh
diff --git a/license_header.txt b/license_header.txt
index 9401f3778..219662d7e 100644
--- a/license_header.txt
+++ b/license_header.txt
@@ -1,7 +1,7 @@
 #
 # CBRAIN Project
 #
-# Copyright (C) 2008-2021
+# Copyright (C) 2008-2023
 # The Royal Institution for the Advancement of Learning
 # McGill University
 #
diff --git a/script/update_cb_all.sh b/script/update_cb_all.sh
index 5e4d081e1..ae524840e 100755
--- a/script/update_cb_all.sh
+++ b/script/update_cb_all.sh
@@ -11,9 +11,9 @@ function usage {
 
 This is CBRAIN's $0 version $VERSION by Pierre Rioux
 
-Usage: $0 [-v] [-[1234567]] path_to_portal_or_bourreau
+Usage: $0 [-v] [[-|+][1234567]] path_to_portal_or_bourreau
 
-This script will attempt to update all the GIT repository for a CBRAIN
+This script will attempt to update all the GIT repositories for a CBRAIN
 installation, including those in the plugins. It has to be invoked
 with a single argument, the path to either the BrainPortal or the Bourreau
 directory of the CBRAIN distribution. For a portal installation,
@@ -31,21 +31,29 @@ These are the steps that are performed:
 
 A) for both Bourreau and BrainPortal:
 
-  - git pull of the main CBRAIN repo
-  - git pull of each installed plugins
-  - bundle install
-  - rake cbrain:plugins:clean:all
-  - rake cbrain:plugins:install:all
+  1 - git pull of the main CBRAIN repo
+  2 - git pull of each installed plugins
+  3 - bundle install
+  4 - rake cbrain:plugins:clean:all
+    - rake cbrain:plugins:install:all
 
 B) for BrainPortal only:
 
-  - rake db:migrate
-  - rake db:sanity:check
-  - rake assets:precompile
-  - chmod -R a+rX BrainPortal/public
+  5 - rake db:migrate
+  6 - rake db:sanity:check
+  7 - rake assets:precompile
+    - chmod -R a+rX BrainPortal/public
 
 Note: you might have to set your RAILS_ENV environment variable
 for the rake tasks to work properly.
+
+With option -v, the outputs of the commands run will be shown.
+
+With option -N, where N is a number between 1 and 7, the script
+will run be starting from step N.
+
+With option +N, where N is a number between 1 and 7, the script
+will run ONLY the step N.
 USAGE
   exit 20
 }
@@ -58,8 +66,11 @@ USAGE
 verbose=""
 test $# -gt 0 && test "X$1" == "X-v" && shift && verbose="1"
 
+# Which steps to execute
+skipto="1"   # first step to execute
+stopat="99"  # last step to execute
+
 # With a -number in argument, will skip to that step
-skipto="1"
 if test $# -gt 0 ; then
   if test "X$1" = "X-1" -o "X$1" = "X-2" -o "X$1" = "X-3" -o \
           "X$1" = "X-4" -o "X$1" = "X-5" -o "X$1" = "X-6" -o \
@@ -69,6 +80,17 @@ if test $# -gt 0 ; then
   fi
 fi
 
+# With a +number in argument, execute ONLY that step
+if test $# -gt 0 ; then
+  if test "X$1" = "X+1" -o "X$1" = "X+2" -o "X$1" = "X+3" -o \
+          "X$1" = "X+4" -o "X$1" = "X+5" -o "X$1" = "X+6" -o \
+          "X$1" = "X+7" ; then # I'm too lazy to check with regex
+    skipto=$( echo "$1" | tr -d + )
+    stopat=$skipto
+    shift
+  fi
+fi
+
 # Verify we have a path to a CBRAIN install
 if test $# -ne 1 ; then
   usage
@@ -126,19 +148,21 @@ function runcapture {
 # ACTUAL UPDATE STEPS
 #============================================================================
 
-if test -z "$skipto" -o "$skipto" -le "1" ; then
+step=1
+if test $step -ge $skipto -a $step -le $stopat ; then
 
-Step 1: GIT Update CBRAIN Base
-runcapture "git pull"
+Step $step: GIT Update CBRAIN Base
+runcapture "git pull --verbose"
 runcapture "git fetch --tags"
 
 fi
 
 
 #============================================================================
-if test -z "$skipto" -o "$skipto" -le "2" ; then
+step=2
+if test $step -ge $skipto -a $step -le $stopat ; then
 
-Step 2: GIT Update CBRAIN Plugins
+Step $step: GIT Update CBRAIN Plugins
 pushd cbrain_plugins >/dev/null || exit
 for plugin in * ; do
   test ! -d "$plugin"                       && continue
@@ -147,7 +171,7 @@ for plugin in * ; do
   test ! -d "$plugin/.git"                  && continue
   echo " => $plugin"
   pushd "$plugin" >/dev/null || exit 20
-  runcapture "git pull"
+  runcapture "git pull --verbose"
   runcapture "git fetch --tags"
   popd >/dev/null || exit 20
 done
@@ -156,17 +180,19 @@ popd >/dev/null || exit 20
 fi
 
 #============================================================================
-if test -z "$skipto" -o "$skipto" -le "3" ; then
+step=3
+if test $step -ge $skipto -a $step -le $stopat ; then
 
-Step 3: Bundle Install
+Step $step: Bundle Install
 runcapture "bundle install"
 
 fi
 
 #============================================================================
-if test -z "$skipto" -o "$skipto" -le "4" ; then
+step=4
+if test $step -ge $skipto -a $step -le $stopat ; then
 
-Step 4: Re-install All Plugins
+Step $step: Re-install All Plugins
 test "$base" == "BrainPortal" && runcapture "rake cbrain:plugins:clean:all"
 test "$base" == "Bourreau"    && runcapture "rake cbrain:plugins:clean:plugins"
 test "$base" == "BrainPortal" && runcapture "rake cbrain:plugins:install:all"
@@ -175,10 +201,11 @@ test "$base" == "Bourreau"    && runcapture "rake cbrain:plugins:install:plugins
 fi
 
 #============================================================================
-if test -z "$skipto" -o "$skipto" -le "5" ; then
+step=5
+if test $step -ge $skipto -a $step -le $stopat ; then
 
 if test "$base" == "BrainPortal" ; then
-  Step 5: Database Migrations
+  Step $step: Database Migrations
   runcapture "rake db:migrate"
 fi
 
@@ -186,20 +213,22 @@ fi
 
 
 #============================================================================
-if test -z "$skipto" -o "$skipto" -le "6" ; then
+step=6
+if test $step -ge $skipto -a $step -le $stopat ; then
 
 if test "$base" == "BrainPortal" ; then
-  Step 6: Database Sanity Checks
+  Step $step: Database Sanity Checks
   runcapture "rake db:sanity:check"
 fi
 
 fi
 
 #============================================================================
-if test -z "$skipto" -o "$skipto" -le "7" ; then
+step=7
+if test $step -ge $skipto -a $step -le $stopat ; then
 
 if test "$base" == "BrainPortal" ; then
-  Step 7: Asset Compilations
+  Step $step: Asset Compilations
   runcapture "rake assets:precompile"
   runcapture "chmod -R a+rX public"
 fi