From 7801df9be07dad2f5c6c4a6c680387a0b2772017 Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Thu, 23 Jul 2015 17:19:52 -0400
Subject: [PATCH 01/85] JSON task/tool descriptors (boutiques)

Main/initial implementation of JSON-based task/tool descriptor
integration. Allows adding tools (task types) by specifying a JSON
descriptor file (with a corresponding JSON schema) that describes the
tool's command-line interface.

The CbrainTask subclass generator either generates a set of Ruby files
suitable for further modification and inclusion as a plugin or
directly defines the task class to integrate the descriptor without
using source files.

The generated view templates (notably task_params) also sport a somewhat
fancier style than what is currently used.
---
 BrainPortal/Gemfile                           |   1 +
 BrainPortal/db/schema.rb                      |   2 +
 .../schema_task_generator.rb                  | 290 +++++++++++
 .../schemas/boutiques.schema.json             | 191 +++++++
 .../templates/bourreau.rb.erb                 | 343 +++++++++++++
 .../templates/edit_help.html.erb              |  91 ++++
 .../templates/portal.rb.erb                   | 299 +++++++++++
 .../templates/show_params.html.erb.erb        | 120 +++++
 .../templates/task_params.html.erb.erb        | 476 ++++++++++++++++++
 BrainPortal/public/stylesheets/cbrain.css     | 230 +++++++++
 10 files changed, 2043 insertions(+)
 create mode 100644 BrainPortal/lib/cbrain_task_generators/schema_task_generator.rb
 create mode 100644 BrainPortal/lib/cbrain_task_generators/schemas/boutiques.schema.json
 create mode 100644 BrainPortal/lib/cbrain_task_generators/templates/bourreau.rb.erb
 create mode 100644 BrainPortal/lib/cbrain_task_generators/templates/edit_help.html.erb
 create mode 100644 BrainPortal/lib/cbrain_task_generators/templates/portal.rb.erb
 create mode 100644 BrainPortal/lib/cbrain_task_generators/templates/show_params.html.erb.erb
 create mode 100644 BrainPortal/lib/cbrain_task_generators/templates/task_params.html.erb.erb

diff --git a/BrainPortal/Gemfile b/BrainPortal/Gemfile
index 6ccecd58f..58fb76b23 100644
--- a/BrainPortal/Gemfile
+++ b/BrainPortal/Gemfile
@@ -34,6 +34,7 @@ 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
diff --git a/BrainPortal/db/schema.rb b/BrainPortal/db/schema.rb
index 250b2fcdc..022f3e81b 100644
--- a/BrainPortal/db/schema.rb
+++ b/BrainPortal/db/schema.rb
@@ -315,6 +315,7 @@
     t.datetime "updated_at"
     t.integer  "group_id"
     t.integer  "ncpus"
+    t.string   "docker_image"
   end
 
