Merge branch 'dev'. This will become 4.2.0

Bourreau/Gemfile

@@ -32,6 +32,7 @@ gem "mysql2"
 gem "sys-proctable", :git => 'git://github.com/djberg96/sys-proctable.git'
 gem "thin"
 gem "pbkdf2-ruby"
+gem "json-schema"
 
 group :development, :test do
   gem "wirble"

Bourreau/config/application.rb

@@ -37,6 +37,10 @@ class Application < Rails::Application
     # Custom directories with classes and modules you want to be autoloadable.
     # config.autoload_paths += %W(#{config.root}/extras)
     config.autoload_paths += Dir["#{config.root}/lib"]
+    config.autoload_paths += Dir["#{config.root}/lib/cbrain_task_generators"]
+
+    # CBRAIN Plugins load paths: add directories for each Userfile model
+    config.autoload_paths += Dir[ * Dir.glob("#{config.root}/cbrain_plugins/installed-plugins/userfiles/*") ]
 
     # CBRAIN Plugins load paths: add directory for the CbrainTask models
     # This directory contains symbolic links to a special loader code
@@ -47,8 +51,14 @@ class Application < Rails::Application
     # properly set up all tasks installed from plugins (and the defaults tasks).
     config.autoload_paths += Dir["#{config.root}/cbrain_plugins/installed-plugins/cbrain_task"]
 
-    # CBRAIN Plugins load paths: add directories for each Userfile model
-    config.autoload_paths += Dir[ * Dir.glob("#{config.root}/cbrain_plugins/installed-plugins/userfiles/*") ]
+    # CBRAIN Plugins load paths: add directory for descriptor-based CbrainTask
+    # models. This directory, similarly to the one above, contains symbolic
+    # links to a special loader code which will call a task generator to
+    # generate the requested CbrainTask subclass on the fly.
+    #
+    # The rake task cbrain:plugins:install:all also takes care of creating the
+    # symlinks for this location.
+    config.autoload_paths += Dir["#{config.root}/cbrain_plugins/installed-plugins/cbrain_task_descriptors"]
 
     # Only load the plugins named here, in the order given (default is alphabetical).
     # :all can be used as a placeholder for all plugins not explicitly named.

Bourreau/lib/cbrain_task_generators

@@ -0,0 +1 @@
+../../BrainPortal/lib/cbrain_task_generators

BrainPortal/Gemfile

@@ -34,12 +34,16 @@ gem "sys-proctable", :git => 'git://github.com/djberg96/sys-proctable.git'
 gem "thin"
 gem "rails_autolink"
 gem "pbkdf2-ruby"
+gem "json-schema"
 gem "test-unit"
 
 group :development do
   gem "wirble"
   gem "looksee"
   gem "hirb"
+  gem "pry"
+  gem "pry-byebug"
+  gem "pry-doc"
 end
 
 group :test do

BrainPortal/app/controllers/application_controller.rb

@@ -34,7 +34,7 @@ class ApplicationController < ActionController::Base
 
   include AuthenticatedSystem
   include SessionHelpers
-  include BasicFilterHelpers
+  include ViewScopes
   include ViewHelpers
   include ApiHelpers
   include PermissionHelpers

BrainPortal/app/controllers/bourreaux_controller.rb

@@ -38,15 +38,13 @@ class BourreauxController < ApplicationController
   API_HIDDEN_ATTRIBUTES = [ :cache_md5 ]  # these are hidden back when APIs calls returns objects
 
   def index #:nodoc:
-    @filter_params["sort_hash"]["order"] ||= "remote_resources.type"
-    @filter_params["sort_hash"]["dir"]   ||= "DESC"
-    @header_scope   = RemoteResource.find_all_accessible_by_user(current_user)
-    @filtered_scope = base_filtered_scope @header_scope.includes(:user, :group)
-    @bourreaux      = base_sorted_scope @filtered_scope
+    @scope = scope_from_session('bourreaux')
+    scope_default_order(@scope, 'type')
 
-    if current_user.has_role? :admin_user
-      @filter_params['details'] = 'on' unless @filter_params.has_key?('details')
-    end
+    @base_scope = RemoteResource
+      .find_all_accessible_by_user(current_user)
+      .includes(:user, :group)
+    @bourreaux = @scope.apply(@base_scope)
 
     respond_to do |format|
       format.html

BrainPortal/app/controllers/custom_filters_controller.rb

@@ -94,11 +94,6 @@ def update #:nodoc:
   # DELETE /custom_filters/1.xml
   def destroy #:nodoc:
     @custom_filter = current_user.custom_filters.find(params[:id])
-    if @custom_filter.filtered_class_controller == "userfiles"
-      current_session[@custom_filter.filtered_class_controller.to_sym]["filter_custom_filters_array"].delete @custom_filter.id.to_s
-    else
-      current_session[@custom_filter.filtered_class_controller.to_sym]["filter_hash"].delete "custom_filter"
-    end
     @custom_filter.destroy
 
     flash[:notice] = "Custom filter '#{@custom_filter.name}' deleted."