   add_index "tool_configs", ["bourreau_id"], :name => "index_tool_configs_on_bourreau_id"
@@ -359,6 +360,7 @@
   add_index "userfiles", ["data_provider_id"], :name => "index_userfiles_on_data_provider_id"
   add_index "userfiles", ["group_id"], :name => "index_userfiles_on_group_id"
   add_index "userfiles", ["hidden", "id"], :name => "index_userfiles_on_hidden_and_id"
+  add_index "userfiles", ["hidden"], :name => "index_userfiles_on_hidden"
   add_index "userfiles", ["immutable", "id"], :name => "index_userfiles_on_immutable_and_id"
   add_index "userfiles", ["name"], :name => "index_userfiles_on_name"
   add_index "userfiles", ["type"], :name => "index_userfiles_on_type"
diff --git a/BrainPortal/lib/cbrain_task_generators/schema_task_generator.rb b/BrainPortal/lib/cbrain_task_generators/schema_task_generator.rb
new file mode 100644
index 000000000..511a65a98
--- /dev/null
+++ b/BrainPortal/lib/cbrain_task_generators/schema_task_generator.rb
@@ -0,0 +1,290 @@
+
+#
+# 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 <http://www.gnu.org/licenses/>.
+#
+
+require 'fileutils'
+
+# This module handles generation of CbrainTasks from schema and descriptor
+# files. The generated code can be added right away to CBRAIN's available tasks
+# or written to file for later modification.
+#
+# NOTE: Only JSON is currently supported
+module SchemaTaskGenerator
+
+  Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
+
+  # Represents a schema to validate task descriptors against
+  class Schema
+
+    # Creates a new Schema from either a file path, a string or a hash
+    # representing the schema.
+    def initialize(schema)
+      @schema = SchemaTaskGenerator.expand_json(schema)
+    end
+
+    # Validates +descriptor+ against the schema. Returns a list of validation
+    # errors or nil if +descriptor+ is valid.
+    def validate(descriptor)
+      JSON::Validator.fully_validate(
+        @schema,
+        SchemaTaskGenerator.expand_json(descriptor),
+        :errors_as_objects => true
+      )
+    end
+
+    # Same as +validate+, but throws exceptions on validation errors instead.
+    # Still returns nil if +descriptor+ is valid.
+    def validate!(descriptor)
+      JSON::Validator.validate!(
+        @schema,
+        SchemaTaskGenerator.expand_json(descriptor),
+        :errors_as_objects => true
+      )
+    end
+
+    # A Schema essentially behaves like a hash, as to allow accessing schema
+    # properties. Forwards all other unknown method calls to Hash, if they
+    # exist.
+    def method_missing(method, *args) #:nodoc:
+      if @schema.respond_to?(method)
+        @schema.send(method, *args)
+      else
+        super
+      end
+    end
+
+  end
+
+  # Encapsulates a CbrainTask generated by this generator
+  class GeneratedTask
+
+    # Name of the generated class. Usually a camel-case form
+    # of descriptor[:name].
+    attr_accessor :name
+    # Descriptor used to generate this task, in hash form.
+    attr_accessor :descriptor
+    # Schema instance used to generate this task.
+    attr_accessor :schema
+    # Validation errors produced when validating the task's descriptor, if any.
+    attr_accessor :validation_errors
+    # Generated Ruby/HTML source for this task. Hash with at least the keys:
+    # [:portal]      BrainPortal side task class Ruby source. Contains a class
+    #                inheriting/implementing PortalTask.
+    # [:bourreau]    Bourreau side task class Ruby source. Contains a class
+    #                inheriting/implementing ClusterTask.
+    # [:task_params] Ruby ERB form template for the task's params (edit) page.
+    # [:show_params] Ruby ERB template for the task's show page.
+    # [:edit_help]   Ruby ERB template for the task's parameter help popup.
+    attr_accessor :source
+
+    # Create a new encapsulated generated CbrainTask from the output of the
+    # generator (+SchemaTaskGenerator+::+generate+ method). +attributes+ is
+    # expected to be a hash matching this object's attributes (:source, :name,
+    # :descriptor, etc.)
+    def initialize(attributes)
+      attributes.each do |name, value|
+        instance_variable_set("@#{name}", value)
+      end
+    end
+
+    # Integrates the encapsulated CbrainTask in this CBRAIN installation.
+    # Unless +register+ is specified to be false, this method will add the
+    # required Tool and ToolConfig if necessary for the CbrainTask to be
+    # useable right away (Since almost all information required to make the
+    # Tool and ToolConfig objects is available in the spec).
+    def integrate(register = true)
+      # As the same code is used to dynamically load tasks descriptors and
+      # create task templates, the class definitions are generated as strings
+      # (Otherwise the source wouldn't be available to write down the generated
+      # templates). This forces the use of eval instead of the much nicer,
+      # faster and easier to maintain alternatives. :(
+      eval @source[Rails.root.to_s =~ /BrainPortal$/ ? :portal : :bourreau]
+
+      # Try and retrieve the just-generated task class
+      task   = @name.camelize.constantize rescue nil
+      task ||= "CbrainTask::#{@name.camelize}".constantize
+
+      # Since the task class doesn't have a matching cbrain_plugins directory
+      # tree, some methods need to be added/redefined to ensure the cooperation
+      # of views and controllers.
+      generated = self
+
+      # The task class has no public_path.
+      task.define_singleton_method(:public_path)    { |public_file| nil }
+
+      # Make sure the task class still has access to its generated source
+      task.define_singleton_method(:generated_from) { generated }
+
+      # Offer access to the raw string version of the view partials for use
+      # in views instead of the cbrain_plugins paths.
+      task.define_singleton_method(:raw_partial) do |partial|
+        ({
+          :task_params => generated.source[:task_params],
+          :show_params => generated.source[:show_params],
+          :edit_help   => generated.source[:edit_help]
+        })[partial];
+      end
+
+      return unless register
+
+      # With the task class and descriptor, we have enough information to
+      # generate a Tool and ToolConfig to register the tool into CBRAIN.
+      # The newly created Tool and ToolConfig (if needed) will initially belong
+      # to the core admin.
+
+      # Create and save a new Tool for this task, unless theres already one.
+      Tool.new(
+        :name              => @descriptor['name'],
+        :user_id           => User.admin.id,
+        :group_id          => User.admin.own_group.id,
+        :category          => "scientific tool",
+        :cbrain_task_class => task.to_s,
+        :description       => @descriptor['description']
+      ).save! unless
+        Tool.exists?(:cbrain_task_class => task.to_s)
+
+      # Create and save a new ToolConfig for this task on this server, unless
+      # theres already one. Only applies to Bourreaux (as it would make no
+      # sense on the portal).
+      return if Rails.root.to_s =~ /BrainPortal$/
+
+      ToolConfig.new(
+        :tool_id      => task.tool.id,
+        :bourreau_id  => RemoteResource.current_resource.id,
+        :group_id     => Group.everyone.id,
+        :version_name => @descriptor['tool-version'],
+        :docker_image => @descriptor['docker-image']
+      ).save! unless
+        ToolConfig.exists?(
+          :tool_id      => task.tool.id,
+          :bourreau_id  => RemoteResource.current_resource.id,
+          :version_name => @descriptor['tool-version']
+        )
+    end
+
+    # Writes the encapsulated CbrainTask as a directory tree under +path+ under
+    # the CBRAIN plugin format;
+    #   source[:portal]      -> <task name>/portal/<task name>.rb
+    #   source[:bourreau]    -> <task name>/bourreau/<task name>.rb
+    #   source[:task_params] -> <task name>/views/_task_params.html.erb
+    #   source[:show_params] -> <task name>/views/_show_params.html.erb
+    #   source[:edit_help]   -> <task name>/views/public/edit_params_help.html
+    def to_directory(path)
+      name = @name.underscore
+      path = Pathname.new(path.to_s) + name
+
+      FileUtils.mkpath(path)
+      Dir.chdir(path) do
+        ['portal', 'bourreau', 'views/public'].each { |d| FileUtils.mkpath(d) }
+
+        IO.write("portal/#{name}.rb",                  @source[:portal])
+        IO.write("bourreau/#{name}.rb",                @source[:bourreau])
+        IO.write("views/_task_params.html.erb",        @source[:task_params])
+        IO.write("views/_show_params.html.erb",        @source[:show_params])
+        IO.write("views/public/edit_params_help.html", @source[:edit_help])
+      end
+    end
+
+  end
+
+  # Generates a CbrainTask from +descriptor+, which is expected to validate
+  # against +schema+. +schema+ is expected to be either a +Schema+ instance,
+  # a path to a schema file, the schema in string format or a hash
+  # representing the schema.
+  # Similarly to +schema+, +descriptor+ is expected to be either a path to a
+  # descriptor file, the descriptor in string format or a hash representing
+  # the descriptor.
+  # By default, the validation of +descriptor+ against +schema+ is strict
+  # and +generate+ will abort at any validation error. Set +strict_validation+
+  # to false if you wish for the generator to try and generate the task despite
+  # validation issues.
+  def self.generate(schema, descriptor, strict_validation = true)
+    descriptor = self.expand_json(descriptor)
+    name       = descriptor['name'].camelize
+    schema     = Schema.new(schema) unless schema.is_a?(Schema)
+    errors     = schema.send(
+      strict_validation ? :'validate!' : :validate,
+      descriptor
+    ) || []
+
+    apply_template = lambda do |template|
+      ERB.new(IO.read(
+        Rails.root.join('lib/cbrain_task_generators/templates', template).to_s
+      ), nil, '%<>>-').result(binding)
+    end
+
+    GeneratedTask.new(
+      :name              => name,
+      :descriptor        => descriptor,
+      :schema            => schema,
+      :validation_errors => errors,
+      :source            => {
+        :portal      => apply_template.('portal.rb.erb'),
+        :bourreau    => apply_template.('bourreau.rb.erb'),
+        :task_params => apply_template.('task_params.html.erb.erb'),
+        :show_params => apply_template.('show_params.html.erb.erb'),
+        :edit_help   => apply_template.('edit_help.html.erb')
+      },
+    )
+  end
+
+  # Utility method to convert a JSON string or file path into a hash.
+  # Returns the hash directly if a hash is given.
+  def self.expand_json(obj)
+    return obj unless obj.is_a?(String)
+
+    JSON.parse!(File.exists?(obj) ? IO.read(obj) : obj)
+  end
+
+  private
+
+  # Utility/helper methods used in templates.
+
+  # Create a function call formatter for +func+ with possible arguments lists
+  # +args+. The generated formatter will accept a list of arguments to format
+  # a call with. (formatter.(['a', 'b']) -> 'func(a, b)')
+  # If given, +block+ will be used to convert each value in +args+
+  # (and the argument passed to the generated function) to an argument list.
+  #
+  # Example:
+  #   a = [{ :a => 1, :b => 2 }, { :a => 2, :b => 4 }]
+  #   f = format_call('f', a) { |a| [ a[:a], a[:b] ] }
+  #   f.({ :a => 1, :b => 2}) # gives 'f(1, 2)'
+  def self.format_call(func, args, &block)
+    args = args.map { |a| block.(a) } if block
+
+    widths = (args.first rescue []).zip(*args).map do |array|
+      array.map { |v| v.length rescue 0 }.max + 1
+    end
+
+    lambda do |args|
+      inner = (block ? block.(args) : args)
+        .reject(&:blank?)
+        .each_with_index
+        .map { |v, i| "%-#{widths[i]}s" % (v + ',') }
+        .join(' ')
+        .gsub(/,\s*$/, '')
+
+      "#{func}(#{inner})"
+    end
+  end
+
+end
diff --git a/BrainPortal/lib/cbrain_task_generators/schemas/boutiques.schema.json b/BrainPortal/lib/cbrain_task_generators/schemas/boutiques.schema.json
new file mode 100644
index 000000000..0d3d3f501
--- /dev/null
+++ b/BrainPortal/lib/cbrain_task_generators/schemas/boutiques.schema.json
@@ -0,0 +1,191 @@
+{
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "id": "http://github.com/boutiques/boutiques-schema",
+    "type": "object",
+    "title": "Tool",
+    "properties": {
+	"name": {
+	    "id": "http://github.com/boutiques/boutiques-schema/name",
+	    "minLength": 1,
+	    "description": "Tool name.",
+	    "type": "string"
+	},
+	"tool-version": {
+	    "id": "http://github.com/boutiques/boutiques-schema/description",
+	    "minLength": 1,
+	    "description": "Tool version.",
+	    "type": "string"
+	},
+	"description": {
+	    "id": "http://github.com/boutiques/boutiques-schema/description",
+	    "minLength": 1,
+	    "description": "Tool description.",
+	    "type": "string"
+	},
+	"command-line": {
+	    "id": "http://github.com/boutiques/boutiques-schema/command-line",
+	    "minLength": 1,
+	    "description": "A string that describes the tool command line, where input and output values are identified by \"keys\". At runtime, command-line keys are substituted with flags and values.",
+	    "type": "string"
+	},
+	"docker-image": {
+	    "id": "http://github.com/boutiques/boutiques-schema/docker-image",
+	    "minLength": 1,
+	    "description": "Name of a Docker image where tool is installed and configured. Example: docker.io/neurodebian.",
+	    "type": "string"
+	},
+	"docker-index": {
+	    "id": "http://github.com/boutiques/boutiques-schema/docker-index",
+	    "minLength": 1,
+	    "description": "Docker index where Docker image is available.",
+	    "default": "http://index.docker.io",
+	    "type": "string"
+	},
+	"schema-version": {
+	    "id": "http://github.com/boutiques/boutiques-schema/schema-version",
+	    "type": "string",
+	    "description": "Version of the schema used.",
+	    "enum": ["0.2-snapshot"]
+	},
+	"inputs": {
+	    "id": "http://github.com/boutiques/boutiques-schema/inputs",
+	    "type": "array",
+	    "items": {
+		"id": "http://github.com/boutiques/boutiques-schema/input",
+		"type": "object",
+		"properties": {
+		    "id": {
+			"id": "http://github.com/boutiques/boutiques-schema/input/id",
+			"minLength": 1,
+			"description": "A short, unique, informative identifier containing only alphanumeric characters and underscores. Typically used to generate variable names. Example: \"data_file\".",
+			"type": "string",
+			"pattern": "^[0-9,_,a-z,A-Z]*$"
+		    },
+		    "name": {
+			"id": "http://github.com/boutiques/boutiques-schema/input/name",
+			"minLength": 1,
+			"description": "A human-readable input name. Example: 'Data file'.",
+			"type": "string"
+		    },
+		    "type": {
+			"id": "http://github.com/boutiques/boutiques-schema/input/type",
+			"type": "string",
+			"description": "Input type.",
+			"enum": ["String", "File", "Flag" , "Number" ]
+		    },
+		    "description": {
+			"id": "http://github.com/boutiques/boutiques-schema/input/description",
+			"minLength": 1,
+			"description": "Input description.",
+			"type": "string"
+		    },
+		    "command-line-key": {
+			"id": "http://github.com/boutiques/boutiques-schema/input/command-line-key",
+			"minLength": 1,
+			"description": "A string contained in command-line, substituted by the input value and/or flag at runtime.",
+			"type": "string"
+		    },
+		    "list": {
+			"id": "http://github.com/boutiques/boutiques-schema/input/list",
+			"description":"True if input is a list of value. An input of type \"Flag\" cannot be a list.",
+			"type": "boolean"
+		    },
+		    "optional":{
+			"id": "http://github.com/boutiques/boutiques-schema/input/optional",
+			"description": "True if input is optional.",
+			"type": "boolean"
+		    },
+		    "command-line-flag":{
+			"id": "http://github.com/boutiques/boutiques-schema/input/command-line-flag",
+			"minLength": 1,
+			"description": "Option flag of the input, involved in the command-line-key substitution. Inputs of type \"Flag\" have to have a command-line flag. Examples: -v, --force.",
+			"type": "string"
+		    },
+		    "default-value":{
+			"id": "http://github.com/boutiques/boutiques-schema/input/default-value",
+			"minLength": 1,
+			"description": "Default value of the input, used by the tool when no option is specified.",
+			"type": "string"
+		    }
+		},
+		"required": [
+		    "name",
+		    "id",
+		    "type"
+		]
+	    }
+	},
+	"output-files": {
+	    "id": "http://github.com/boutiques/boutiques-schema/output-files",
+	    "type": "array",
+	    "items": {
+		"id": "http://github.com/boutiques/boutiques-schema/output",
+		"type": "object",
+		"properties": {
+		    "id": {
+			"id": "http://github.com/boutiques/boutiques-schema/output/id",
+			"minLength": 1,
+			"description": "A short, unique, informative identifier containing only alphanumeric characters and underscores. Typically used to generate variable names. Example: \"data_file\"",
+			"pattern": "^[0-9,_,a-z,A-Z]*$",
+			"type": "string"
+		    },
+		    "name": {
+			"id": "http://github.com/boutiques/boutiques-schema/output/name",
+			"description": "A human-readable output name. Example: 'Data file'",
+			"minLength": 1,
+			"type": "string"
+		    },
+		    "description": {
+			"id": "http://github.com/boutiques/boutiques-schema/output/description",
+			"description": "Output description.",
+			"minLength": 1,
+			"type": "string"
+		    },
+		    "command-line-key": {
+			"id": "http://github.com/boutiques/boutiques-schema/output/command-line-key",
+			"description": "A string contained in command-line, substituted by the output value and/or flag at runtime.",
+			"minLength": 1,
+			"type": "string"
+		    },
+		    "path-template": {
+			"id": "http://github.com/boutiques/boutiques-schema/output/path-template",
+			"description": "Describes the output file path relatively to the execution directory. May contain input command-line-keys. Example: \"results/[INPUT1]_brain.mnc\".",
+			"minLength": 1,
+			"type": "string"
+		    },
+		    "list": {
+			"id": "http://github.com/boutiques/boutiques-schema/output/list",
+			"description": "True if output is a list of value.",
+			"type": "boolean"
+		    },
+		    "optional":{
+			"id": "http://github.com/boutiques/boutiques-schema/output/optional",
+			"description": "True if output may not be produced by the tool.",
+			"type": "boolean"
+		    },
+		    "command-line-flag":{
+			"id": "http://github.com/boutiques/boutiques-schema/output/command-line-flag",
+			"minLength": 1,
+			"description": "Option flag of the output, involved in the command-line-key substitution. Examples: -o, --output",
+			"type": "string"
+		    }
+		    
+		},
+		"required": [
+		    "id",
+		    "name",
+		    "path-template"
+		]
+	    }
+	}
+    },
+    "required": [
+	"name",
+	"description",
+	"command-line",
+	"schema-version",
+	"inputs",
+	"output-files"
+    ]
+}
+
diff --git a/BrainPortal/lib/cbrain_task_generators/templates/bourreau.rb.erb b/BrainPortal/lib/cbrain_task_generators/templates/bourreau.rb.erb
new file mode 100644
index 000000000..d7dc7eef2
--- /dev/null
+++ b/BrainPortal/lib/cbrain_task_generators/templates/bourreau.rb.erb
@@ -0,0 +1,343 @@
+
+#
+# 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 <http://www.gnu.org/licenses/>.
+#
+
+# NOTE: This is a working template generated from a descriptor:
+# [Schema]         <%= schema['id'] %>
+# [Schema version] <%= descriptor['schema-version'] %>
+# [Tool]           <%= descriptor['name'] %>
+# [Version]        <%= descriptor['tool-version'] || '?' %>
+# See the CbrainTask Programmer Guide (CBRAIN Wiki) for a more complete picture
+# of how CbrainTasks are constructed.
+% # NOTE: This template's weird indentation is there to try and make the
+% # generated code as legible as possible.
+
+# Bourreau-side CbrainTask subclass to launch <%= name %>
+class CbrainTask::<%= name %> < ClusterTask
+
+  Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
+
+  # Descriptor-based tasks are, by default, easily restartable and recoverable
+  include RestartableTask
+  include RecoverableTask
+
+% # Maximum width of a given +key+'s value in a +list+ of hashes
+% max_width = lambda do |list, key|
+%   list.map { |i| i[key].to_s.length rescue 0 }.max
+% end
+%
+% # Parameter groups
+% inputs   = descriptor['inputs'].dup
+% outputs  = descriptor['output-files'].dup
+% files    = inputs.select  { |i| i['type'] == 'File'   }
+% required = outputs.select { |o| ! o['optional']       }
+% globs    = outputs.select { |o| o['list']             }
+% in_keys  = inputs.select  { |i| i['command-line-key'] }
+% out_keys = outputs.select { |o| o['command-line-key'] }
+% flags    = (inputs + outputs).select { |p| p['command-line-flag'] }
+%
+  # Setup the cluster's environment to execute <%= name %>; create the relevant
+  # directories, prepare symlinks to input files, set environment variables,
+  # etc. Returns true if the task was correctly set up.
+  def setup #:nodoc:
+% unless files.empty?
+    params = self.params
+
+    # An error occured. Log +message+ and return false immediately.
+    retn  = Proc.new { |r| return r }
+    error = lambda do |message|
+      self.addlog(message)
+      retn.(false)
+    end
+
+    # Resolve all input userfiles IDs to their Userfile instances and set the
+    # results data provider if missing.
+%   resolve = format_call('resolve_file_parameter', files) { |file| [
+%     ":'#{file['id']}'",
+%     'error'
+%   ] }
+%   files.each do |file|
+    <%= resolve.(file) %>
+%   end
+
+    # And make them all available to <%= name %>
+%   make_available = format_call('make_available', files) { |file| [
+%     "params[:'#{file['id']}']",
+%     "'.'"
+%   ] }
+%   files.each do |file|
+    <%= make_available.(file) %>
+%   end
+
+% end
+    true
+  end
+
+  # The set of shell commands to run on the cluster to execute <%= name %>.
+  # Any output on stdout or stderr will be captured and logged for information
+  # or debugging purposes.
+  # Note that this function also generates the list of output filenames
+  # in params.
+  def cluster_commands #:nodoc:
+% if in_keys.empty? && out_keys.empty?
+%   unless outputs.empty?
+    # Output filenames
+    self.params.merge!({
+%     id_width = max_width.(outputs, 'id') + ":''".length
+%     outputs.each do |output|
+      <%=
+        "%-#{id_width}s => %s" % [
+          ":'#{output['id']}'",
+          "'#{output['path-template']}',"
+        ]
+      %>
+%     end
+    })
+
+%   end
+    # Command-line
+    [ '<%= descriptor['command-line'] %>' ]
+% else
+    params = self.params
+
+    # <%= name %>'s command line and output file names is constructed from a
+    # set of key-value pairs (keys) which are substituted in the command line
+    # and output templates. For example, if we have { '[1]' => '5' } for keys,
+    # a command line such as "foo [1] -e [1]" would turn into "foo 5 -e 5".
+
+%   unless in_keys.empty?
+    # Substitution keys for input parameters
+    keys = {
+%     key_width = max_width.(in_keys, 'command-line-key') + "'".length
+%     in_keys.each do |key|
+      <%=
+        "'%-#{key_width}s => params[:'%s']," % [
+          key['command-line-key'] + "'",
+          key['id']
+        ]
+      %>
+%     end
+    }
+
+%   end
+%   unless out_keys.empty?
+    # Substitution keys for output files
+%     if in_keys.empty?
+    keys = {
+%     else
+    keys.merge!({
+%     end
+%
+%     key_width  = max_width.(out_keys, 'command-line-key') + "''".length
+%     path_width = max_width.(out_keys, 'path-template')    + "'',".length
+%     out_keys.each do |key|
+      <%=
+        "%-#{key_width}s => substitute_keys(%-#{path_width}s keys)," % [
+          "'#{key['command-line-key']}'",
+          "'#{key['path-template']}',"
+        ]
+      %>
+%     end
+    })
+
+%   end
+%   unless flags.empty?
+    # Input/output command-line flags used with keys in command-line
+    # substitution.
+    flags = {
+%     key_width = max_width.(flags, 'command-line-key')  + "''".length
+%     flags.each do |flag|
+      <%=
+        "%-#{key_width}s => %s" % [
+          "'#{flag['command-line-key']}'",
+          "'#{flag['command-line-flag']}',"
+        ]
+      %>
+%     end
+    }
+
+%   end
+%   unless outputs.empty?
+    # Generate output filenames
+    params.merge!({
+%     id_width   = max_width.(outputs, 'id')          + ":''".length
+%     path_width = max_width.(outputs, 'path-template') + "'',".length
+%     outputs.each do |output|
+      <%=
+        "%-#{id_width}s => substitute_keys(%-#{path_width}s keys)," % [
+          ":'#{output['id']}'",
+          "'#{output['path-template']}',"
+        ]
+      %>
+%     end
+    })
+
+%   end
+    # Generate the final command-line to run <%= name %>
+    [ substitute_keys(<<-'CMD', keys<%= flags.empty? ? '' : ', flags' %>) ]
+      <%= descriptor['command-line'] %>
+    CMD
+% end
+  end
+
+  # Called after the task is done, this method saves <%= name %>'s output files
+  # to the Bourreau's cache and registers them into CBRAIN for later retrieval.
+  # Returns true on success.
+  def save_results #:nodoc:
+    # Additional checks to see if <%= name %> succeeded would belong here.
+
+% if outputs.empty?
+    # No output files to save; nothing to do
+    true
+% else
+    # No matter how many errors occur, we need to save as many output
+    # files as possible and carry the error state to the end.
+    params    = self.params
+    succeeded = true
+
+    # Extract out the output files parameters from params. They will be re-added
+    # once their existence is validated and their registration into CBRAIN is
+    # complete.
+    outputs = params.extract!(*[
+%   outputs.each do |output|
+      :'<%= output['id'] %>',
+%   end
+    ])
+
+%   unless required.empty?
+    # Make sure that every required output +path+ actually exists
+    # (or that its +glob+ matches something).
+    ensure_exists = lambda do |path|
+      return if File.exists(path)
+      self.addlog("Missing output file #{path}")
+      succeeded &&= false
+    end
+    ensure_matches = lambda do |glob|
+      return unless Dir.glob(glob).empty?
+      self.addlog("No output files matching #{glob}")
+      succeeded &&= false
+    end
+
+%     required.select { |o| ! o['list'] }.each do |output|
+    ensure_exists(outputs[:'<%= output['id'] %>'])
+%     end
+%     required.select { |o|   o['list'] }.each do |output|
+    ensure_matches(outputs[:'<%= output['id'] %>'])
+%     end
+
+%   end
+%   unless globs.empty?
+    # Expand output file globs/patterns inside outputs for output file lists.
+    [
+%     globs.each do |output|
+      :'<%= output['id'] %>',
+%     end
+    ].each do |param|
+      outputs[param] = Dir.glob(outputs[param])
+    end
+
+%   end
+    # Save (and register) all generated files to the results data provider
+    outputs.each do |param, paths|
+      paths = [paths] unless paths.is_a?(Enumerable)
+      paths.each do |path|
+        next unless path.present? && File.exists?(path)
+
+        self.addlog("Saving result file #{path}")
+        name = File.basename(path)
+
+        output = safe_userfile_find_or_new((
+          File.directory?(path) ? FileCollection : Userfile.suggested_file_type(name)
+        ), :name => name)
+        unless output.save
+          self.addlog("Failed to save file #{path}")
+          succeeded &&= false
+          next
+        end
+
+        output.cache_copy_from_local_file(path)
+        params[param] ||= []
+        params[param]  << output.id
+        self.addlog("Saved result file #{path}")
+%   if (single_file = files.first if files.count == 1 && ! files.first['list'])
+
+        # As all output files were generated from a single input file,
+        # the outputs can all be made children of the one parent input file.
+        parent = params[:'<%= single_file['id'] %>']
+        output.move_to_child_of(parent)
+        self.addlog_to_userfiles_these_created_these([parent], [output])
+%   end
+      end
+    end
+
+    succeeded
+% end
+  end
+
+  private
+
+  # Generic helper methods
+
+  # Make a given set of userfiles +files+ available to <%= name %> at
+  # +directory+. Simple variation on +ClusterTask+::+make_available+
+  # to allow +files+ to be an Enumerable of files to make available under
+  # +directory+.
+  def make_available(files, directory)
+    files = [files] unless files.is_a?(Enumerable)
+    files.compact.each { |file| super(file, directory + '/') }
+  end
+
+  # Resolve/replace input userfiles IDs for parameter +param+
+  # to their Userfile instances, calling +failed+ if a file cannot be resolved.
+  # Also try and set the results data provider if its missing.
+  def resolve_file_parameter(param, failed)
+    value = params[param]
+    return if value.nil?
+
+    files = (value.is_a?(Enumerable) ? value : [value]).map do |file|
+      file = Userfile.find_by_id(file) unless file.is_a?(Userfile)
+      failed.("Could not find file with ID #{file}") unless file
+      file
+    end
+
+    params[param] = value.is_a?(Enumerable) ? files : files.first
+    self.results_data_provider_id ||= files.first.data_provider_id rescue nil
+  end
+
+  # Substitute each parameter value in +keys+ in +str+ prepended by the
+  # corresponding flag in +flags+, if available.
+  # substitute_keys('f -e [1]', { '[1]' => 5 })                    => 'f -e 5'
+  # substitute_keys('f -e [1]', { '[1]' => 5 }, { '[1]' => '-z' }) => 'f -e -z 5'
+  def substitute_keys(str, keys, flags = {})
+    keys.inject(str) do |str, (key, value)|
+      flag = flags[key]
+      next str.gsub(key, flag) if flag && value == true
+
+      value = (value.is_a?(Enumerable) ? value.dup : [value])
+        .reject(&:nil?)
+        .map { |v| (v.is_a?(Userfile) ? v.name : v.to_s).bash_escape }
+        .join(' ')
+
+      str.gsub(key, flag && value.present? ? "#{flag} #{value}" : value)
+    end
+  end
+
+end
diff --git a/BrainPortal/lib/cbrain_task_generators/templates/edit_help.html.erb b/BrainPortal/lib/cbrain_task_generators/templates/edit_help.html.erb
new file mode 100644
index 000000000..fc3fc3d35
--- /dev/null
+++ b/BrainPortal/lib/cbrain_task_generators/templates/edit_help.html.erb
@@ -0,0 +1,91 @@
+
+<!--
+#
+# 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 <http://www.gnu.org/licenses/>.  
+#
+-->
+
+<!--
+# NOTE: This is a working template generated from a descriptor:
+# [Schema]         <%= schema['id'] %>
+# [Schema version] <%= descriptor['schema-version'] %>
+# [Tool]           <%= descriptor['name'] %>
+# [Version]        <%= descriptor['tool-version'] || '?' %>
+# See the CbrainTask Programmer Guide (CBRAIN Wiki) for a more complete picture
+# of how CbrainTasks are constructed.
+-->
+<%-
+# NOTE: This template's weird indentation is there to try and make the
+# generated code as legible as possible.
+-%>
+
+<%-
+  # Parameter groups
+  params  = descriptor['inputs'].select { |i| i['type'] != 'File' }
+  inputs  = descriptor['inputs'].select { |i| i['type'] == 'File' }
+  outputs = descriptor['output-files'].dup
+-%>
+<%# Format a parameter (+param+) attributes as a list element (<li>) -%>
+<%- format_param = lambda do |param| -%>
+  <li>
+    <strong>
+      <%= param['name'] %>
+  <%- if param['command-line-flag']-%>
+      (<code class="cmd-flag"><%= param['command-line-flag'] %></code>)
+  <%- end -%>
+  <%- if param['description'] -%>
+    </strong>:
+    <%= param['description'] %>
+  <%- else -%>
+    </strong>
+  <%- end -%>
+  </li>
+<%- end -%>
+<h1><%= descriptor['name'] %></h1>
+<%- if descriptor['tool-version'] -%>
+<h4><%= descriptor['tool-version'] %></h4>
+<%- end -%>
+<br />
+
+<%- if descriptor['description'] -%>
+<%= descriptor['description'] %>
+<br />
+
+<%- end -%>
+<%- unless params.empty? -%>
+<h2>Parameters</h2>
+<ul>
+  <%- params.each { |param| format_param.(param) } -%>
+</ul>
+
+<%- end -%>
+<%- unless inputs.empty? -%>
+<h2>Input files</h2>
+<ul>
+  <%- inputs.each { |input| format_param.(input) } -%>
+</ul>
+
+<%- end -%>
+<%- unless outputs.empty? -%>
+<h2>Output files</h2>
+<ul>
+  <%- outputs.each { |output| format_param.(output) } -%>
+</ul>
+<%- end -%>
diff --git a/BrainPortal/lib/cbrain_task_generators/templates/portal.rb.erb b/BrainPortal/lib/cbrain_task_generators/templates/portal.rb.erb
new file mode 100644
index 000000000..5f9c1b6a7
--- /dev/null
+++ b/BrainPortal/lib/cbrain_task_generators/templates/portal.rb.erb
@@ -0,0 +1,299 @@
+
+#
+# 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 <http://www.gnu.org/licenses/>.
+#
+
+# NOTE: This is a working template generated from a descriptor:
+# [Schema]         <%= schema['id'] %>
+# [Schema version] <%= descriptor['schema-version'] %>
+# [Tool]           <%= descriptor['name'] %>
+# [Version]        <%= descriptor['tool-version'] || '?' %>
+# See the CbrainTask Programmer Guide (CBRAIN Wiki) for a more complete picture
+# of how CbrainTasks are constructed.
+% # NOTE: This template's weird indentation is there to try and make the
+% # generated code as legible as possible.
+
+# Portal-side CbrainTask subclass to launch <%= name %>
+class CbrainTask::<%= name %> < PortalTask
+
+  Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
+
+% # Maximum width of a given +key+'s value in a +list+ of hashes
+% max_width = lambda do |list, key|
+%   list.map { |i| i[key].to_s.length rescue 0 }.max
+% end
+%
+% # Parameter groups
+% params     = descriptor['inputs'].dup
+% outputs    = descriptor['output-files'].dup
+% required   = params.select { |i| ! i['optional']     }
+% optional   = params.select { |i| i['optional']       }
+% defaults   = params.select { |i| i['default-value']  }
+% files      = params.select { |i| i['type'] == 'File' }
+% file_lists = files.select  { |i| i['list']           }
+%
+% # Special case; we only have one file input parameter and it only
+% # allows single files.
+% single_file  = files.first if files.count == 1 && file_lists.empty?
+% if single_file
+%   # The parameter's validation is made in final_task_list and is no longer
+%   # optional if it was.
+%   params.delete(single_file)
+%   required.delete(single_file)
+%   optional.delete(single_file)
+% end
+%
+% unless defaults.empty?
+  # Default values for some (all?) of <%= name %>'s parameters. Those values
+  # reflect the defaults taken by the tool's developer; feel free to change
+  # them to match your platform's requirements.
+  def self.default_launch_args #:nodoc:
+    {
+%   id_width = max_width.(defaults, 'id') + "'".length
+%   defaults.each do |default|
+      <%=
+        ":'%-#{id_width}s => %s," % [
+          default['id'] + "'",
+          default['default-value'].inspect
+        ]
+      %>
+%   end
+    }
+  end
+
+% end
+  # Callback called just before the task's form is rendered. At this point,
+  # the task's params hash contains at least the default list of input
+  # userfiles under the key :interface_userfile_ids. 
+  def before_form #:nodoc:
+% file_types = descriptor['inputs']
+%   .select { |i| ! i['optional'] && i['type'] == 'File' }
+%   .map    { |i| i['cbrain-file-type'] }
+%   .uniq
+% unless file_types.empty?
+    # Resolve interface_userfile_ids to actual userfile objects
+    files = Userfile.find_all_by_id(self.params[:interface_userfile_ids])
+
+%   if file_types.length == 1 && !file_types.first
+    # At least one file is required.
+    cb_error "Error: this task requires at least one input file" if files.empty?
+%   else
+    # Some input files are not optional and specific file types are
+    # required. Make sure the given input files are adequate.
+
+    # Ensure that +files+ contains at least one file of type +type+
+    ensure_one = lambda do |files, type|
+      type = type.constantize unless type.is_a?(Class)
+      cb_error "Error: this task requires at least one file of type '#{type.name}'" unless
+        files.any? { |f| f.is_a?(type) }
+    end
+
+%     file_types.compact.each do |type|
+    ensure_one.(files, '<%= type %>')
+%     end
+%   end
+
+% end
+    ""
+  end
+
+  # Callback called just after the task's form has been submitted by the user.
+  # At this point, all the task's params will be filled. This is where most
+  # validations happens.
+  def after_form #:nodoc:
+% unless params.empty?
+    params = self.params
+
+%   unless file_lists.empty?
+    # Assign the default input file list from interface_userfile_ids to unset
+    # file list parameters.
+    [
+%     file_lists.each do |param|
+      :'<%= param['id'] %>',
+%     end
+    ].each do |list|
+      params[list] = params[:interface_userfile_ids].dup unless
+        params[list].is_a?(Enumerable) # Allows explicitly empty lists
+    end
+
+%   end
+    # Sanitize every input parameter according to their expected type
+
+%   sanitize_param = format_call('sanitize_param', params) { |param| [
+%     ":'#{param['id']}'",
+%     ":#{param['type'].downcase}",
+%     (param['cbrain-file-type'] ? ":file_type => '#{param['cbrain-file-type']}'" : nil)
+%   ] }
+%
+%   unless required.empty?
+    # Required parameters
+%     required.each do |param|
+    <%= sanitize_param.(param) %>
+%     end
+
+%   end
+%   unless optional.empty?
+    # Optional parameters
+%     calls      = optional.map { |param| [ sanitize_param.(param), param ] }
+%     call_width = calls.map { |c, p| c.length }.max
+%     calls.each do |call, param|
+    <%= "%-#{call_width}s unless params[:'%s'].nil?" % [ call, param['id'] ] %>
+%     end
+
+%   end
+% end
+    ""
+  end
+
+  # Final set of tasks to be launched based on this task's parameters. Only
+  # useful if the parameters set for this task represent a set of tasks
+  # instead of just one.
+  def final_task_list #:nodoc:
+% if single_file
+    # Create a list of tasks out of the default input file list
+    # (interface_userfile_ids), each file going into parameter '<%= single_file['id'] %>'
+    self.params[:interface_userfile_ids].map do |id|
+      task = self.dup
+
+      # Set and sanitize the one file parameter for each id
+      task.params[:'<%= single_file['id']%>'] = id
+%   if single_file['cbrain-file-type']
+      task.sanitize_param(:'<%= single_file['id'] %>', :file, :file_type => '<%= single_file['cbrain-file-type']%>')
+%   else
+      task.sanitize_param(:'<%= single_file['id'] %>', :file)
+%   end
+
+      task.description ||= ''
+      task.description  += " <%= single_file['id']%>: #{Userfile.find(id).name}"
+      task.description.strip!
+      task
+    end
+% else
+    [ self ]
+% end
+  end
+
+  # Task parameters to leave untouched by the edit task mechanism. Usually
+  # for parameters added in after_form or final_task_list, as those wouldn't
+  # be present on the form and thus lost when the task is edited.
+  def untouchable_params_attributes #:nodoc:
+% if outputs.empty?
+    { }
+% else
+    # Output parameters will be present after the task has run and need to be
+    # preserved.
+    {
+%   id_width = max_width.(outputs, 'id') + "'".length
+%   outputs.each do |output|
+      <%= ":'%-#{id_width}s => true," % (output['id'] + "'") %>
+%   end
+    }
+% end
+  end
+
+  # Generic helper methods
+
+  # Ensure that the parameter +name+ is not null and matches a generic tool
+  # parameter +type+ (:file, :numeric, :string or :flag) before converting the
+  # parameter's value to the corresponding Ruby type (if appropriate).
+  # For example, sanitize_param(:deviation, :numeric) would validate that
+  # self.params[:deviation] is a number and then convert it to a Ruby Float or
+  # Integer.
+  #
+  # Available +options+:
+  # [file_type] Userfile type to validate a parameter of +type+ :file against.
+  #
+  # If the parameter's value is an array, every value in the array is checked
+  # and expected to match +type+.
+  #
+  # Raises an exception for task parameter +name+ if the parameter's value
+  # is not adequate.
+  def sanitize_param(name, type, options = {})
+    # Taken userfile names. An error will be raised if two input files have the
+    # same name.
+    @taken_files ||= Set.new
+
+    # Fetch the parameter and convert to an Enumerable if required
+    values = self.params[name] rescue nil
+    values = [values] unless values.is_a?(Enumerable)
+
+    # Validate and convert each value
+    values.map! do |value|
+      case type
+      # Try to convert to integer and then float. Cant? then its not a number.
+      when :number
+        if (number = Integer(value) rescue Float(value) rescue nil)
+          value = number
+        elsif value.blank?
+          params_errors.add(name, ": value missing")
+        else
+          params_errors.add(name, ": not a number (#{value})")
+        end
+
+      # Nothing special required for strings, bar for symbols being acceptable strings.
+      when :string
+        value = value.to_s if value.is_a?(Symbol)
+        params_errors.add(name, " not a string (#{value})") unless value.is_a?(String)
+
+      # Try to match against various common representation of true and false
+      when :flag
+        if value.is_a?(String)
+          value = true  if value =~ /^(true|t|yes|y|on|1)$/i
+          value = false if value =~ /^(false|f|no|n|off|0|)$/i
+        end
+
+        if ! [ true, false ].include?(value)
+          params_errors.add(name, ": not true or false (#{value})")
+        end
+
+      # Make sure the file ID is valid, accessible, not already used and
+      # of the correct type.
+      when :file
+        unless (id = Integer(value) rescue nil)
+          params_errors.add(name, ": invalid or missing userfile (ID #{value})")
+          next value
+        end
+
+        unless (file = Userfile.find_accessible_by_user(value, self.user))
+          params_errors.add(name, ": cannot find userfile (ID #{value})")
+          next value
+        end
+
+        if @taken_files.include?(file.name)
+          params_errors.add(name, ": file name already in use (#{file.name})")
+        else
+          @taken_files.add(file.name)
+        end
+
+        if type = options[:file_type]
+          type = type.constantize unless type.is_a?(Class)
+          params_errors.add(name, ": incorrect userfile type (#{file.name})") if
+            type && ! file.is_a?(type)
+        end
+      end
+
+      value
+    end
+
+    # Store the value back
+    self.params[name] = values.first unless self.params[name].is_a?(Enumerable)
+  end
+
+end
diff --git a/BrainPortal/lib/cbrain_task_generators/templates/show_params.html.erb.erb b/BrainPortal/lib/cbrain_task_generators/templates/show_params.html.erb.erb
new file mode 100644
index 000000000..80dbe879d
--- /dev/null
+++ b/BrainPortal/lib/cbrain_task_generators/templates/show_params.html.erb.erb
@@ -0,0 +1,120 @@
+
+<%%-
+#
+# 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 <http://www.gnu.org/licenses/>.
+#
+-%>
+
+<%%-
+# NOTE: This is a working template generated from a descriptor:
+# [Schema]         <%= schema['id'] %>
+# [Schema version] <%= descriptor['schema-version'] %>
+# [Tool]           <%= descriptor['name'] %>
+# [Version]        <%= descriptor['tool-version'] || '?' %>
+# See the CbrainTask Programmer Guide (CBRAIN Wiki) for a more complete picture
+# of how CbrainTasks are constructed.
+-%>
+<%-
+# NOTE: This template's weird indentation is there to try and make the
+# generated code as legible as possible.
+-%>
+
+<%-
+  # Parameter groups
+  params  = descriptor['inputs'].select { |i| i['type'] != 'File' }
+  inputs  = descriptor['inputs'].select { |i| i['type'] == 'File' }
+  outputs = descriptor['output-files'].dup
+-%>
+<%- unless [params, inputs, outputs].all?(&:empty?) -%>
+<%%
+  # Format a parameter (input or output) +value+ for display. Mostly for
+  # arrays (parameter lists).
+  format_param = lambda do |value|
+    value = [value] unless value.is_a?(Enumerable)
+    value.map(&:to_s).join(', ')
+  end
+
+  # Format a set of one or more Userfile IDs for display.
+  # Similar to format_param.
+  format_files = lambda do |value|
+    value = [value] unless value.is_a?(Enumerable)
+    format_param.(value.map { |v| link_to_userfile_if_accessible(v) }).html_safe
+  end
+%%>
+<%- end -%>
+<div class="task-show">
+<%- if [params, inputs, outputs].all?(&:empty?) -%>
+  No parameters, no inputs, no ouputs.
+<%- else -%>
+  <table>
+  <%- unless params.empty? -%>
+    <tbody class="tsk-sw-param">
+      <tr>
+        <th colspan="2" class="tsk-sw-hdr">
+          Parameters
+        </th>
+      </tr>
+    <%- params.each do |param| -%>
+      <tr>
+        <td class="tsk-sw-name"><%= param['name'] %></td>
+        <td class="tsk-sw-val">
+          <%%= format_param.(params[:'<%= param['id'] %>']) %>
+        </td>
+      </tr>
+    <%- end -%>
+    </tbody>
+  <%- end -%>
+  <%- unless inputs.empty? -%>
+    <tbody class="tsk-sw-input">
+      <tr>
+        <th colspan="2" class="tsk-sw-hdr">
+          Input files
+        </th>
+      </tr>
+    <%- inputs.each do |input| -%>
+      <tr>
+        <td class="tsk-sw-name"><%= input['name'] %></td>
+        <td class="tsk-sw-val">
+          <%%= format_files.(params[:'<%= input['id'] %>']) %>
+        </td>
+      </tr>
+    <%- end -%>
+    </tbody>
+  <%- end -%>
+  <%- unless outputs.empty? -%>
+    <tbody class="tsk-sw-output">
+      <tr>
+        <th colspan="2" class="tsk-sw-hdr">
+          Output files
+        </th>
+      </tr>
+    <%- outputs.each do |output| -%>
+      <tr>
+        <td class="tsk-sw-name"><%= output['name'] %></td>
+        <td class="tsk-sw-val">
+          <%%= format_files.(params[:'<%= output['id'] %>']) %>
+        </td>
+      </tr>
+    <%- end -%>
+    </tbody>
+  <%- end -%>
+  </table>
+<%- end -%>
+</div>
diff --git a/BrainPortal/lib/cbrain_task_generators/templates/task_params.html.erb.erb b/BrainPortal/lib/cbrain_task_generators/templates/task_params.html.erb.erb
new file mode 100644
index 000000000..c3ef92277
--- /dev/null
+++ b/BrainPortal/lib/cbrain_task_generators/templates/task_params.html.erb.erb
@@ -0,0 +1,476 @@
+
+<%%-
+#
+# 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 <http://www.gnu.org/licenses/>.
+#
+-%>
+
+<%%-
+# NOTE: This is a working template generated from a descriptor:
+# [Schema]         <%= schema['id'] %>
+# [Schema version] <%= descriptor['schema-version'] %>
+# [Tool]           <%= descriptor['name'] %>
+# [Version]        <%= descriptor['tool-version'] || '?' %>
+# See the CbrainTask Programmer Guide (CBRAIN Wiki) for a more complete picture
+# of how CbrainTasks are constructed.
+-%>
+<%-
+# NOTE: This template's weird indentation is there to try and make the
+# generated code as legible as possible.
+-%>
+
+<%-
+  # Parameter groups
+  params   = descriptor['inputs'].dup
+  required = params.select { |i| ! i['optional'] }
+  optional = params.select { |i|   i['optional'] }
+
+  # Single input file case
+  files       = params.select { |i| i['type'] == 'File' }
+  single_file = files.first if files.count == 1 && ! files.any? { |f| f['list'] }
+-%>
+<%% input_files = Userfile.find_all_by_id(params[:interface_userfile_ids]) rescue [] %>
+
+<%%#
+  Generate a parameter label for HTML input with id +id+.
+  +name+ corresponds to the tool parameter name to display,
+  +optional+ indicates that the parameter is optional (or not) and
+  +flag+ is the parameter's command-line flag if available.
+%%>
+<%% label = lambda do |id, name, optional: false, flag: nil| %>
+  <label class="tsk-prm-lbl" for="<%%= id.to_la_id %>">
+    <%%= name %>
+    <%% if flag %>
+      (<code class="cmd-flag"><%%= flag %></code>)
+    <%% end %>
+    <%% unless optional %>
+      <span class="required">*</span>
+    <%% end %>
+  </label>
+<%% end %>
+
+<%%#
+  Generate a generic parameter input field with HTML id +id+ and name +name+.
+  +type+ is the kind of input field to generate (text or hidden),
+  +value+ is the input field's initial value,
+  +optional+ indicates that the parameter is optional (and the name should not
+  directly be placed on the tag) and
+  +placeholder+ is the placeholder text to fill the input with while awaiting
+  user input
+%%>
+<%% input = lambda do |id, name, type: 'text', value: nil, optional: false, placeholder: nil| %>
+  <%% value = @task.params[name.to_sym] if name && value.nil? %>
+  <input <%% if id %>
+          id="<%%= id.to_la_id %>"
+         <%% end %>
+         class="tsk-prm-in"
+         type="<%%= type %>"
+         <%% if name %>
+           <%%= optional ? 'data-name' : 'name' %>="<%%= name.to_la %>"
+         <%% end %>
+         <%% if value %>
+           value="<%%= value %>"
+         <%% end %>
+         <%% if placeholder %>
+           placeholder="<%%= placeholder %>"
+         <%% end %>
+  />
+<%% end %>
+
+<%%#
+  Generate a list of inputs suitable for a list parameter with HTML id +id+
+  and name +name+. +values+, +optional+ and +placeholder+ work similarly to
+  input's corresponding arguments.
+%%>
+<%% input_list = lambda do |id, name, values: nil, optional: false, placeholder: nil| %>
+  <%%
+    values = @task.params[name.to_sym] if name && values.nil?
+    values = ([values] unless values.is_a?(Enumerable)).compact
+    first = values.pop
+  %>
+  <ul class="tsk-prm-list">
+    <li>
+      <%%
+        input.(id, name,
+          value:       first,
+          optional:    optional,
+          placeholder: placeholder
+        )
+      %>
+      <span class="tsk-prm-add ui-icon ui-icon-plus"></span>
+    </li>
+    <%% values.each do |value| %>
+      <li>
+        <%%
+          input.(nil, name,
+            value:       value,
+            optional:    optional,
+            placeholder: placeholder
+          )
+        %>
+        <span class="tsk-prm-add ui-icon ui-icon-minus"></span>
+      </li>
+    <%% end %>
+  </ul>
+<%% end %>
+
+<%%#
+  Generate a fancy checkbox for flag or optional parameters with HTML +id+.
+  If +name+ is given, a checkbox suitable for flag parameters is generated
+  while one for optional arguments is generated otherwhise. The checkbox's
+  initial state (checked or not) is +check+.
+%%>
+<%% checkbox = lambda do |id, name: nil, check: nil| %>
+  <%%#
+    FIXME for some obscure reason, naming the 'check' parameter 'checked'
+    makes the first parameter (id) become nil regardless of the value passed
+    in. This only seems to occur in the context of Rails' template renderer.
+  %>
+  <%%
+    id    = name ? id.to_la_id : "tsk-prm-opt-#{id}"
+    type  = name ? 'chk' : 'opt'
+  %>
+  <%% if name %>
+    <%% check = @task.params[name.to_sym] if check.nil? %>
+    <%%#
+      As a checkbox's value is not sent if left unchecked, a hidden 'back' field
+      sends the unchecked state is used to send. Rails overwrites this 'back'
+      value with the checbox's when the checkbox is checked, as the checkbox is
+      after the 'back' field.
+    %>
+    <input class="tsk-prm-chk-in"
+           type="hidden"
+           name="<%%= name.to_la %>"
+           value="0"
+    />
+    <input class="tsk-prm-chk"
+           type="checkbox"
+           id="<%%= id %>"
+           name="<%%= name.to_la %>"
+           value="1"
+           <%% if check %>
+             checked="checked"
+           <%% end %>
+    />
+  <%% else %>
+    <input class="tsk-prm-opt"
+           type="checkbox"
+           id="<%%= id %>"
+           <%% if check %>
+             checked="checked"
+           <%% end %>
+    />
+  <%% end %>
+  <label class="tsk-prm-<%%= type %>-lbl" for="<%%= id %>">
+    <span class="tsk-prm-<%%= type %>-icon ui-icon ui-icon-check"></span>
+  </label>
+<%% end %>
+
+<%%#
+  Generate a drop-down list for a set of +options+ (value, label pairs) with
+  HTML id +id+ and name +name+.
+  +nothing+ corresponds to the text displayed if +options+ is empty and
+  +optional+ indicates if the parameter is optional (or not)
+%%>
+<%% dropdown = lambda do |id, name, options = [], nothing: '(Nothing to select)', optional: false| %>
+  <%% value = @task.params[name.to_sym] if name %>
+  <%%
+    input.(id, name,
+      type:     'hidden',
+      value:    value,
+      optional: optional
+    )
+  %>
+  <div class="tsk-prm-sel">
+    <span class="tsk-prm-sel-icon ui-icon ui-icon-triangle-1-s"></span>
+    <%% if options.empty? %>
+      <span class="tsk-prm-sel-lbl disabled">
+        <%%= nothing %>
+      </span>
+    <%% else %>
+      <span class="tsk-prm-sel-lbl">
+        <%% if (pair = options.select { |o| o.first == value }.first) %>
+          <%%= pair.last %>
+        <%% end %>
+      </span>
+      <ul class="tsk-prm-sel-opt">
+        <%% options.each do |value, label| %>
+          <li data-value="<%%= value %>"><%%= label %></li>
+        <%% end %>
+      </ul>
+    <%% end %>
+  </div>
+<%% end %>
+
+<%%# Generate a parameter's description block for +desc+ %>
+<%% description = lambda do |desc| %>
+  <span class="tsk-prm-desc">
+    <%%= desc %>
+  </span>
+<%% end %>
+
+<%# Generate a complete HTML block for a given parameter +param+ -%>
+<%- parameter = lambda do |param| -%>
+  <%-
+    id    = param['id']
+    type  = param['type'].downcase.to_sym
+    opt   = !!(param['optional'] && type != :flag)
+    list  = param['list']
+  -%>
+  <%-
+    classes  = [ 'tsk-prm', type.to_s ]
+    classes << 'list' if list
+  -%>
+    <%% id = '<%= id %>' %>
+    <li class="<%%= id %> <%= classes.join(' ') %>">
+      <%%
+  <%- if type == :flag -%>
+        # Flag input toggle
+        checkbox.(id, name: id)
+
+  <%- end -%>
+        # Name/Label
+        label.(id, %q{ <%= param['name'] %> },
+  <%- if param['command-line-flag'] -%>
+          optional: <%= param['optional'] %>,
+          flag:     '<%= param['command-line-flag'] %>'
+  <%- else -%>
+          optional: <%= param['optional'] %>
+  <%- end -%>
+        )
+
+  <%- if opt -%>
+        # Optional parameter enable/disable toggle
+        checkbox.(id)
+
+  <%- end -%>
+  <%- if type == :file -%>
+    <%- if single_file -%>
+        # Automatic single file input
+        dropdown.(id, id,
+          [], nothing: '(Automatically selected)',
+          optional: <%= opt %>
+        )
+    <%- elsif param['cbrain-file-type'] -%>
+        # File input dropdown
+        type = '<%= param['cbrain-file-type'] %>'.constantize rescue nil
+        dropdown.(id, id,
+          input_files
+            .select { |f| f.is_a?(type) if type }
+            .map    { |f| [ f.id.to_s, f.name ] },
+          optional: <%= opt %>
+        )
+    <%- else -%>
+        # File input dropdown
+        dropdown.(id, id,
+          input_files.map { |f| [ f.id.to_s, f.name ] },
+          optional: <%= opt %>
+        )
+    <%- end -%>
+
+  <%- elsif [ :string, :number ].include?(type) -%>
+    <%-
+      arg_width = [
+        'optional',
+        ('placeholder' if type == :number),
+      ].compact.map(&:length).max + ':'.length
+    -%>
+    <%- if list -%>
+        # Input field list
+        input_list.(id, id,
+    <%- else -%>
+        # Input field
+        input.(id, id,
+    <%- end -%>
+    <%- if type == :number -%>
+          optional:    <%= opt.to_s %>,
+          placeholder: '0.0'
+    <%- else -%>
+          optional: <%= opt.to_s %>
+    <%- end -%>
+        )
+
+  <%- end -%>
+  <%- if param['description'] -%>
+        # Description
+        description.(<<-'DESC')
+          <%= param['description'] %>
+        DESC
+  <%- end -%>
+      %>
+    </li>
+
+<%- end -%>
+<div class="task-params">
+  <%- if params.empty? -%>
+  <%= name %> has no parameters.
+  <%- else -%>
+  <ul>
+    <%- required.each(&parameter) -%>
+    <%- optional.each(&parameter) -%>
+  </ul>
+  <%- end -%>
+</div>
+
+<script type="application/javascript">
+$(function () {
+  "use strict";
+
+  var parameters = $('.tsk-prm');
+
+  /*
+   * Remove the checked attribute of checkboxes and use their internal
+   * state instead.
+   */
+  parameters.find("input[type='checkbox'][checked='checked']").each(function () {
+    $(this)
+      .removeAttr('checked')
+      .prop('checked', true);
+  });
+
+  /* Optional parameters */
+
+  /* Clicking on the parameter's checkbox toggles the parameter's state */
+  parameters.delegate('.tsk-prm-opt', 'change', function () {
+    var opt   = $(this),
+        param = opt.parent();
+
+    /*
+     * When an optional parameter is enabled, add its name attribute
+     * (stored in a data-* field) to send them with the POST.
+     */
+    if (opt.prop('checked')) {
+      param.find('.tsk-prm-in').each(function () {
+        var name = $(this).data('name');
+
+        /* Lists need to be sent with [] for proper server-side handling */
+        if (param.hasClass('list')) name += '[]';
+
+        $(this).attr('name', name);
+      });
+
+    /*
+     * When an optional parameter is disabled, clear its value(s) and name
+     * attribute.
+     */
+    } else {
+      /* Main value and name attribute */
+      param
+        .find('.tsk-prm-in')
+        .removeAttr('name')
+        .val('');
+
+      /* Display value for drop-down inputs */
+      param
+        .find('.tsk-prm-sel-lbl')
+        .text('');
+
+      /* Remove all extra inputs in input lists */
+      param
+        .find('.tsk-prm-list > li')
+        .slice(1)
+        .remove();
+    }
+  });
+
+  /* Changing a parameter's value automatically marks it as active */
+  parameters.delegate('.tsk-prm-in', 'change', function () {
+    $(this)
+      .closest('.tsk-prm')
+      .find('.tsk-prm-opt')
+      .prop('checked', true)
+      .trigger('change');
+  });
+
+  /* Activate optional parameters with default values */
+  parameters.find(".tsk-prm-in[value]").trigger('change');
+
+  /* Drop-down lists */
+
+  /*
+   * Clicking anywhere but the drop-down closes it without changing the
+   * selection.
+   */
+  $('.task-params').click(function () {
+    $(this)
+      .find('.tsk-prm-sel-opt')
+      .hide();
+  });
+
+  /* Clicking on the drop-down's label or icon toggles its visibility */
+  parameters.delegate('.tsk-prm-sel', 'click', function (event) {
+    event.stopPropagation();
+
+    $(this)
+      .children('.tsk-prm-sel-opt')
+      .toggle();
+  });
+
+  /* Clicking on a drop-down item selects it */
+  parameters.delegate('.tsk-prm-sel-opt > li', 'click', function () {
+    var item  = $(this),
+        param = item.closest('.tsk-prm');
+
+    /* Set the backing input element's value */
+    param
+      .find('.tsk-prm-in')
+      .val(item.data('value'))
+      .trigger('change');
+
+    /* Display the newly selected value in the drop-down's label */
+    param
+      .find('.tsk-prm-sel-lbl')
+      .text(item.text());
+  });
+
+  /* Add/remove buttons for list parameters */
+
+  /* Clicking on a '+' button adds a new value row and enables the parameter */
+  parameters.delegate('.tsk-prm-add', 'click', function () {
+    var name = $(this)
+      .siblings('.tsk-prm-in')
+      .data('name');
+
+    $(this)
+      .closest('ul')
+      .append(
+        '<li>' +
+          '<input ' +
+            'class="tsk-prm-in" ' +
+            'type="text" ' +
+            'name="' + name + '" ' +
+            'data-name="' + name + '" ' +
+          '/> ' +
+          '<span class="tsk-prm-rm ui-icon ui-icon-minus"></span>' +
+        '</li>'
+      )
+      .siblings('.tsk-prm-opt')
+      .prop('checked', true)
+      .trigger('change');
+  });
+
+  /* Clicking on a '-' button removes the row */
+  parameters.delegate('.tsk-prm-rm', 'click', function () {
+    $(this)
+      .closest('li')
+      .remove();
+  });
+});
+</script>
diff --git a/BrainPortal/public/stylesheets/cbrain.css b/BrainPortal/public/stylesheets/cbrain.css
index 1b325b96c..1d77bf1d9 100644
--- a/BrainPortal/public/stylesheets/cbrain.css
+++ b/BrainPortal/public/stylesheets/cbrain.css
@@ -541,6 +541,10 @@ h1.warning {
   float: left;
 }
 