BrainPortal/app/controllers/data_providers_controller.rb

@@ -36,15 +36,13 @@ class DataProvidersController < ApplicationController
   API_HIDDEN_ATTRIBUTES = [ :cloud_storage_client_identifier, :cloud_storage_client_token ]
 
   def index #:nodoc:
-    @filter_params["sort_hash"]["order"] ||= "data_providers.name"
+    @scope = scope_from_session('data_providers')
+    scope_default_order(@scope, 'name')
 
-    @header_scope   = DataProvider.find_all_accessible_by_user(current_user)
-    @filtered_scope = base_filtered_scope @header_scope.includes(:user, :group)
-    @data_providers = base_sorted_scope @filtered_scope
-
-    if current_user.has_role? :admin_user
-      @filter_params['details'] = 'on' unless @filter_params.has_key?('details')
-    end
+    @base_scope = DataProvider
+      .find_all_accessible_by_user(current_user)
+      .includes(:user, :group)
+    @data_providers = @scope.apply(@base_scope)
 
     respond_to do |format|
       format.html
@@ -291,12 +289,24 @@ def browse
       return
     end
 
-    @filter_params["browse_hash"] ||= {}
-    @per_page  = @filter_params["browse_hash"]["per_page"]
-    validate_pagination_values # validates @per_page and @current_page
-    as_user_id = params[:as_user_id].presence || @filter_params["browse_hash"]["as_user_id"].presence || current_user.id
-    @as_user   = current_user.available_users.where(:id => as_user_id).first || current_user
-    @filter_params["browse_hash"]["as_user_id"] = @as_user.id.to_s
+    # Load up the default scope for DP browsing and handle 'name_like'.
+    @scope = scope_from_session(default_scope_name)
+    scope_filter_from_params(@scope, :name_like, {
+      :attribute => 'name',
+      :operator  => 'match'
+    })
+
+    # Browsing as a different user? Make sure the target user is set.
+    @as_user = current_user
+      .available_users
+      .where(:id => (
+        params['as_user_id'] ||
+        @scope.custom['as_user_id'] ||
+        current_user.id
+      ))
+      .first
+    @as_user ||= current_user
+    @scope.custom['as_user_id'] = @as_user.id
 
     begin
       # [ base, size, type, mtime ]
@@ -362,22 +372,16 @@ def browse
 
     end
 
-    # Search by name
-    if @filter_params["browse_hash"]["name_like"].present?
-      search_term   = @filter_params["browse_hash"]["name_like"].to_s.downcase
-      @fileinfolist = @fileinfolist.select{|file| file.name.to_s.downcase.index(search_term)}
-    end
+    # Now that @fileinfolist is complete, apply @scope's elements and paginate
+    # before display.
+    @fileinfolist = @scope.apply(@fileinfolist)
 
-    @file_count   = @fileinfolist.count
-    unless request.format.to_sym == :xml || request.format.to_sym == :json
-      @fileinfolist = WillPaginate::Collection.create(@current_page, @per_page) do |pager|
-        pager.replace(@fileinfolist[(@current_page-1)*@per_page, @per_page] || [])
-        pager.total_entries = @file_count
-        pager
-      end
-    end
+    @scope.pagination ||= Scope::Pagination.from_hash({ :per_page => 25 })
+    @files = @scope.pagination.apply(@fileinfolist) unless
+      [:xml, :json].include?(request.format.to_sym)
 
-    current_session.save_preferences_for_user(current_user, :data_providers, :browse_hash)
+    scope_to_session(@scope)
+    current_session.save_preferences
 
     respond_to do |format|
       format.html
@@ -399,12 +403,16 @@ def browse
   # This method is (unfortunately) also used to unregister files, and delete them (on the browsable side)
   def register
     # TODO: refactor completely!
-    @provider  = DataProvider.find_accessible_by_user(params[:id], current_user)
+    @provider = DataProvider.find_accessible_by_user(params[:id], current_user)
 