+.cmd-flag {
+  color: #0471b4;
+}
+
 /* % ######################################################### */
 /* % General styles for definition lists */
 /* % ######################################################### */
@@ -1595,6 +1599,232 @@ th.center_align_heading {
   margin-right: 0em;
 }
 
+/* Show task parameters */
+.task-show > table {
+  border: 0;
+}
+
+.tsk-sw-hdr,
+.tsk-sw-name,
+.tsk-sw-val {
+  background: inherit;
+  border: 0;
+  text-align: left;
+}
+
+.tsk-sw-hdr {
+  font-family: sans-serif;
+  font-size: 1.1em;
+  font-weight: bold;
+  padding: 30px 5px 10px 5px;
+  text-align: left;
+}
+
+.tsk-sw-name {
+  padding-right: 40px;
+}
+
+.tsk-sw-param > tr > .tsk-sw-hdr {
+  padding-top: 5px;
+}
+
+.tsk-sw-param > tr > .tsk-sw-val {
+  font-family: monospace;
+}
+
+/* Edit task parameters */
+.task-params > ul {
+  list-style: none;
+  padding-left: 20px;
+  padding: 0;
+}
+
+.task-params > ul > li {
+  margin-bottom: 30px;
+  margin-top: 10px;
+}
+
+/* label */
+.tsk-prm-lbl {
+  display: block;
+  font-size: 1.1em;
+  font-weight: bold;
+  margin-bottom: 5px;
+  margin-left: 25px;
+}
+
+.tsk-prm-lbl > .required {
+  color: red;
+}
+
+.tsk-prm.flag > .tsk-prm-lbl {
+  margin-left: 30px;
+}
+
+/* optional */
+.tsk-prm-opt,
+.tsk-prm-chk {
+  display: none;
+}
+
+.tsk-prm-opt-lbl,
+.tsk-prm-chk-lbl {
+  background: #ffffff;
+  border: 1px solid #888888;
+  display: inline-block;
+  float: left;
+  height: 22px;
+  width: 22px;
+}
+
+.tsk-prm-opt-lbl {
+  border-right: 0;
+}
+
+.tsk-prm-opt-lbl > .tsk-prm-opt-icon,
+.tsk-prm-chk-lbl > .tsk-prm-chk-icon {
+  background-image: url("images/ui-icons_ffffff_256x240.png");
+  margin-left: 3px;
+  margin-top: 2px;
+  visibility: hidden;
+}
+
+.tsk-prm-opt:checked + .tsk-prm-opt-lbl,
+.tsk-prm-opt[checked=checked] + .tsk-prm-opt-lbl,
+.tsk-prm-chk:checked + .tsk-prm-chk-lbl,
+.tsk-prm-chk[checked=checked] + .tsk-prm-chk-lbl {
+  background: #0471b4;
+}
+
+.tsk-prm-opt:checked + .tsk-prm-opt-lbl > .tsk-prm-opt-icon,
+.tsk-prm-opt[checked=checked] + .tsk-prm-opt-lbl > .tsk-prm-opt-icon,
+.tsk-prm-chk:checked + .tsk-prm-chk-lbl > .tsk-prm-chk-icon,
+.tsk-prm-chk[checked=checked] + .tsk-prm-chk-lbl > .tsk-prm-chk-icon {
+  visibility: visible;
+}
+
+/* input */
+.tsk-prm-in,
+.tsk-prm-sel {
+  background: #ffffff;
+  border: 1px solid #888888;
+  color: #000000;
+  display: block;
+  font-family: monospace;
+  font-size: 15px;
+  margin-left: 23px;
+  min-height: 18px;
+  padding: 2px 5px;
+  position: relative;
+  width: auto;
+}
+
+.tsk-prm.string > .tsk-prm-in,
+.tsk-prm.string > .tsk-prm-list > li > .tsk-prm-in {
+  width: 600px;
+}
+
+.tsk-prm.number > .tsk-prm-in,
+.tsk-prm.number > .tsk-prm-list > li > .tsk-prm-in,
+.tsk-prm-sel {
+  min-width: 175px;
+}
+
+/* selection */
+.tsk-prm-sel-lbl {
+  overflow: hidden;
+  white-space: nowrap;
+}
+
+.tsk-prm-sel-lbl.disabled {
+  color: #888888;
+  font-style: italic;
+}
+
+.tsk-prm-sel > .tsk-prm-sel-icon {
+  background-image: url("images/ui-icons_666666_256x240.png");
+  float: right;
+  margin-top: 2px;
+}
+
+.tsk-prm-sel-opt {
+  border: 1px solid #888888;
+  display: none;
+  left: -1px;
+  list-style: none;
+  max-height: 200px;
+  overflow-y: auto;
+  padding: 0;
+  position: absolute;
+  top: 22px;
+  min-width: 185px;
+  z-index: 501;
+}
+
+.tsk-prm-sel-opt > li {
+  background: #ffffff;
+  color: #000000;
+  display: block;
+  font-family: monospace;
+  font-size: 15px;
+  padding: 4px 5px;
+  width: auto;
+}
+
+.tsk-prm-sel-opt > li:hover {
+  background: #fff3d3;
+}
+
+.tsk-prm-sel-opt > li:active {
+  background: #ffe49a;
+}
+
+/* list */
+.tsk-prm-list {
+  list-style: none;
+  margin-left: 23px;
+  padding: 0;
+}
+
+.tsk-prm-list > li {
+  margin-bottom: 3px;
+}
+
+.tsk-prm-list > li > .tsk-prm-in {
+  display: inline-block;
+  margin-left: 0;
+}
+
+.tsk-prm-list > li > .tsk-prm-add,
+.tsk-prm-list > li > .tsk-prm-rm {
+  background-image: url("images/ui-icons_666666_256x240.png");
+  display: inline-block;
+  cursor: pointer;
+  position: relative;
+  top: 3px;
+}
+
+.tsk-prm-add:hover,
+.tsk-prm-rm:hover {
+  background-color: #dddddd;
+}
+
+.tsk-prm-add:active,
+.tsk-prm-rm:active {
+  background-color: #ffffff;
+}
+
+/* description */
+.tsk-prm-desc {
+  display: block;
+  margin-top: 5px;
+  margin-left: 25px;
+  max-width: 600px;
+}
+
+.tsk-prm.flag > .tsk-prm-desc {
+  margin-left: 30px;
+}
 
 
 /* % ######################################################### */

From b0eff7b5443f01744f3d158e8c7bd0fff9587ead Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Fri, 24 Jul 2015 16:05:37 -0400
Subject: [PATCH 02/85] Automatic JSON descriptor integration (auto-load)

Descriptors can now be added to plugins under cbrain_task_descriptors/
in the plugin's root directory. Once the plugin is installed, these
descriptors are then automatically loaded as CbrainTask subclasses as
with the rest of the plugin's task classes. No Ruby source files are
created by the generator; the task views and autoloading process have
been modified to avoid that requirement.
---
 Bourreau/Gemfile                              |   1 +
 Bourreau/config/application.rb                |  14 +-
 Bourreau/lib/cbrain_task_generators           |   1 +
 BrainPortal/app/models/cluster_task.rb        |  19 +-
 BrainPortal/app/models/portal_task.rb         |  19 +-
 BrainPortal/app/views/tasks/_params.html.erb  |  19 +-
 BrainPortal/app/views/tasks/show.html.erb     |   7 +-
 BrainPortal/config/application.rb             |  14 +-
 BrainPortal/config/initializers/cbrain.rb     |   7 +-
 .../schema_task_generator.rb                  |  34 +-
 .../schemas/boutiques.schema.json             | 358 +++++++++---------
 .../templates/edit_help.html.erb              |   6 +-
 BrainPortal/lib/tasks/cbrain_plugins.rake     | 129 +++----
 13 files changed, 341 insertions(+), 287 deletions(-)
 create mode 120000 Bourreau/lib/cbrain_task_generators

diff --git a/Bourreau/Gemfile b/Bourreau/Gemfile
index c4d0edba4..dd632c5f4 100644
--- a/Bourreau/Gemfile
+++ b/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"
diff --git a/Bourreau/config/application.rb b/Bourreau/config/application.rb
index 908d06d1f..736e2560d 100644
--- a/Bourreau/config/application.rb
+++ b/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.
diff --git a/Bourreau/lib/cbrain_task_generators b/Bourreau/lib/cbrain_task_generators
new file mode 120000
index 000000000..6cc485eef
--- /dev/null
+++ b/Bourreau/lib/cbrain_task_generators
@@ -0,0 +1 @@
+../../BrainPortal/lib/cbrain_task_generators
\ No newline at end of file
diff --git a/BrainPortal/app/models/cluster_task.rb b/BrainPortal/app/models/cluster_task.rb
index 50c0b5f8c..070f07525 100644
--- a/BrainPortal/app/models/cluster_task.rb
+++ b/BrainPortal/app/models/cluster_task.rb
@@ -1674,14 +1674,17 @@ def task_is_proper_subclass #:nodoc:
 end
 
 # Patch: pre-load all model files for the subclasses
-Dir.chdir(CBRAIN::TasksPlugins_Dir) do
-  Dir.glob("*.rb").each do |model|
-    next if model == "cbrain_task_class_loader.rb"
-    model.sub!(/.rb$/,"")
-    unless CbrainTask.const_defined? model.classify
-      #puts_blue "Loading CbrainTask subclass #{model.classify} from #{model}.rb ..."
-      require_dependency "#{CBRAIN::TasksPlugins_Dir}/#{model}.rb"
+[ CBRAIN::TasksPlugins_Dir, CBRAIN::TaskDescriptorsPlugins_Dir ].each do |dir|
+  Dir.chdir(dir) do
+    Dir.glob("*.rb").each do |model|
+      next if [
+        'cbrain_task_class_loader.rb',
+        'cbrain_task_descriptor_loader.rb'
+      ].include?(model)
+
+      model.sub!(/.rb$/, '')
+      require_dependency "#{dir}/#{model}.rb" unless
+        CbrainTask.const_defined? model.classify
     end
   end
 end
-
diff --git a/BrainPortal/app/models/portal_task.rb b/BrainPortal/app/models/portal_task.rb
index 7c77bdb28..e4c647cf3 100644
--- a/BrainPortal/app/models/portal_task.rb
+++ b/BrainPortal/app/models/portal_task.rb
@@ -702,14 +702,17 @@ def task_is_proper_subclass #:nodoc:
 end
 
 # Patch: pre-load all model files for the subclasses
-Dir.chdir(CBRAIN::TasksPlugins_Dir) do
-  Dir.glob("*.rb").each do |model|
-    next if model == "cbrain_task_class_loader.rb"
-    model.sub!(/.rb$/,"")
-    unless CbrainTask.const_defined? model.classify
-#      puts_blue "Loading CbrainTask subclass #{model.classify} from #{model}.rb ..."
-      require_dependency "#{CBRAIN::TasksPlugins_Dir}/#{model}.rb"
+[ CBRAIN::TasksPlugins_Dir, CBRAIN::TaskDescriptorsPlugins_Dir ].each do |dir|
+  Dir.chdir(dir) do
+    Dir.glob("*.rb").each do |model|
+      next if [
+        'cbrain_task_class_loader.rb',
+        'cbrain_task_descriptor_loader.rb'
+      ].include?(model)
+
+      model.sub!(/.rb$/, '')
+      require_dependency "#{dir}/#{model}.rb" unless
+        CbrainTask.const_defined? model.classify
     end
   end
 end
-
diff --git a/BrainPortal/app/views/tasks/_params.html.erb b/BrainPortal/app/views/tasks/_params.html.erb
index 909381b61..c5588ddb4 100644
--- a/BrainPortal/app/views/tasks/_params.html.erb
+++ b/BrainPortal/app/views/tasks/_params.html.erb
@@ -22,9 +22,14 @@
 #
 -%>
 
+<% locals = { :params  => @task.params, :form => form } %>
+
 <h2>Task Parameters
-  <% public_path = @task.public_path("edit_params_help.html") %>
-  <% if public_path %>
+  <% if @task.class.respond_to?(:raw_partial) %>
+    <%= overlay_content_link "(Help)", :class => "task_help_link", :enclosing_element => "span" do %>
+      <%= render :inline => @task.class.raw_partial(:edit_help), :locals => locals %>
+    <% end %>
+  <% elsif (public_path = @task.public_path("edit_params_help.html")) %>
     <%= overlay_ajax_link "(Help)", public_path.to_s, :class  => "task_help_link" %>
   <% end %>
   :
@@ -32,7 +37,9 @@
 
 <div class="generalbox">
 <%= error_messages_for(@task) %>
-<%= render :partial => task_partial('task_params'),
-           :locals  => { :params  => @task.params, :form => form }
- %>
-</div>
\ No newline at end of file
+<% if @task.class.respond_to?(:raw_partial) %>
+  <%= render :inline => @task.class.raw_partial(:task_params), :locals => locals %>
+<% else %>
+  <%= render :partial => task_partial('task_params'), :locals => locals %>
+<% end %>
+</div>
diff --git a/BrainPortal/app/views/tasks/show.html.erb b/BrainPortal/app/views/tasks/show.html.erb
index 00fb7acc2..6be2002a8 100644
--- a/BrainPortal/app/views/tasks/show.html.erb
+++ b/BrainPortal/app/views/tasks/show.html.erb
@@ -141,7 +141,12 @@
     <%= build_tabs do |tb| %>
        <%= tb.tab("Summary") do %>
          <% begin %>
-           <%= render :partial => task_partial('show_params'), :locals => { :task => @task, :params => @task.params } %>
+           <% locals = { :task => @task, :params  => @task.params } %>
+           <% if @task.class.respond_to?(:raw_partial) %>
+             <%= render :inline => @task.class.raw_partial(:show_params), :locals => locals %>
+           <% else %>
+             <%= render :partial => task_partial('show_params'), :locals => locals %>
+           <% end %>
          <% rescue ActionView::MissingTemplate %>
            <pre>Problem loading summary view (no template provided by task author).</pre>
          <% rescue => ex %>
diff --git a/BrainPortal/config/application.rb b/BrainPortal/config/application.rb
index a816e6871..32fdf7056 100644
--- a/BrainPortal/config/application.rb
+++ b/BrainPortal/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.
diff --git a/BrainPortal/config/initializers/cbrain.rb b/BrainPortal/config/initializers/cbrain.rb
index b5f29ace4..1e10fad39 100644
--- a/BrainPortal/config/initializers/cbrain.rb
+++ b/BrainPortal/config/initializers/cbrain.rb
@@ -43,9 +43,10 @@ class CBRAIN
                       "PID-#{Process.pid}"
 
   # CBRAIN plugins locations
-  Plugins_Dir          = "#{Rails.root.to_s}/cbrain_plugins"
-  TasksPlugins_Dir     = "#{Plugins_Dir}/installed-plugins/cbrain_task" # singular; historical
-  UserfilesPlugins_Dir = "#{Plugins_Dir}/installed-plugins/userfiles"
+  Plugins_Dir                = "#{Rails.root.to_s}/cbrain_plugins"
+  UserfilesPlugins_Dir       = "#{Plugins_Dir}/installed-plugins/userfiles"
+  TasksPlugins_Dir           = "#{Plugins_Dir}/installed-plugins/cbrain_task" # singular; historical
+  TaskDescriptorsPlugins_Dir = "#{Plugins_Dir}/installed-plugins/cbrain_task_descriptors"
 
   $CBRAIN_StartTime_Revision = "???"  # Will be filled in by validation script
 
diff --git a/BrainPortal/lib/cbrain_task_generators/schema_task_generator.rb b/BrainPortal/lib/cbrain_task_generators/schema_task_generator.rb
index 511a65a98..e5b316d07 100644
--- a/BrainPortal/lib/cbrain_task_generators/schema_task_generator.rb
+++ b/BrainPortal/lib/cbrain_task_generators/schema_task_generator.rb
@@ -26,11 +26,17 @@
 # files. The generated code can be added right away to CBRAIN's available tasks
 # or written to file for later modification.
 #
-# NOTE: Only JSON is currently supported
+# NOTE: Only JSON and a single schema (boutiques) is currently supported
 module SchemaTaskGenerator
 
   Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
 
+  # Directory where descriptor schemas are located
+  SCHEMA_DIR = "#{Rails.root.to_s}/lib/cbrain_task_generators/schemas"
+
+  # Default schema file to use when validating auto-loaded descriptors
+  DEFAULT_SCHEMA_FILE = 'boutiques.schema.json'
+
   # Represents a schema to validate task descriptors against
   class Schema
 
@@ -150,14 +156,20 @@ def integrate(register = true)
       # The newly created Tool and ToolConfig (if needed) will initially belong
       # to the core admin.
 
+      name         = @descriptor['name']
+      version      = @descriptor['tool-version'] || '(unknown)'
+      description  = @descriptor['description']  || ''
+      docker_image = @descriptor['docker-image']
+      resource     = RemoteResource.current_resource
+
       # Create and save a new Tool for this task, unless theres already one.
       Tool.new(
-        :name              => @descriptor['name'],
+        :name              => name,
         :user_id           => User.admin.id,
         :group_id          => User.admin.own_group.id,
         :category          => "scientific tool",
         :cbrain_task_class => task.to_s,
-        :description       => @descriptor['description']
+        :description       => description
       ).save! unless
         Tool.exists?(:cbrain_task_class => task.to_s)
 
@@ -168,15 +180,16 @@ def integrate(register = true)
 
       ToolConfig.new(
         :tool_id      => task.tool.id,
-        :bourreau_id  => RemoteResource.current_resource.id,
+        :bourreau_id  => resource.id,
         :group_id     => Group.everyone.id,
-        :version_name => @descriptor['tool-version'],
-        :docker_image => @descriptor['docker-image']
+        :version_name => version,
+        :description  => "#{name} #{version} on #{resource.name}",
+        :docker_image => docker_image
       ).save! unless
         ToolConfig.exists?(
           :tool_id      => task.tool.id,
           :bourreau_id  => RemoteResource.current_resource.id,
-          :version_name => @descriptor['tool-version']
+          :version_name => version
         )
     end
 
@@ -246,6 +259,13 @@ def self.generate(schema, descriptor, strict_validation = true)
     )
   end
 
+  # Returns the default Schema instance to use when validating descriptors
+  # without a specific schema or when auto-loading descriptors.
+  # (constructed from DEFAULT_SCHEMA_FILE)
+  def self.default_schema
+    @@default_schema ||= Schema.new("#{SCHEMA_DIR}/#{DEFAULT_SCHEMA_FILE}")
+  end
+
   # Utility method to convert a JSON string or file path into a hash.
   # Returns the hash directly if a hash is given.
   def self.expand_json(obj)
diff --git a/BrainPortal/lib/cbrain_task_generators/schemas/boutiques.schema.json b/BrainPortal/lib/cbrain_task_generators/schemas/boutiques.schema.json
index 0d3d3f501..22c2c0335 100644
--- a/BrainPortal/lib/cbrain_task_generators/schemas/boutiques.schema.json
+++ b/BrainPortal/lib/cbrain_task_generators/schemas/boutiques.schema.json
@@ -4,188 +4,186 @@
     "type": "object",
     "title": "Tool",
     "properties": {
-	"name": {
-	    "id": "http://github.com/boutiques/boutiques-schema/name",
-	    "minLength": 1,
-	    "description": "Tool name.",
-	    "type": "string"
-	},
-	"tool-version": {
-	    "id": "http://github.com/boutiques/boutiques-schema/description",
-	    "minLength": 1,
-	    "description": "Tool version.",
-	    "type": "string"
-	},
-	"description": {
-	    "id": "http://github.com/boutiques/boutiques-schema/description",
-	    "minLength": 1,
-	    "description": "Tool description.",
-	    "type": "string"
-	},
-	"command-line": {
-	    "id": "http://github.com/boutiques/boutiques-schema/command-line",
-	    "minLength": 1,
-	    "description": "A string that describes the tool command line, where input and output values are identified by \"keys\". At runtime, command-line keys are substituted with flags and values.",
-	    "type": "string"
-	},
-	"docker-image": {
-	    "id": "http://github.com/boutiques/boutiques-schema/docker-image",
-	    "minLength": 1,
-	    "description": "Name of a Docker image where tool is installed and configured. Example: docker.io/neurodebian.",
-	    "type": "string"
-	},
-	"docker-index": {
-	    "id": "http://github.com/boutiques/boutiques-schema/docker-index",
-	    "minLength": 1,
-	    "description": "Docker index where Docker image is available.",
-	    "default": "http://index.docker.io",
-	    "type": "string"
-	},
-	"schema-version": {
-	    "id": "http://github.com/boutiques/boutiques-schema/schema-version",
-	    "type": "string",
-	    "description": "Version of the schema used.",
-	    "enum": ["0.2-snapshot"]
-	},
-	"inputs": {
-	    "id": "http://github.com/boutiques/boutiques-schema/inputs",
-	    "type": "array",
-	    "items": {
-		"id": "http://github.com/boutiques/boutiques-schema/input",
-		"type": "object",
-		"properties": {
-		    "id": {
-			"id": "http://github.com/boutiques/boutiques-schema/input/id",
-			"minLength": 1,
-			"description": "A short, unique, informative identifier containing only alphanumeric characters and underscores. Typically used to generate variable names. Example: \"data_file\".",
-			"type": "string",
-			"pattern": "^[0-9,_,a-z,A-Z]*$"
-		    },
-		    "name": {
-			"id": "http://github.com/boutiques/boutiques-schema/input/name",
-			"minLength": 1,
-			"description": "A human-readable input name. Example: 'Data file'.",
-			"type": "string"
-		    },
-		    "type": {
-			"id": "http://github.com/boutiques/boutiques-schema/input/type",
-			"type": "string",
-			"description": "Input type.",
-			"enum": ["String", "File", "Flag" , "Number" ]
-		    },
-		    "description": {
-			"id": "http://github.com/boutiques/boutiques-schema/input/description",
-			"minLength": 1,
-			"description": "Input description.",
-			"type": "string"
-		    },
-		    "command-line-key": {
-			"id": "http://github.com/boutiques/boutiques-schema/input/command-line-key",
-			"minLength": 1,
-			"description": "A string contained in command-line, substituted by the input value and/or flag at runtime.",
-			"type": "string"
-		    },
-		    "list": {
-			"id": "http://github.com/boutiques/boutiques-schema/input/list",
-			"description":"True if input is a list of value. An input of type \"Flag\" cannot be a list.",
-			"type": "boolean"
-		    },
-		    "optional":{
-			"id": "http://github.com/boutiques/boutiques-schema/input/optional",
-			"description": "True if input is optional.",
-			"type": "boolean"
-		    },
-		    "command-line-flag":{
-			"id": "http://github.com/boutiques/boutiques-schema/input/command-line-flag",
-			"minLength": 1,
-			"description": "Option flag of the input, involved in the command-line-key substitution. Inputs of type \"Flag\" have to have a command-line flag. Examples: -v, --force.",
-			"type": "string"
-		    },
-		    "default-value":{
-			"id": "http://github.com/boutiques/boutiques-schema/input/default-value",
-			"minLength": 1,
-			"description": "Default value of the input, used by the tool when no option is specified.",
-			"type": "string"
-		    }
-		},
-		"required": [
-		    "name",
-		    "id",
-		    "type"
-		]
-	    }
-	},
-	"output-files": {
-	    "id": "http://github.com/boutiques/boutiques-schema/output-files",
-	    "type": "array",
-	    "items": {
-		"id": "http://github.com/boutiques/boutiques-schema/output",
-		"type": "object",
-		"properties": {
-		    "id": {
-			"id": "http://github.com/boutiques/boutiques-schema/output/id",
-			"minLength": 1,
-			"description": "A short, unique, informative identifier containing only alphanumeric characters and underscores. Typically used to generate variable names. Example: \"data_file\"",
-			"pattern": "^[0-9,_,a-z,A-Z]*$",
-			"type": "string"
-		    },
-		    "name": {
-			"id": "http://github.com/boutiques/boutiques-schema/output/name",
-			"description": "A human-readable output name. Example: 'Data file'",
-			"minLength": 1,
-			"type": "string"
-		    },
-		    "description": {
-			"id": "http://github.com/boutiques/boutiques-schema/output/description",
-			"description": "Output description.",
-			"minLength": 1,
-			"type": "string"
-		    },
-		    "command-line-key": {
-			"id": "http://github.com/boutiques/boutiques-schema/output/command-line-key",
-			"description": "A string contained in command-line, substituted by the output value and/or flag at runtime.",
-			"minLength": 1,
-			"type": "string"
-		    },
-		    "path-template": {
-			"id": "http://github.com/boutiques/boutiques-schema/output/path-template",
-			"description": "Describes the output file path relatively to the execution directory. May contain input command-line-keys. Example: \"results/[INPUT1]_brain.mnc\".",
-			"minLength": 1,
-			"type": "string"
-		    },
-		    "list": {
-			"id": "http://github.com/boutiques/boutiques-schema/output/list",
-			"description": "True if output is a list of value.",
-			"type": "boolean"
-		    },
-		    "optional":{
-			"id": "http://github.com/boutiques/boutiques-schema/output/optional",
-			"description": "True if output may not be produced by the tool.",
-			"type": "boolean"
-		    },
-		    "command-line-flag":{
-			"id": "http://github.com/boutiques/boutiques-schema/output/command-line-flag",
-			"minLength": 1,
-			"description": "Option flag of the output, involved in the command-line-key substitution. Examples: -o, --output",
-			"type": "string"
-		    }
-		    
-		},
-		"required": [
-		    "id",
-		    "name",
-		    "path-template"
-		]
-	    }
-	}
+        "name": {
+            "id": "http://github.com/boutiques/boutiques-schema/name",
+            "minLength": 1,
+            "description": "Tool name.",
+            "type": "string"
+        },
+        "tool-version": {
+            "id": "http://github.com/boutiques/boutiques-schema/description",
+            "minLength": 1,
+            "description": "Tool version.",
+            "type": "string"
+        },
+        "description": {
+            "id": "http://github.com/boutiques/boutiques-schema/description",
+            "minLength": 1,
+            "description": "Tool description.",
+            "type": "string"
+        },
+        "command-line": {
+            "id": "http://github.com/boutiques/boutiques-schema/command-line",
+            "minLength": 1,
+            "description": "A string that describes the tool command line, where input and output values are identified by \"keys\". At runtime, command-line keys are substituted with flags and values.",
+            "type": "string"
+        },
+        "docker-image": {
+            "id": "http://github.com/boutiques/boutiques-schema/docker-image",
+            "minLength": 1,
+            "description": "Name of a Docker image where tool is installed and configured. Example: docker.io/neurodebian.",
+            "type": "string"
+        },
+        "docker-index": {
+            "id": "http://github.com/boutiques/boutiques-schema/docker-index",
+            "minLength": 1,
+            "description": "Docker index where Docker image is available.",
+            "default": "http://index.docker.io",
+            "type": "string"
+        },
+        "schema-version": {
+            "id": "http://github.com/boutiques/boutiques-schema/schema-version",
+            "type": "string",
+            "description": "Version of the schema used.",
+            "enum": ["0.2-snapshot"]
+        },
+        "inputs": {
+            "id": "http://github.com/boutiques/boutiques-schema/inputs",
+            "type": "array",
+            "items": {
+                "id": "http://github.com/boutiques/boutiques-schema/input",
+                "type": "object",
+                "properties": {
+                    "id": {
+                        "id": "http://github.com/boutiques/boutiques-schema/input/id",
+                        "minLength": 1,
+                        "description": "A short, unique, informative identifier containing only alphanumeric characters and underscores. Typically used to generate variable names. Example: \"data_file\".",
+                        "type": "string",
+                        "pattern": "^[0-9,_,a-z,A-Z]*$"
+                    },
+                    "name": {
+                        "id": "http://github.com/boutiques/boutiques-schema/input/name",
+                        "minLength": 1,
+                        "description": "A human-readable input name. Example: 'Data file'.",
+                        "type": "string"
+                    },
+                    "type": {
+                        "id": "http://github.com/boutiques/boutiques-schema/input/type",
+                        "type": "string",
+                        "description": "Input type.",
+                        "enum": ["String", "File", "Flag" , "Number" ]
+                    },
+                    "description": {
+                        "id": "http://github.com/boutiques/boutiques-schema/input/description",
+                        "minLength": 1,
+                        "description": "Input description.",
+                        "type": "string"
+                    },
+                    "command-line-key": {
+                        "id": "http://github.com/boutiques/boutiques-schema/input/command-line-key",
+                        "minLength": 1,
+                        "description": "A string contained in command-line, substituted by the input value and/or flag at runtime.",
+                        "type": "string"
+                    },
+                    "list": {
+                        "id": "http://github.com/boutiques/boutiques-schema/input/list",
+                        "description":"True if input is a list of value. An input of type \"Flag\" cannot be a list.",
+                        "type": "boolean"
+                    },
+                    "optional":{
+                        "id": "http://github.com/boutiques/boutiques-schema/input/optional",
+                        "description": "True if input is optional.",
+                        "type": "boolean"
+                    },
+                    "command-line-flag":{
+                        "id": "http://github.com/boutiques/boutiques-schema/input/command-line-flag",
+                        "minLength": 1,
+                        "description": "Option flag of the input, involved in the command-line-key substitution. Inputs of type \"Flag\" have to have a command-line flag. Examples: -v, --force.",
+                        "type": "string"
+                    },
+                    "default-value":{
+                        "id": "http://github.com/boutiques/boutiques-schema/input/default-value",
+                        "minLength": 1,
+                        "description": "Default value of the input, used by the tool when no option is specified."
+                    }
+                },
+                "required": [
+                    "name",
+                    "id",
+                    "type"
+                ]
+            }
+        },
+        "output-files": {
+            "id": "http://github.com/boutiques/boutiques-schema/output-files",
+            "type": "array",
+            "items": {
+                "id": "http://github.com/boutiques/boutiques-schema/output",
+                "type": "object",
+                "properties": {
+                    "id": {
+                        "id": "http://github.com/boutiques/boutiques-schema/output/id",
+                        "minLength": 1,
+                        "description": "A short, unique, informative identifier containing only alphanumeric characters and underscores. Typically used to generate variable names. Example: \"data_file\"",
+                        "pattern": "^[0-9,_,a-z,A-Z]*$",
+                        "type": "string"
+                    },
+                    "name": {
+                        "id": "http://github.com/boutiques/boutiques-schema/output/name",
+                        "description": "A human-readable output name. Example: 'Data file'",
+                        "minLength": 1,
+                        "type": "string"
+                    },
+                    "description": {
+                        "id": "http://github.com/boutiques/boutiques-schema/output/description",
+                        "description": "Output description.",
+                        "minLength": 1,
+                        "type": "string"
+                    },
+                    "command-line-key": {
+                        "id": "http://github.com/boutiques/boutiques-schema/output/command-line-key",
+                        "description": "A string contained in command-line, substituted by the output value and/or flag at runtime.",
+                        "minLength": 1,
+                        "type": "string"
+                    },
+                    "path-template": {
+                        "id": "http://github.com/boutiques/boutiques-schema/output/path-template",
+                        "description": "Describes the output file path relatively to the execution directory. May contain input command-line-keys. Example: \"results/[INPUT1]_brain.mnc\".",
+                        "minLength": 1,
+                        "type": "string"
+                    },
+                    "list": {
+                        "id": "http://github.com/boutiques/boutiques-schema/output/list",
+                        "description": "True if output is a list of value.",
+                        "type": "boolean"
+                    },
+                    "optional":{
+                        "id": "http://github.com/boutiques/boutiques-schema/output/optional",
+                        "description": "True if output may not be produced by the tool.",
+                        "type": "boolean"
+                    },
+                    "command-line-flag":{
+                        "id": "http://github.com/boutiques/boutiques-schema/output/command-line-flag",
+                        "minLength": 1,
+                        "description": "Option flag of the output, involved in the command-line-key substitution. Examples: -o, --output",
+                        "type": "string"
+                    }
+                },
+                "required": [
+                    "id",
+                    "name",
+                    "path-template"
+                ]
+            }
+        }
     },
     "required": [
-	"name",
-	"description",
-	"command-line",
-	"schema-version",
-	"inputs",
-	"output-files"
+        "name",
+        "description",
+        "command-line",
+        "schema-version",
+        "inputs",
+        "output-files"
     ]
 }
 
diff --git a/BrainPortal/lib/cbrain_task_generators/templates/edit_help.html.erb b/BrainPortal/lib/cbrain_task_generators/templates/edit_help.html.erb
index fc3fc3d35..8bce1e8f8 100644
--- a/BrainPortal/lib/cbrain_task_generators/templates/edit_help.html.erb
+++ b/BrainPortal/lib/cbrain_task_generators/templates/edit_help.html.erb
@@ -58,10 +58,12 @@
   <%- end -%>
   </li>
 <%- end -%>
-<h1><%= descriptor['name'] %></h1>
+<h1>
+  <%= descriptor['name'] %>
 <%- if descriptor['tool-version'] -%>
-<h4><%= descriptor['tool-version'] %></h4>
+  <%= descriptor['tool-version'] %>
 <%- end -%>
+</h1>
 <br />
 
 <%- if descriptor['description'] -%>
diff --git a/BrainPortal/lib/tasks/cbrain_plugins.rake b/BrainPortal/lib/tasks/cbrain_plugins.rake
index 24b93365d..32020c8a5 100644
--- a/BrainPortal/lib/tasks/cbrain_plugins.rake
+++ b/BrainPortal/lib/tasks/cbrain_plugins.rake
@@ -31,10 +31,11 @@ namespace :cbrain do
       # Unfortunately we don't have access to cbrain.rb where some useful constants are defined in the
       # CBRAIN class, such as CBRAIN::TasksPlugins_Dir ; if we ever change where plugins are stored, we
       # have to update this here and the cbrain.rb file too.
-      plugins_dir           = Rails.root            + "cbrain_plugins"
-      installed_plugins_dir = plugins_dir           + "installed-plugins"
-      tasks_plugins_dir     = installed_plugins_dir + "cbrain_task"
-      userfiles_plugins_dir = installed_plugins_dir + "userfiles"
+      plugins_dir             = Rails.root            + "cbrain_plugins"
+      installed_plugins_dir   = plugins_dir           + "installed-plugins"
+      userfiles_plugins_dir   = installed_plugins_dir + "userfiles"
+      tasks_plugins_dir       = installed_plugins_dir + "cbrain_task"
+      descriptors_plugins_dir = installed_plugins_dir + "cbrain_task_descriptors"
 
       Dir.chdir(plugins_dir.to_s) do
         packages = Dir.glob('*').reject { |path| path =~ /^(installed-plugins)$/ }.select { |f| File.directory?(f) }
@@ -46,64 +47,57 @@ namespace :cbrain do
           puts "Checking plugins in package '#{package}'..."
           Dir.chdir(package) do
 