-    @filter_params["browse_hash"] ||= {}
-    as_user_id = params[:as_user_id].presence || @filter_params["browse_hash"]["as_user_id"].presence || current_user.id
-    @as_user = current_user.available_users.where(:id => as_user_id).first || current_user
-    @filter_params["browse_hash"]["as_user_id"] = @as_user.id.to_s
+    scope      = scope_from_session('data_providers#browse')
+    @as_user   = current_user
+      .available_users
+      .where(:id => scope.custom['as_user_id'] ||= (
+        params['as_user_id'] || current_user.id
+      ))
+      .first
+    @as_user ||= current_user
 
     unless @provider.is_browsable?(current_user)
       flash[:error] = "You cannot register files from this provider."
@@ -648,11 +656,17 @@ def register
 
   # Report inconsistencies in the data provider.
   def report
+    @scope    = scope_from_session(default_scope_name)
     @provider = DataProvider.find(params[:id])
     @issues   = @provider.provider_report(params[:reload])
 
+    scope_default_order(@scope, :severity)
+    @scope.pagination ||= Scope::Pagination.from_hash({ :per_page => 25 })
+    @view_scope = @scope.apply(@issues, paginate: true)
+
     respond_to do |format|
-      format.html # report.html.erb
+      format.html
+      format.js
       format.xml  { render :xml  => { :issues => @issues } }
       format.json { render :json => { :issues => @issues } }
     end

BrainPortal/app/controllers/exception_logs_controller.rb

@@ -17,25 +17,29 @@
 # 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 <http://www.gnu.org/licenses/>.  
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 
 # Controller for viewing or managing exception logs.
 class ExceptionLogsController < ApplicationController
-  
+
   Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
 
-  before_filter :login_required 
+  before_filter :login_required
   before_filter :admin_role_required
 
   def index #:nodoc:
-    @filter_params["sort_hash"]["order"] ||= 'exception_logs.created_at'
-    @filter_params["sort_hash"]["dir"]   ||= 'DESC'
-    
-    @filtered_scope = base_filtered_scope
-    @exception_logs = base_sorted_scope(@filtered_scope).paginate(:page => @current_page, :per_page => @per_page)
+    @scope = scope_from_session('exception_logs')
+    scope_default_order(@scope, 'created_at', :desc)
+
+    @base_scope = ExceptionLog
+    @view_scope = @scope.apply(@base_scope)
 
-    current_session.save_preferences_for_user(current_user, :exception_logs, :per_page)
+    @scope.pagination ||= Scope::Pagination.from_hash({ :per_page => 50 })
+    @exception_logs = @scope.pagination.apply(@view_scope)
+
+    scope_to_session(@scope)
+    current_session.save_preferences
 
     respond_to do |format|
       format.html # index.html.erb
@@ -56,7 +60,7 @@ def show #:nodoc:
   def destroy #:nodoc:
     @exception_logs = ExceptionLog.find(params[:exception_log_ids])
     @exception_logs.each(&:destroy)
-    
+
     flash[:notice] = "#{view_pluralize(@exception_logs.count, "exception")} deleted."
 
     respond_to do |format|

BrainPortal/app/controllers/feedbacks_controller.rb

@@ -17,23 +17,23 @@
 # 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 <http://www.gnu.org/licenses/>.  
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 
 #RESTful controller for the Feedback resource.
 class FeedbacksController < ApplicationController
   before_filter :login_required
-  
+
   Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
-  
+
   # GET /feedbacks
   # GET /feedbacks.xml
   def index #:nodoc:
-    @filter_params["sort_hash"]["order"] ||= 'feedbacks.created_at'
-    @filter_params["sort_hash"]["dir"] ||= 'DESC'
-    
-    @filtered_scope = base_filtered_scope
-    @feedbacks      = base_sorted_scope @filtered_scope.includes(:user)
+    @scope = scope_from_session('feedbacks')
+    scope_default_order(@scope, 'created_at', :desc)
+
+    @base_scope = Feedback.includes(:user)
+    @feedbacks  = @scope.apply(@base_scope)
 
     respond_to do |format|
       format.js
@@ -106,7 +106,7 @@ def update #:nodoc:
   def destroy #:nodoc:
     @feedback = Feedback.find(params[:id])
     @feedback.destroy
-    
+
     respond_to do |format|
       format.html { redirect_to :action => :index, :status => 303 }
       format.js   { redirect_to :action => :index, :format => :js, :status => 303 }