-            # Setup each userfile plugin
-
-            files = Dir.glob('userfiles/*').select { |f| File.directory?(f) }
-            puts "Found #{files.size} file(s) to set up..."
-            files.each do |u_slash_f|                                  # "userfiles/abcd"
-              myfile           = Pathname.new(u_slash_f).basename.to_s # "abcd"
-              symlink_location = userfiles_plugins_dir + myfile
-              plugin_location  = plugins_dir           + package + u_slash_f
-              symlink_value    = plugin_location.relative_path_from(symlink_location.parent)
-              #puts "#{u_slash_f} #{myfile}\n TS=#{symlink_location}\n PL=#{plugin_location}\n LL=#{symlink_value}"
-
-              if File.exists?(symlink_location)
-                if File.symlink?(symlink_location)
-                  if File.readlink(symlink_location) == symlink_value.to_s
-                    puts "-> Userfile already setup: '#{myfile}'."
+            # Setup a single unit (userfiles, tasks or descriptors)
+            setup = lambda do |glob, name, directory, condition: nil, after: nil|
+              files = Dir.glob(glob)
+              files.select!(&condition) if condition
+              puts "Found #{files.size} #{name}(s) to set up..."
+              files.each do |u_slash_f|
+                plugin           = Pathname.new(u_slash_f).basename.to_s
+                symlink_location = directory   + plugin
+                plugin_location  = plugins_dir + package + u_slash_f
+                symlink_value    = plugin_location.relative_path_from(symlink_location.parent)
+
+                if File.exists?(symlink_location)
+                  if File.symlink?(symlink_location)
+                    if File.readlink(symlink_location) == symlink_value.to_s
+                      puts "-> #{name.capitalize} already setup: '#{plugin}'."
+                      next
+                    end
+                    puts "-> Error: there is already a symlink with an unexpected value here:\n   #{symlink_location}"
                     next
                   end
-                  puts "-> Error: there is already a symlink with an unexpected value here:\n   #{symlink_location}"
+                  puts "-> Error: there is already an entry (file or directory) here:\n   #{symlink_location}"
                   next
                 end
-                puts "-> Error: there is already an entry (file or directory) here:\n   #{symlink_location}"
-                next
-              end
 
-              puts "-> Creating symlink for userfile '#{myfile}'."
-              File.symlink symlink_value, symlink_location
-              #puts "  #{symlink_value} as #{symlink_location}"
+                puts "-> Creating symlink for #{name} '#{plugin}'."
+                File.symlink symlink_value, symlink_location
+
+                after.(symlink_location) if after
+              end
             end
 
+            # Setup each userfile plugin
+            setup.('userfiles/*', 'userfile', userfiles_plugins_dir,
+              condition: lambda { |f| File.directory?(f) }
+            )
 
             # Setup each cbrain_task plugin
-
-            tasks = Dir.glob('cbrain_task/*').select { |f| File.directory?(f) }
-            puts "Found #{tasks.size} tasks(s) to set up..."
-            tasks.each do |u_slash_t|                                  # "cbrain_task/abcd"
-              mytask           = Pathname.new(u_slash_t).basename.to_s # "abcd"
-              symlink_location = tasks_plugins_dir + mytask
-              plugin_location  = plugins_dir       + package + u_slash_t
-              symlink_value    = plugin_location.relative_path_from(symlink_location.parent)
-
-              if File.exists?(symlink_location)
-                if File.symlink?(symlink_location)
-                  if File.readlink(symlink_location) == symlink_value.to_s
-                    puts "-> Task already setup: '#{mytask}'."
-                    next
-                  end
-                  puts "-> Error: there is already a symlink with an unexpected value here:\n   #{symlink_location}"
-                  next
-                end
-                puts "-> Error: there is already an entry (file or directory) here:\n   #{symlink_location}"
-                next
+            setup.('cbrain_task/*', 'task', tasks_plugins_dir,
+              condition: lambda { |f| File.directory?(f) },
+              after: lambda do |symlink_location|
+                File.symlink "cbrain_task_class_loader.rb", "#{symlink_location}.rb"
               end
+            )
 
-              puts "-> Creating symlink for task '#{mytask}'."
-              File.symlink symlink_value, symlink_location
-              File.symlink "cbrain_task_class_loader.rb", "#{symlink_location}.rb" # intelligent loader wrapper
-              #puts "  #{symlink_value} as #{symlink_location}"
-            end
+            # Setup each cbrain_task descriptor plugin
+            setup.('cbrain_task_descriptors/*', 'descriptor', descriptors_plugins_dir,
+              condition: lambda { |f| File.extname(f) == '.json' },
+              after: lambda do |symlink_location|
+                File.symlink "cbrain_task_descriptor_loader.rb", "#{symlink_location.sub(/.json$/, '.rb')}"
+              end
+            )
 
           end # chdir package
         end # each package
@@ -203,26 +197,25 @@ namespace :cbrain do
       # Unfortunately we don't have access to cbrain.rb where some useful constants are defined in the
       # CBRAIN class, such as CBRAIN::TasksPlugins_Dir ; if we ever change where plugins are stored, we
       # have to update this here and the cbrain.rb file too.
-      plugins_dir           = Rails.root            + "cbrain_plugins"
-      installed_plugins_dir = plugins_dir           + "installed-plugins"
-      tasks_plugins_dir     = installed_plugins_dir + "cbrain_task"
-      userfiles_plugins_dir = installed_plugins_dir + "userfiles"
-
-      puts "Erasing all symlinks for userfiles installed from CBRAIN plugins..."
-      Dir.chdir(userfiles_plugins_dir.to_s) do
-        Dir.glob('*').select { |f| File.symlink?(f) }.each do |f|
-          puts "-> Erasing link for userfile '#{f}'."
-          File.unlink(f)
+      plugins_dir             = Rails.root            + "cbrain_plugins"
+      installed_plugins_dir   = plugins_dir           + "installed-plugins"
+      userfiles_plugins_dir   = installed_plugins_dir + "userfiles"
+      tasks_plugins_dir       = installed_plugins_dir + "cbrain_task"
+      descriptors_plugins_dir = installed_plugins_dir + "cbrain_task_descriptors"
+
+      erase = lambda do |name, dir|
+        puts "Erasing all symlinks for #{name.pluralize} installed from CBRAIN plugins..."
+        Dir.chdir(dir.to_s) do
+          Dir.glob('*').select { |f| File.symlink?(f) }.each do |f|
+            puts "-> Erasing link for #{name} '#{f}'."
+            File.unlink(f)
+          end
         end
       end
 
-      puts "Erasing all symlinks for tasks installed from CBRAIN plugins..."
-      Dir.chdir(tasks_plugins_dir.to_s) do
-        Dir.glob('*').select { |f| File.symlink?(f) }.each do |f|
-          puts "-> Erasing link for task '#{f}'."
-          File.unlink(f)
-        end
-      end
+      erase.('userfile',   userfiles_plugins_dir)
+      erase.('task',       tasks_plugins_dir)
+      erase.('descriptor', descriptors_plugins_dir)
 
     end
 

From 57d07e87ce10b2eca93b3568653e4d6c432ee460 Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Tue, 28 Jul 2015 15:44:49 -0400
Subject: [PATCH 03/85] Version switcher CbrainTask wrapper, minor fixes

Switching between multiple tool versions is now supported via a special
'versions switcher' class which wraps the classes generated by the
generator and turns itself into the correct generated CbrainTask
subclass when a tool config is assigned.

Note that this functionality currently breaks if the admin manually adds
another tool config with a different version without a matching
descriptor.
---
 BrainPortal/app/models/cluster_task.rb        |   2 +-
 BrainPortal/app/models/portal_task.rb         |   2 +-
 BrainPortal/app/views/tasks/_params.html.erb  |  15 +-
 BrainPortal/app/views/tasks/show.html.erb     |  11 +-
 .../schema_task_generator.rb                  | 185 ++++++++++++++++--
 .../templates/bourreau.rb.erb                 |   6 +-
 .../templates/portal.rb.erb                   |   2 +-
 7 files changed, 196 insertions(+), 27 deletions(-)

diff --git a/BrainPortal/app/models/cluster_task.rb b/BrainPortal/app/models/cluster_task.rb
index 070f07525..347c9a40b 100644
--- a/BrainPortal/app/models/cluster_task.rb
+++ b/BrainPortal/app/models/cluster_task.rb
@@ -1684,7 +1684,7 @@ def task_is_proper_subclass #:nodoc:
 
       model.sub!(/.rb$/, '')
       require_dependency "#{dir}/#{model}.rb" unless
-        CbrainTask.const_defined? model.classify
+        [ model.classify, model.camelize ].any? { |m| CbrainTask.const_defined?(m) rescue nil }
     end
   end
 end
diff --git a/BrainPortal/app/models/portal_task.rb b/BrainPortal/app/models/portal_task.rb
index e4c647cf3..0085574d0 100644
--- a/BrainPortal/app/models/portal_task.rb
+++ b/BrainPortal/app/models/portal_task.rb
@@ -712,7 +712,7 @@ def task_is_proper_subclass #:nodoc:
 
       model.sub!(/.rb$/, '')
       require_dependency "#{dir}/#{model}.rb" unless
-        CbrainTask.const_defined? model.classify
+        [ model.classify, model.camelize ].any? { |m| CbrainTask.const_defined?(m) rescue nil }
     end
   end
 end
diff --git a/BrainPortal/app/views/tasks/_params.html.erb b/BrainPortal/app/views/tasks/_params.html.erb
index c5588ddb4..c870f878e 100644
--- a/BrainPortal/app/views/tasks/_params.html.erb
+++ b/BrainPortal/app/views/tasks/_params.html.erb
@@ -22,12 +22,17 @@
 #
 -%>
 
-<% locals = { :params  => @task.params, :form => form } %>
+<%
+  locals      = { :params  => @task.params, :form => form }
+  raw_partial = lambda do |partial|
+    @task.class.raw_partial(partial) if @task.class.respond_to?(:raw_partial)
+  end
+%>
 
 <h2>Task Parameters
-  <% if @task.class.respond_to?(:raw_partial) %>
+  <% if raw_partial.(:edit_help) %>
     <%= overlay_content_link "(Help)", :class => "task_help_link", :enclosing_element => "span" do %>
-      <%= render :inline => @task.class.raw_partial(:edit_help), :locals => locals %>
+      <%= render :inline => raw_partial.(:edit_help), :locals => locals %>
     <% end %>
   <% elsif (public_path = @task.public_path("edit_params_help.html")) %>
     <%= overlay_ajax_link "(Help)", public_path.to_s, :class  => "task_help_link" %>
@@ -37,8 +42,8 @@
 
 <div class="generalbox">
 <%= error_messages_for(@task) %>
-<% if @task.class.respond_to?(:raw_partial) %>
-  <%= render :inline => @task.class.raw_partial(:task_params), :locals => locals %>
+<% if raw_partial.(:task_params) %>
+  <%= render :inline => raw_partial.(:task_params), :locals => locals %>
 <% else %>
   <%= render :partial => task_partial('task_params'), :locals => locals %>
 <% end %>
diff --git a/BrainPortal/app/views/tasks/show.html.erb b/BrainPortal/app/views/tasks/show.html.erb
index 6be2002a8..d3cae6c5c 100644
--- a/BrainPortal/app/views/tasks/show.html.erb
+++ b/BrainPortal/app/views/tasks/show.html.erb
@@ -141,9 +141,14 @@
     <%= build_tabs do |tb| %>
        <%= tb.tab("Summary") do %>
          <% begin %>
-           <% locals = { :task => @task, :params  => @task.params } %>
-           <% if @task.class.respond_to?(:raw_partial) %>
-             <%= render :inline => @task.class.raw_partial(:show_params), :locals => locals %>
+           <%
+             locals = { :task => @task, :params  => @task.params }
+             raw_partial = lambda do |partial|
+               @task.class.raw_partial(partial) if @task.class.respond_to?(:raw_partial)
+             end
+           %>
+           <% if raw_partial.(:show_params) %>
+             <%= render :inline => raw_partial.(:show_params), :locals => locals %>
            <% else %>
              <%= render :partial => task_partial('show_params'), :locals => locals %>
            <% end %>
diff --git a/BrainPortal/lib/cbrain_task_generators/schema_task_generator.rb b/BrainPortal/lib/cbrain_task_generators/schema_task_generator.rb
index e5b316d07..93a2ba1de 100644
--- a/BrainPortal/lib/cbrain_task_generators/schema_task_generator.rb
+++ b/BrainPortal/lib/cbrain_task_generators/schema_task_generator.rb
@@ -114,9 +114,19 @@ def initialize(attributes)
     # Integrates the encapsulated CbrainTask in this CBRAIN installation.
     # Unless +register+ is specified to be false, this method will add the
     # required Tool and ToolConfig if necessary for the CbrainTask to be
-    # useable right away (Since almost all information required to make the
+    # useable right away (since almost all information required to make the
     # Tool and ToolConfig objects is available in the spec).
-    def integrate(register = true)
+    # Also, unless +multi_version+ is specified to be false, this method will
+    # wrap the encapsulated CbrainTask in a version switcher class to allow
+    # different CbrainTask classes for each tool version.
+    # Returns the newly generated CbrainTask subclass.
+    def integrate(register: true, multi_version: true)
+      # Make sure the task class about to be generated does not already exist,
+      # to avoid mixing the classes up.
+      name = SchemaTaskGenerator.classify(@name)
+      Object.send(:remove_const, name)     if Object.const_defined?(name)
+      CbrainTask.send(:remove_const, name) if CbrainTask.const_defined?(name)
+
       # As the same code is used to dynamically load tasks descriptors and
       # create task templates, the class definitions are generated as strings
       # (Otherwise the source wouldn't be available to write down the generated
@@ -125,8 +135,8 @@ def integrate(register = true)
       eval @source[Rails.root.to_s =~ /BrainPortal$/ ? :portal : :bourreau]
 
       # Try and retrieve the just-generated task class
-      task   = @name.camelize.constantize rescue nil
-      task ||= "CbrainTask::#{@name.camelize}".constantize
+      task   = name.constantize rescue nil
+      task ||= "CbrainTask::#{name}".constantize
 
       # Since the task class doesn't have a matching cbrain_plugins directory
       # tree, some methods need to be added/redefined to ensure the cooperation
@@ -146,23 +156,48 @@ def integrate(register = true)
           :task_params => generated.source[:task_params],
           :show_params => generated.source[:show_params],
           :edit_help   => generated.source[:edit_help]
-        })[partial];
+        })[partial]
       end
 
-      return unless register
+      # If multi-versioning is enabled, replace the task class object constant
+      # in CbrainTask (or Object) by a version switcher wrapper class.
+      if multi_version
+        # Build the corresponding switcher and add the task's version and class
+        # to it.
+        version  = @descriptor['tool-version']
+        switcher = SchemaTaskGenerator.version_switcher(name)
+        switcher.known_versions[version] = task
+
+        # Redefine the CbrainTask or Object constant pointing to the task's
+        # class to point to the switcher instead.
+        mod = [ Object, CbrainTask ]
+          .select { |m| m.const_defined?(name) }
+          .first
+        if mod
+          mod.send(:remove_const, name)
+          mod.const_set(name, switcher)
+        end
+      end
 
       # With the task class and descriptor, we have enough information to
       # generate a Tool and ToolConfig to register the tool into CBRAIN.
-      # The newly created Tool and ToolConfig (if needed) will initially belong
-      # to the core admin.
+      register(task) if register
+
+      task
+    end
 
+    # Register a newly generated CbrainTask subclass (+task+) in this CBRAIN
+    # installation, creating the appropriate Tool and ToolConfig objects from
+    # the information contained in the descriptor. The newly created Tool and
+    # ToolConfig will initially belong to the core admin.
+    def register(task)
       name         = @descriptor['name']
       version      = @descriptor['tool-version'] || '(unknown)'
       description  = @descriptor['description']  || ''
       docker_image = @descriptor['docker-image']
       resource     = RemoteResource.current_resource
 
-      # Create and save a new Tool for this task, unless theres already one.
+      # Create and save a new Tool for the task, unless theres already one.
       Tool.new(
         :name              => name,
         :user_id           => User.admin.id,
@@ -173,7 +208,7 @@ def integrate(register = true)
       ).save! unless
         Tool.exists?(:cbrain_task_class => task.to_s)
 
-      # Create and save a new ToolConfig for this task on this server, unless
+      # Create and save a new ToolConfig for the task on this server, unless
       # theres already one. Only applies to Bourreaux (as it would make no
       # sense on the portal).
       return if Rails.root.to_s =~ /BrainPortal$/
@@ -188,7 +223,7 @@ def integrate(register = true)
       ).save! unless
         ToolConfig.exists?(
           :tool_id      => task.tool.id,
-          :bourreau_id  => RemoteResource.current_resource.id,
+          :bourreau_id  => resource.id,
           :version_name => version
         )
     end
@@ -231,7 +266,7 @@ def to_directory(path)
   # validation issues.
   def self.generate(schema, descriptor, strict_validation = true)
     descriptor = self.expand_json(descriptor)
-    name       = descriptor['name'].camelize
+    name       = self.classify(descriptor['name'])
     schema     = Schema.new(schema) unless schema.is_a?(Schema)
     errors     = schema.send(
       strict_validation ? :'validate!' : :validate,
@@ -259,6 +294,123 @@ def self.generate(schema, descriptor, strict_validation = true)
     )
   end
 
+  # Generate (or retrieve if it has been generated already) a version switcher
+  # class for CbrainTask subclasses named +name+. The version switcher class
+  # will behave just like a blank CbrainTask subclass until it is assigned
+  # a ToolConfig. It will then replace its methods with the ones from the
+  # CbrainTask subclass corresponding to that particular version:
+  #   class A < PortalTask
+  #     def f; :a; end
+  #   end
+  #
+  #   class B < PortalTask
+  #     def f; :b; end
+  #   end
+  #
+  #   s = version_switcher('A')
+  #   s.known_versions['1.1'] = A
+  #   s.known_versions['1.2'] = B
+  #
+  #   s.tool_config = ToolConfig.new(:version => '1.1')
+  #   s.f # :a
+  def self.version_switcher(name)
+    base = Rails.root.to_s =~ /BrainPortal$/ ? PortalTask : ClusterTask
+    @@version_switchers       ||= {}
+    @@version_switchers[name] ||= Class.new(base) do
+
+      # Versions known to this version switcher and their associated CbrainTask
+      # subclasses.
+      def self.known_versions
+        class_variable_set(:@@known_versions, {}) unless
+          class_variable_defined?(:@@known_versions)
+
+        class_variable_get(:@@known_versions)
+      end
+
+      # Add a few singleton methods on the object to perform a version switch
+      # once the tool config is set.
+      after_initialize do
+        # FIXME: the simplest and most straightforward way to make the version
+        # switcher task instance become an instance of the version-specific
+        # class would be to directly change the instance's class.
+        # At the time of writing, this is impossible in Ruby.
+        # This method (+as_version+) tries its best to mimic the missing
+        # functionality.
+
+        # Convert this blank CbrainTask object (instance of the version switcher
+        # class) to a more-or-less real instance of the class corresponding to
+        # +version+ by including all of its methods in, replacing the defaults
+        # from PortalTask or ClusterTask.
+        define_singleton_method(:as_version) do |version|
+          cb_error "Unknown or invalid version '#{version}'" unless
+            (version_class = self.class.known_versions[version])
+
+          # Use the Ruby 2.0 refinement API to include version_class methods
+          # inside this object's singleton class (or metaclass)
+          metaclass = class << self; self; end
+          metaclass.include(Module.new { include refine(version_class) { } })
+
+          # And try to make the object appear to be a version_class.
+          define_singleton_method(:class) { version_class }
+          define_singleton_method(:kind_of?) { |klass| is_a?(klass) }
+          define_singleton_method(:is_a?) do |klass|
+            klass <= version_class || super(klass)
+          end
+          define_singleton_method(:instance_of?) do |klass|
+            klass == version_class || super(klass)
+          end
+
+          # An object can only be given methods for a single version, and
+          # exactly once. Conflicts and odd issues could occur otherwise.
+          # Thus, there is no longer a need for :as_version or the tool_config
+          # setter hooks.
+          [ :as_version, :tool_config=, :tool_config_id= ].each do |m|
+            metaclass.send(:remove_method, m) rescue nil
+          end
+        end
+
+        # If we dont have a tool config already, try to catch the exact moment
+        # when the version switcher instance gets assigned its tool config and
+        # invoke as_version when it happens.
+        if self.tool_config
+          self.as_version(self.tool_config.version_name)
+        else
+          [ :tool_config=, :tool_config_id= ].each do |method|
+            define_singleton_method(method) do |*args|
+              value = super(*args)
+              self.as_version(self.tool_config.version_name) if self.tool_config
+              value
+            end
+          end
+        end
+      end
+
+      # Just like generated task classes, the version switcher doesn't have a
+      # cbrain_plugins directory structure and needs a few methods for views
+      # and controllers, adjusted to reflect that a ToolConfig is needed to
+      # access the real task class.
+
+      # No public path
+      def self.public_path(public_file)
+        nil
+      end
+
+      # No generated source (yet)
+      def self.generated_from
+        nil
+      end
+
+      # Stubbed out raw view partials
+      def self.raw_partial(partial)
+        ({
+          :task_params => %q{ No version specified },
+          :show_params => %q{ No version specified }
+        })[partial]
+      end
+
+    end
+  end
+
   # Returns the default Schema instance to use when validating descriptors
   # without a specific schema or when auto-loading descriptors.
   # (constructed from DEFAULT_SCHEMA_FILE)
@@ -274,6 +426,15 @@ def self.expand_json(obj)
     JSON.parse!(File.exists?(obj) ? IO.read(obj) : obj)
   end
 
+  # Utility method to convert a string (+str+) to an identifier suitable for a
+  # Ruby class name. Similar to Rails' classify, but tries to handle more cases.
+  def self.classify(str)
+    str.gsub!('-', '_')
+    str.gsub!(/\W/, '')
+    str.gsub!(/^\d/, '')
+    str.camelize
+  end
+
   private
 
   # Utility/helper methods used in templates.
diff --git a/BrainPortal/lib/cbrain_task_generators/templates/bourreau.rb.erb b/BrainPortal/lib/cbrain_task_generators/templates/bourreau.rb.erb
index d7dc7eef2..b0d84c7fc 100644
--- a/BrainPortal/lib/cbrain_task_generators/templates/bourreau.rb.erb
+++ b/BrainPortal/lib/cbrain_task_generators/templates/bourreau.rb.erb
@@ -237,10 +237,10 @@ class CbrainTask::<%= name %> < ClusterTask
     end
 
 %     required.select { |o| ! o['list'] }.each do |output|
-    ensure_exists(outputs[:'<%= output['id'] %>'])
+    ensure_exists.(outputs[:'<%= output['id'] %>'])
 %     end
 %     required.select { |o|   o['list'] }.each do |output|
-    ensure_matches(outputs[:'<%= output['id'] %>'])
+    ensure_matches.(outputs[:'<%= output['id'] %>'])
 %     end
 
 %   end
@@ -292,8 +292,6 @@ class CbrainTask::<%= name %> < ClusterTask
 % end
   end
 
-  private
-
   # Generic helper methods
 
   # Make a given set of userfiles +files+ available to <%= name %> at
diff --git a/BrainPortal/lib/cbrain_task_generators/templates/portal.rb.erb b/BrainPortal/lib/cbrain_task_generators/templates/portal.rb.erb
index 5f9c1b6a7..265da8a03 100644
--- a/BrainPortal/lib/cbrain_task_generators/templates/portal.rb.erb
+++ b/BrainPortal/lib/cbrain_task_generators/templates/portal.rb.erb
@@ -170,7 +170,7 @@ class CbrainTask::<%= name %> < PortalTask
     # Create a list of tasks out of the default input file list
     # (interface_userfile_ids), each file going into parameter '<%= single_file['id'] %>'
     self.params[:interface_userfile_ids].map do |id|
-      task = self.dup
+      task = self.clone
 
       # Set and sanitize the one file parameter for each id
       task.params[:'<%= single_file['id']%>'] = id

From 43cd13f20a78894cd017415f6939fa7f00f0b03d Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Tue, 28 Jul 2015 16:10:03 -0400
Subject: [PATCH 04/85] Missing version fallback

as_version now tries to fall back to the first defined tool version
if the given version cannot be found in known_versions.
---
 .../schema_task_generator.rb                   | 18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

diff --git a/BrainPortal/lib/cbrain_task_generators/schema_task_generator.rb b/BrainPortal/lib/cbrain_task_generators/schema_task_generator.rb
index 93a2ba1de..db6d75c5b 100644
--- a/BrainPortal/lib/cbrain_task_generators/schema_task_generator.rb
+++ b/BrainPortal/lib/cbrain_task_generators/schema_task_generator.rb
@@ -342,8 +342,22 @@ def self.known_versions
         # +version+ by including all of its methods in, replacing the defaults
         # from PortalTask or ClusterTask.
         define_singleton_method(:as_version) do |version|
-          cb_error "Unknown or invalid version '#{version}'" unless
-            (version_class = self.class.known_versions[version])
+          # Try to get the version-specific class corresponding to +version+,
+          # falling back on the first defined version in known_versions if it
+          # cannot be found.
+          known = self.class.known_versions
+          unless (version_class = known[version])
+            cb_error "No known versions for #{self.class.name}!?" unless
+              known.present?
+
+            logger.warn(
+              "WARNING: " +
+              "Unknown version #{version} for #{self.class.name}, " +
+              "using #{known.first[0]} instead"
+            )
+
+            version, version_class = known.first
+          end
 
           # Use the Ruby 2.0 refinement API to include version_class methods
           # inside this object's singleton class (or metaclass)

From b2f67b0b609a16cda5877491fbc05153be46a535 Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Tue, 28 Jul 2015 18:00:36 -0400
Subject: [PATCH 05/85] Rails generator for descriptor-based CbrainTasks

The new generator, descriptor_task, uses SchemaTaskGenerator to generate
a CbrainTask source set and outputs it in the CBRAIN plugin format (just
like the to_directory method) under cbrain_plugins/cbrain-plugins-local.
The source descriptor, schema and strict mode are specified as
command-line arguments.
---
 .../lib/generators/descriptor_task/USAGE      | 23 +++++++
 .../descriptor_task_generator.rb              | 60 +++++++++++++++++++
 2 files changed, 83 insertions(+)
 create mode 100644 BrainPortal/lib/generators/descriptor_task/USAGE
 create mode 100644 BrainPortal/lib/generators/descriptor_task/descriptor_task_generator.rb

diff --git a/BrainPortal/lib/generators/descriptor_task/USAGE b/BrainPortal/lib/generators/descriptor_task/USAGE
new file mode 100644
index 000000000..e1289b29e
--- /dev/null
+++ b/BrainPortal/lib/generators/descriptor_task/USAGE
@@ -0,0 +1,23 @@
+Description:
+  Generate a working CbrainTask template from a JSON descriptor. This template
+  can be used as a working base for adding custom functionality to a CbrainTask
+  beyond what is automatically generated by CBRAIN's descriptor integration
+  mechanism.
+
+  If no schema (--schema) is specified, CBRAIN's default JSON descriptor
+  schema is used.
+
+Example:
+
+    rails generate descriptor_task ~/descriptors/my_tool.json
+
+  will create:
+
+    cbrain_plugins/cbrain-plugins-local/cbrain_task/portal/my_tool.rb
+    cbrain_plugins/cbrain-plugins-local/cbrain_task/bourreau/my_tool.rb
+    cbrain_plugins/cbrain-plugins-local/cbrain_task/views/_task_params.html.erb
+    cbrain_plugins/cbrain-plugins-local/cbrain_task/views/_show_params.html.erb
+    cbrain_plugins/cbrain-plugins-local/cbrain_task/views/public/edit_params_help.html
+
+  Note that the path component 'cbrain-plugin-local' is a name given to a
+  dummy CBRAIN plugins package; feel free to rename it as needed.
diff --git a/BrainPortal/lib/generators/descriptor_task/descriptor_task_generator.rb b/BrainPortal/lib/generators/descriptor_task/descriptor_task_generator.rb
new file mode 100644
index 000000000..81ebe8fe9
--- /dev/null
+++ b/BrainPortal/lib/generators/descriptor_task/descriptor_task_generator.rb
@@ -0,0 +1,60 @@
+
+#
+# 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 <http://www.gnu.org/licenses/>.
+#
+
+class DescriptorTaskGenerator < Rails::Generators::Base
+
+  Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
+
+  source_root File.expand_path('.', __FILE__)
+
+  argument :json_descriptor, :type => :string,
+    :desc => %q{JSON descriptor to generate the CbrainTask subclass from}
+
+  class_option :schema, :type => :string, :required => false,
+    :desc => %q{JSON descriptor schema to validate the descriptor with}
+
+  class_option :strict, :type => :boolean, :default => false,
+    :desc => %q{Abort generation if the provided descriptor doesn't validate}
+
+  def create_task #:nodoc:
+    generated = SchemaTaskGenerator.generate(
+      options[:schema] || SchemaTaskGenerator.default_schema,
+      json_descriptor,
+      options[:strict]
+    )
+
+    name, source = generated.name, generated.source
+    base = "cbrain_plugins/cbrain-plugins-local/cbrain_task/#{name}"
+
+    empty_directory "#{base}"
+    empty_directory "#{base}/portal"
+    empty_directory "#{base}/bourreau"
+    empty_directory "#{base}/views/public"
+
+    create_file "#{base}/portal/#{generated.name}.rb",        source[:portal]
+    create_file "#{base}/bourreau/#{generated.name}.rb",      source[:bourreau]
+    create_file "#{base}/views/_task_params.html.erb",        source[:task_params]
+    create_file "#{base}/views/_show_params.html.erb",        source[:show_params]
+    create_file "#{base}/views/public/edit_params_help.html", source[:edit_help]
+  end
+
+end

From f8b26fc1244443d7b1c68844528cdf4b5314b25e Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Thu, 30 Jul 2015 18:51:38 -0400
Subject: [PATCH 06/85] Disabled version switching, minor fixes

The currently implemented way of specializing the 'version switcher'
instance to the version-specific class (bulk-importing methods) crashes
Ruby when trying to garbage-collect the object.

At the time of writing, there is no known good way to implemented the
required functionality in Ruby without resorting to even deeper and
messier hacks. As such, the functionality has been disabled for now (its
off by default, and neither the auto-loader or Rails generator enable
it).

This changeset also adds a warning when a to-be-generated task class has
already been defined before and corrects some minor issues.
---
 .../schema_task_generator.rb                  | 63 +++++++++++--------
 .../templates/portal.rb.erb                   |  2 +-
 2 files changed, 39 insertions(+), 26 deletions(-)

diff --git a/BrainPortal/lib/cbrain_task_generators/schema_task_generator.rb b/BrainPortal/lib/cbrain_task_generators/schema_task_generator.rb
index db6d75c5b..6d9b4c9ee 100644
--- a/BrainPortal/lib/cbrain_task_generators/schema_task_generator.rb
+++ b/BrainPortal/lib/cbrain_task_generators/schema_task_generator.rb
@@ -116,16 +116,22 @@ def initialize(attributes)
     # required Tool and ToolConfig if necessary for the CbrainTask to be
     # useable right away (since almost all information required to make the
     # Tool and ToolConfig objects is available in the spec).
-    # Also, unless +multi_version+ is specified to be false, this method will
-    # wrap the encapsulated CbrainTask in a version switcher class to allow
-    # different CbrainTask classes for each tool version.
+    # Also, if +multi_version+ is specified, this method will wrap the
+    # encapsulated CbrainTask in a version switcher class to allow different
+    # CbrainTask classes for each tool version.
     # Returns the newly generated CbrainTask subclass.
-    def integrate(register: true, multi_version: true)
+    def integrate(register: true, multi_version: false)
       # Make sure the task class about to be generated does not already exist,
       # to avoid mixing the classes up.
       name = SchemaTaskGenerator.classify(@name)
-      Object.send(:remove_const, name)     if Object.const_defined?(name)
-      CbrainTask.send(:remove_const, name) if CbrainTask.const_defined?(name)
+      [ Object, CbrainTask ].select { |m| m.const_defined?(name) }.each do |m|
+        Rails.logger.warn(
+          "WARNING: #{name} is already defined in #{m.name}; " +
+          "undefining to avoid collisions"
+        ) unless multi_version
+
+        m.send(:remove_const, name)
+      end
 
       # As the same code is used to dynamically load tasks descriptors and
       # create task templates, the class definitions are generated as strings
@@ -170,12 +176,9 @@ def integrate(register: true, multi_version: true)
 
         # Redefine the CbrainTask or Object constant pointing to the task's
         # class to point to the switcher instead.
-        mod = [ Object, CbrainTask ]
-          .select { |m| m.const_defined?(name) }
-          .first
-        if mod
-          mod.send(:remove_const, name)
-          mod.const_set(name, switcher)
+        [ Object, CbrainTask ].select { |m| m.const_defined?(name) }.each do |m|
+          m.send(:remove_const, name)
+          m.const_set(name, switcher)
         end
       end
 
@@ -337,6 +340,16 @@ def self.known_versions
         # This method (+as_version+) tries its best to mimic the missing
         # functionality.
 
+        # FIXME: unfortunately, while the technique +as_version+ uses is
+        # more-or-less sound Ruby-wise (it bulk-imports the version class
+        # instance methods into the version switcher instance's singleton
+        # class), it apparently overrides/messes up some sensitive core Ruby
+        # methods which make Ruby segfault when the object is garbage collected.
+
+        # As such, this version switching functionality is not currently in use,
+        # for lack of a working technique to try to 'convert' the version
+        # switcher instance.
+
         # Convert this blank CbrainTask object (instance of the version switcher
         # class) to a more-or-less real instance of the class corresponding to
         # +version+ by including all of its methods in, replacing the defaults
@@ -351,18 +364,26 @@ def self.known_versions
               known.present?
 
             logger.warn(
-              "WARNING: " +
-              "Unknown version #{version} for #{self.class.name}, " +
-              "using #{known.first[0]} instead"
+              "WARNING: Unknown version #{version} for #{self.class.name}, " +
+              "using #{known.first[0]} instead."
             )
 
             version, version_class = known.first
           end
 
+          # An object can only be given methods for a single version, and
+          # exactly once. Conflicts and odd issues could occur otherwise.
+          # Thus, there is no longer a need for :as_version or the tool_config
+          # setter hooks.
+          [ :as_version, :tool_config=, :tool_config_id= ].each do |m|
+            self.singleton_class.send(:remove_method, m) rescue nil
+          end
+
           # Use the Ruby 2.0 refinement API to include version_class methods
           # inside this object's singleton class (or metaclass)
-          metaclass = class << self; self; end
-          metaclass.include(Module.new { include refine(version_class) { } })
+          self.singleton_class.include(Module.new do
+            include refine(version_class) { }
+          end)
 
           # And try to make the object appear to be a version_class.
           define_singleton_method(:class) { version_class }
@@ -373,14 +394,6 @@ def self.known_versions
           define_singleton_method(:instance_of?) do |klass|
             klass == version_class || super(klass)
           end
-
-          # An object can only be given methods for a single version, and
-          # exactly once. Conflicts and odd issues could occur otherwise.
-          # Thus, there is no longer a need for :as_version or the tool_config
-          # setter hooks.
-          [ :as_version, :tool_config=, :tool_config_id= ].each do |m|
-            metaclass.send(:remove_method, m) rescue nil
-          end
         end
 
         # If we dont have a tool config already, try to catch the exact moment
diff --git a/BrainPortal/lib/cbrain_task_generators/templates/portal.rb.erb b/BrainPortal/lib/cbrain_task_generators/templates/portal.rb.erb
index 265da8a03..5f9c1b6a7 100644
--- a/BrainPortal/lib/cbrain_task_generators/templates/portal.rb.erb
+++ b/BrainPortal/lib/cbrain_task_generators/templates/portal.rb.erb
@@ -170,7 +170,7 @@ class CbrainTask::<%= name %> < PortalTask
     # Create a list of tasks out of the default input file list
     # (interface_userfile_ids), each file going into parameter '<%= single_file['id'] %>'
     self.params[:interface_userfile_ids].map do |id|
-      task = self.clone
+      task = self.dup
 
       # Set and sanitize the one file parameter for each id
       task.params[:'<%= single_file['id']%>'] = id

From d9369f24359a15a7f40eab7f63d26a8327b72471 Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Fri, 31 Jul 2015 14:40:31 -0400
Subject: [PATCH 07/85] Support for path-template-stripped-extensions

As per boutiques' spec, the specified extension list is now stripped from
input strings and file names before replacement in the path template.
---
 .../templates/bourreau.rb.erb                 | 57 ++++++++++++++-----
 1 file changed, 43 insertions(+), 14 deletions(-)

diff --git a/BrainPortal/lib/cbrain_task_generators/templates/bourreau.rb.erb b/BrainPortal/lib/cbrain_task_generators/templates/bourreau.rb.erb
index b0d84c7fc..0e865cb7d 100644
--- a/BrainPortal/lib/cbrain_task_generators/templates/bourreau.rb.erb
+++ b/BrainPortal/lib/cbrain_task_generators/templates/bourreau.rb.erb
@@ -149,12 +149,20 @@ class CbrainTask::<%= name %> < ClusterTask
 %     key_width  = max_width.(out_keys, 'command-line-key') + "''".length
 %     path_width = max_width.(out_keys, 'path-template')    + "'',".length
 %     out_keys.each do |key|
+%       stripped = key['path-template-stripped-extensions']
       <%=
-        "%-#{key_width}s => substitute_keys(%-#{path_width}s keys)," % [
+        "%-#{key_width}s => apply_template(%-#{path_width}s keys%s" % [
           "'#{key['command-line-key']}'",
-          "'#{key['path-template']}',"
+          "'#{key['path-template']}',",
+          stripped ? ', strip: [' : '),'
         ]
       %>
+%       if stripped
+%         stripped.each do |ext|
+        '<%= ext %>',
+%         end
+      ]),
+%       end
 %     end
     })
 
@@ -182,7 +190,7 @@ class CbrainTask::<%= name %> < ClusterTask
 %     path_width = max_width.(outputs, 'path-template') + "'',".length
 %     outputs.each do |output|
       <%=
-        "%-#{id_width}s => substitute_keys(%-#{path_width}s keys)," % [
+        "%-#{id_width}s => apply_template(%-#{path_width}s keys)," % [
           ":'#{output['id']}'",
           "'#{output['path-template']}',"
         ]
@@ -192,7 +200,7 @@ class CbrainTask::<%= name %> < ClusterTask
 
 %   end
     # Generate the final command-line to run <%= name %>
-    [ substitute_keys(<<-'CMD', keys<%= flags.empty? ? '' : ', flags' %>) ]
+    [ apply_template(<<-'CMD', keys<%= flags.empty? ? '' : ', flags: flags' %>) ]
       <%= descriptor['command-line'] %>
     CMD
 % end
@@ -226,7 +234,7 @@ class CbrainTask::<%= name %> < ClusterTask
     # Make sure that every required output +path+ actually exists
     # (or that its +glob+ matches something).
     ensure_exists = lambda do |path|
-      return if File.exists(path)
+      return if File.exists?(path)
       self.addlog("Missing output file #{path}")
       succeeded &&= false
     end
@@ -320,21 +328,42 @@ class CbrainTask::<%= name %> < ClusterTask
     self.results_data_provider_id ||= files.first.data_provider_id rescue nil
   end
 
-  # Substitute each parameter value in +keys+ in +str+ prepended by the
-  # corresponding flag in +flags+, if available.
-  # substitute_keys('f -e [1]', { '[1]' => 5 })                    => 'f -e 5'
-  # substitute_keys('f -e [1]', { '[1]' => 5 }, { '[1]' => '-z' }) => 'f -e -z 5'
-  def substitute_keys(str, keys, flags = {})
-    keys.inject(str) do |str, (key, value)|
+  # Apply substitution keys +keys+ to +template+ in order to format a
+  # command-line or output file name.
+  # Substitute each value in +keys+ in +template+, prepended by the
+  # corresponding flag in +flags+ (if available) and stripped of the
+  # endings in +strip+:
+  #   apply_template('f [1]', { '[1]' => 5 })
+  #     => 'f 5'
+  #
+  #   apply_template('f [1]', { '[1]' => 5 },
+  #     flags: { '[1]' => '-z' }
+  #   ) => 'f -z 5'
+  #
+  #   apply_template('f [1]', { '[1]' => '5.z' },
+  #     flags: { '[1]' => '-z' },
+  #     strip: [ '.z' ]
+  #   ) => 'f -z 5'
+  def apply_template(template, keys, flags: {}, strip: [])
+    keys.inject(template) do |template, (key, value)|
       flag = flags[key]
-      next str.gsub(key, flag) if flag && value == true
+      next template.gsub(key, flag) if flag && value == true
 
       value = (value.is_a?(Enumerable) ? value.dup : [value])
         .reject(&:nil?)
-        .map { |v| (v.is_a?(Userfile) ? v.name : v.to_s).bash_escape }
+        .map do |v|
+          v = v.name if v.is_a?(Userfile)
+          v = v.dup  if v.is_a?(String)
+
+          strip.find do |e|
+            v.sub!(/#{Regexp.quote(e)}$/, '')
+          end if v.is_a?(String)
+
+          v.to_s.bash_escape
+        end
         .join(' ')
 
-      str.gsub(key, flag && value.present? ? "#{flag} #{value}" : value)
+      template.gsub(key, flag && value.present? ? "#{flag} #{value}" : value)
     end
   end
 

From c3367e7674601afddcbe9ff82813c78324449bfd Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Fri, 31 Jul 2015 15:00:44 -0400
Subject: [PATCH 08/85] Mark optional fields as active on focus

Optional fields are now set as active (and sent to the server) as soon
as they are selected (focus event) instead of waiting fo user input
(change event).
---
 .../templates/task_params.html.erb.erb               | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/BrainPortal/lib/cbrain_task_generators/templates/task_params.html.erb.erb b/BrainPortal/lib/cbrain_task_generators/templates/task_params.html.erb.erb
index c3ef92277..f635e1310 100644
--- a/BrainPortal/lib/cbrain_task_generators/templates/task_params.html.erb.erb
+++ b/BrainPortal/lib/cbrain_task_generators/templates/task_params.html.erb.erb
@@ -348,7 +348,7 @@ $(function () {
   /* Optional parameters */
 
   /* Clicking on the parameter's checkbox toggles the parameter's state */
-  parameters.delegate('.tsk-prm-opt', 'change', function () {
+  parameters.delegate('.tsk-prm-opt', 'change activate.tsk-prm', function () {
     var opt   = $(this),
         param = opt.parent();
 
@@ -391,16 +391,16 @@ $(function () {
   });
 
   /* Changing a parameter's value automatically marks it as active */
-  parameters.delegate('.tsk-prm-in', 'change', function () {
+  parameters.delegate('.tsk-prm-in', 'focus activate.tsk-prm', function () {
     $(this)
       .closest('.tsk-prm')
       .find('.tsk-prm-opt')
       .prop('checked', true)
-      .trigger('change');
+      .trigger('activate.tsk-prm');
   });
 
   /* Activate optional parameters with default values */
-  parameters.find(".tsk-prm-in[value]").trigger('change');
+  parameters.find(".tsk-prm-in[value]").trigger('activate.tsk-prm');
 
   /* Drop-down lists */
 
@@ -432,7 +432,7 @@ $(function () {
     param
       .find('.tsk-prm-in')
       .val(item.data('value'))
-      .trigger('change');
+      .trigger('activate.tsk-prm');
 
     /* Display the newly selected value in the drop-down's label */
     param
@@ -463,7 +463,7 @@ $(function () {
       )
       .siblings('.tsk-prm-opt')
       .prop('checked', true)
-      .trigger('change');
+      .trigger('activate.tsk-prm');
   });
 
   /* Clicking on a '-' button removes the row */

From 75e82e42f149188d8a6735a68ca84a66f9519b1f Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Fri, 31 Jul 2015 16:13:55 -0400
Subject: [PATCH 09/85] More intuitive automatic file selection indicator

The first few files are now listed in gray instead of displaying
'(Automatically selected)' and the selection arrow is no longer
displayed.
---
 .../templates/task_params.html.erb.erb               | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/BrainPortal/lib/cbrain_task_generators/templates/task_params.html.erb.erb b/BrainPortal/lib/cbrain_task_generators/templates/task_params.html.erb.erb
index f635e1310..461ba596f 100644
--- a/BrainPortal/lib/cbrain_task_generators/templates/task_params.html.erb.erb
+++ b/BrainPortal/lib/cbrain_task_generators/templates/task_params.html.erb.erb
@@ -199,12 +199,12 @@
     )
   %>
   <div class="tsk-prm-sel">
-    <span class="tsk-prm-sel-icon ui-icon ui-icon-triangle-1-s"></span>
     <%% if options.empty? %>
       <span class="tsk-prm-sel-lbl disabled">
         <%%= nothing %>
       </span>
     <%% else %>
+      <span class="tsk-prm-sel-icon ui-icon ui-icon-triangle-1-s"></span>
       <span class="tsk-prm-sel-lbl">
         <%% if (pair = options.select { |o| o.first == value }.first) %>
           <%%= pair.last %>
@@ -226,6 +226,14 @@
   </span>
 <%% end %>
 
+<%%# Give a short (up to +max+ characters) representation of +list+ %>
+<%%
+  short_repr = lambda do |list, max|
+    str = list.map(&:to_s).join(', ')
+    str.length <= max ? str : (str[0, max - 3] + '...')
+  end
+%%>
+
 <%# Generate a complete HTML block for a given parameter +param+ -%>
 <%- parameter = lambda do |param| -%>
   <%-
@@ -265,7 +273,7 @@
     <%- if single_file -%>
         # Automatic single file input
         dropdown.(id, id,
-          [], nothing: '(Automatically selected)',
+          [], nothing: short_repr.(input_files.map(&:name), 65),
           optional: <%= opt %>
         )
     <%- elsif param['cbrain-file-type'] -%>

From b0a7124e8b23654e09d9822d4eb260ad93388884 Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Wed, 5 Aug 2015 16:58:11 -0400
Subject: [PATCH 10/85] Session data controller, CbrainSession refactor to
 reduce coupling (!)

CbrainSession now acts as an independent model wrapping
ActiveRecord::SessionStore::Session, and no longer concerns itself with:
- Session value format; the undocumented API relying on special suffixes
  (_clear, _remove, _hash, _array, etc.) in session keys has been
  removed.
- Controller-specific keys; CbrainSession no longer directly considers
  keys named from controllers (bar a single method kept for backwards
  compatibility.
- Filtering and sorting; all methods related to sorting and filtering
  have been removed, as they should belong in their own module or class.
All methods have been re-worked to be as simple as possible, documented
and meet CBRAIN's coding style.

This changeset also adds a new controller to allow direct API access to
session data, which is intended to be used from client-side JS scripts.

Note that as this changeset removes the filtering/sorting methods from
CbrainSession, it breaks the filtering and sorting capabilities offered
by the basic_filter_helpers and filter_helper modules. This
functionality will be restored by the upcoming refactor of those
modules.
---
 .../controllers/data_providers_controller.rb  |   2 +-
 .../controllers/exception_logs_controller.rb  |   2 +-
 .../app/controllers/groups_controller.rb      |   8 +-
 .../app/controllers/messages_controller.rb    |   2 +-
 .../app/controllers/portal_controller.rb      |  10 +-
 .../controllers/session_data_controller.rb    |  61 +++
 .../app/controllers/sessions_controller.rb    |   4 +-
 .../app/controllers/tasks_controller.rb       |   4 +-
 .../app/controllers/userfiles_controller.rb   |  63 +--
 .../app/controllers/users_controller.rb       |   4 +-
 BrainPortal/app/models/cbrain_session.rb      | 509 ++++++++----------
 .../app/views/userfiles/_file_menu.html.erb   |  10 +-
 .../userfiles/_userfiles_display.html.erb     |   6 +-
 BrainPortal/config/routes.rb                  |   4 +-
 BrainPortal/lib/basic_filter_helpers.rb       |  34 +-
 BrainPortal/lib/session_helpers.rb            |   2 +-
 16 files changed, 343 insertions(+), 382 deletions(-)
 create mode 100644 BrainPortal/app/controllers/session_data_controller.rb

diff --git a/BrainPortal/app/controllers/data_providers_controller.rb b/BrainPortal/app/controllers/data_providers_controller.rb
index af546a153..0dceb9913 100644
--- a/BrainPortal/app/controllers/data_providers_controller.rb
+++ b/BrainPortal/app/controllers/data_providers_controller.rb
@@ -377,7 +377,7 @@ def browse
       end
     end
 
-    current_session.save_preferences_for_user(current_user, :data_providers, :browse_hash)
+    current_session.save_preferences
 
     respond_to do |format|
       format.html
diff --git a/BrainPortal/app/controllers/exception_logs_controller.rb b/BrainPortal/app/controllers/exception_logs_controller.rb
index 3f6f8cd8e..6efdbd9de 100644
--- a/BrainPortal/app/controllers/exception_logs_controller.rb
+++ b/BrainPortal/app/controllers/exception_logs_controller.rb
@@ -35,7 +35,7 @@ def index #:nodoc:
     @filtered_scope = base_filtered_scope
     @exception_logs = base_sorted_scope(@filtered_scope).paginate(:page => @current_page, :per_page => @per_page)
 
-    current_session.save_preferences_for_user(current_user, :exception_logs, :per_page)
+    current_session.save_preferences
 
     respond_to do |format|
       format.html # index.html.erb
diff --git a/BrainPortal/app/controllers/groups_controller.rb b/BrainPortal/app/controllers/groups_controller.rb
index 34f5cb8c6..7e30695a8 100644
--- a/BrainPortal/app/controllers/groups_controller.rb
+++ b/BrainPortal/app/controllers/groups_controller.rb
@@ -87,7 +87,7 @@ def index  #:nodoc:
       @group_id_2_brain_portal_counts  = BrainPortal.group("group_id").count
     end
 
-    current_session.save_preferences_for_user(current_user, :groups, :button_view, :per_page)
+    current_session.save_preferences
 
     respond_to do |format|
       format.js
@@ -235,9 +235,9 @@ def switch #:nodoc:
     redirect_action     = params[:redirect_action]     || :index
     redirect_id         = params[:redirect_id]
 
-    current_session.param_chain("userfiles", "filter_hash").delete("group_id")
-    current_session.param_chain("tasks"    , "filter_hash").delete("group_id")
-    current_session.persistent_userfile_ids_clear
+    current_session.params_for(:userfiles)['filter_hash'].delete('group_id')
+    current_session.params_for(:tasks)['filter_hash'].delete('group_id')
+    current_session[:persistent_userfiles].clear rescue nil
 
     redirect_path = { :controller => redirect_controller, :action => redirect_action }
     redirect_path[:id] = redirect_id unless redirect_id.blank?
diff --git a/BrainPortal/app/controllers/messages_controller.rb b/BrainPortal/app/controllers/messages_controller.rb
index 416c1d863..5b4c4419a 100644
--- a/BrainPortal/app/controllers/messages_controller.rb
+++ b/BrainPortal/app/controllers/messages_controller.rb
@@ -48,7 +48,7 @@ def index #:nodoc:
 
     @messages = scope.paginate(:page => @current_page, :per_page => @per_page)
 
-    current_session.save_preferences_for_user(current_user, :messages, :per_page)
+    current_session.save_preferences
 
     respond_to do |format|
       format.html # index.html.erb
diff --git a/BrainPortal/app/controllers/portal_controller.rb b/BrainPortal/app/controllers/portal_controller.rb
index 1543c6f6d..72c821503 100644
--- a/BrainPortal/app/controllers/portal_controller.rb
+++ b/BrainPortal/app/controllers/portal_controller.rb
@@ -51,9 +51,10 @@ def welcome #:nodoc:
       @active_users = CbrainSession.active_users
       @active_users.unshift(current_user) unless @active_users.include?(current_user)
       if request.post?
-        unless params[:session_clear].blank?
-          CbrainSession.session_class.where(["updated_at < ?", params[:session_clear].to_i.seconds.ago]).delete_all
-        end
+        CbrainSession.clean_sessions
+        CbrainSession.purge_sessions(params[:session_clear].to_i.seconds.ago) unless
+          params[:session_clear].blank?
+
         if params[:lock_portal] == "lock"
           BrainPortal.current_resource.lock!
           BrainPortal.current_resource.addlog("User #{current_user.login} locked this portal.")
@@ -68,9 +69,6 @@ def welcome #:nodoc:
           flash.now[:error] = ""
         end
       end
-    #elsif current_user.has_role? :site_manager
-    #  @active_users = CbrainSession.active_users.where( :site_id  => current_user.site_id )
-    #  @active_users.unshift(current_user) unless @active_users.include?(current_user)
     end
 
     bourreau_ids = Bourreau.find_all_accessible_by_user(current_user).raw_first_column("remote_resources.id")
diff --git a/BrainPortal/app/controllers/session_data_controller.rb b/BrainPortal/app/controllers/session_data_controller.rb
new file mode 100644
index 000000000..3ab04eae0
--- /dev/null
+++ b/BrainPortal/app/controllers/session_data_controller.rb
@@ -0,0 +1,61 @@
+
+#
+# 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 <http://www.gnu.org/licenses/>.
+#
+
+# JSON/XML controller for server-side session data, such as filters, sorting
+# options, selections, etc.
+class SessionDataController < ApplicationController
+
+  Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
+
+  api_available
+  before_filter :login_required
+
+  # GET /session_data
+  def show #:nodoc:
+    @session = current_session.to_h.reject do |k,v|
+      CbrainSession.internal_keys.include?(k)
+    end
+
+    respond_to do |format|
+      format.xml  { render :xml  => @session }
+      format.json { render :json => @session }
+    end
+  end
+
+  # POST /session_data
+  def update #:nodoc:
+    mode    = request.query_parameters[:mode].to_sym rescue :replace
+    changes = request.request_parameters.reject do |k,v|
+      CbrainSession.internal_keys.include?(k)
+    end
+
+    current_session.update(changes, mode)
+    show
+
+  rescue => ex
+    respond_to do |format|
+      format.xml  { render :xml  => { :error => ex.message }, :status => :unprocessable_entity }
+      format.json { render :json => { :error => ex.message }, :status => :unprocessable_entity }
+    end
+  end
+
+end
diff --git a/BrainPortal/app/controllers/sessions_controller.rb b/BrainPortal/app/controllers/sessions_controller.rb
index 0bd5ab01e..16c651315 100644
--- a/BrainPortal/app/controllers/sessions_controller.rb
+++ b/BrainPortal/app/controllers/sessions_controller.rb
@@ -76,7 +76,7 @@ def destroy #:nodoc:
     current_session.deactivate if current_session
     current_user.addlog("Logged out") if current_user
     portal.addlog("User #{current_user.login} logged out") if current_user
-    current_session.clear_data!
+    current_session.clear
     #reset_session
     flash[:notice] = "You have been logged out."
 
@@ -235,7 +235,7 @@ def user_tracking(portal) #:nodoc:
     current_session.activate
     user   = current_user
 
-    current_session.load_preferences_for_user(user)
+    current_session.load_preferences
 
     # Record the best guess for browser's remote host name
     reqenv  = request.env
diff --git a/BrainPortal/app/controllers/tasks_controller.rb b/BrainPortal/app/controllers/tasks_controller.rb
index 294abd0f6..3bb1b8c2d 100644
--- a/BrainPortal/app/controllers/tasks_controller.rb
+++ b/BrainPortal/app/controllers/tasks_controller.rb
@@ -103,7 +103,7 @@ def index #:nodoc:
       pager
     end
 
-    current_session.save_preferences_for_user(current_user, :tasks, :per_page)
+    current_session.save_preferences
 
     @bourreau_status = bourreaux.map { |b| [b.id, b.online?] }.to_h
     respond_to do |format|
@@ -210,7 +210,7 @@ def new #:nodoc:
     @tool_config = @task.tool_config # for acces in view
 
     # Filter list of files as provided by the get request
-    file_ids = (params[:file_ids] || []) | current_session.persistent_userfile_ids_list
+    file_ids = (params[:file_ids] || []) | (current_session[:persistent_userfiles] || [])
     @files            = Userfile.find_accessible_by_user(file_ids, current_user, :access_requested => :write) rescue []
     if @files.empty?
       flash[:error] = "You must select at least one file to which you have write access."
diff --git a/BrainPortal/app/controllers/userfiles_controller.rb b/BrainPortal/app/controllers/userfiles_controller.rb
index 7e1dac0eb..15fdc08b8 100644
--- a/BrainPortal/app/controllers/userfiles_controller.rb
+++ b/BrainPortal/app/controllers/userfiles_controller.rb
@@ -152,7 +152,7 @@ def index #:nodoc:
     @archived_total  = @filtered_scope.where(:archived => true).count
     @immutable_total = @filtered_scope.where(:immutable => true).count
 
-    current_session.save_preferences_for_user(current_user, :userfiles, :view_hidden, :tree_sort, :view_all, :details, :per_page)
+    current_session.save_preferences
     respond_to do |format|
       format.html
       format.js
@@ -948,48 +948,39 @@ def change_provider #:nodoc:
   # Adds the selected userfile IDs to the session's persistent list
   def manage_persistent
 
-    if (params[:operation] || 'clear') =~ /(clear|add|remove|replace)/i
-      filelist  = params[:file_ids] || []
-      operation = Regexp.last_match[1].downcase
-    elsif (params[:operation]) =~ /select/i
-      operation      = "add"
-      # Reduce userfiles list according to @filter_params
-      filelist       = []
-      header_scope   = header_scope(@filter_params)
-      filtered_scope = filter_scope(@filter_params, header_scope)
-      filtered_scope.each do |f|
-        filelist << f.id.to_s if f.available?
-      end
+    operation  = (params[:operation] || 'clear').downcase
+    persistent = (current_session[:persistent_userfiles] || Set.new)
+
+    if operation =~ /select/
+      files = filter_scope(@filter_params, header_scope(@filter_params))
+        .select(&:available?)
+        .map(&:id)
+        .map(&:to_s)
     else
-      operation = 'clear'
+      files = params[:file_ids] || []
     end
 
-    flash[:notice] = ""
+    case operation
+    when /add/, /select/
+      persistent += files
 
-    cleared_count = added_count = removed_count = 0
+    when /remove/
+      persistent -= files
 
-    if operation == 'clear' || operation == 'replace'
-      cleared_count = current_session.persistent_userfile_ids_clear
-      flash[:notice] += "#{view_pluralize(cleared_count, "file")} cleared from persistent list.\n" if cleared_count > 0
-    end
+    when /clear/
+      persistent.clear
 
-    if operation == 'add'   || operation == 'replace'
-      added_count   = current_session.persistent_userfile_ids_add(filelist)
-      flash[:notice] += "#{view_pluralize(added_count, "file")} added to persistent list.\n" if added_count > 0
+    when /replace/
+      persistent.replace(files)
     end
 
-    if operation == 'remove'
-      removed_count = current_session.persistent_userfile_ids_remove(filelist)
-      flash[:notice] += "#{view_pluralize(removed_count, "file")} removed from persistent list.\n" if removed_count > 0
+    if persistent.size > 0
+      flash[:notice] = "#{view_pluralize(persistent.size, 'file')} now persistently selected."
+    else
+      flash[:notice] = "Peristent selection list now empty."
     end
 
-    persistent_ids = current_session.persistent_userfile_ids_list
-    flash[:notice] += "Total of #{view_pluralize(persistent_ids.size, "file")} now in the persistent list of files.\n" if
-      persistent_ids.size > 0 && (added_count > 0 || removed_count > 0 || cleared_count > 0)
-
-    flash[:notice] += "No changes made to the persistent list of userfiles." if
-      added_count == 0 && removed_count == 0 && cleared_count == 0
-
+    current_session[:persistent_userfiles] = persistent
     redirect_to :action => :index, :page => params[:page]
   end
 
@@ -1367,9 +1358,9 @@ def archive_management
   # Adds the persistent userfile ids to the params[:file_ids] argument
   def auto_add_persistent_userfile_ids #:nodoc:
     params[:file_ids] ||= []
-    if params[:ignore_persistent].blank?
-      params[:file_ids] = params[:file_ids] | current_session.persistent_userfile_ids_list
-    end
+    params[:file_ids]  |= current_session[:persistent_userfiles].to_a if
+      params[:ignore_persistent].blank? &&
+      current_session[:persistent_userfiles].present?
   end
 
   # Verify that all files selected for an operation
diff --git a/BrainPortal/app/controllers/users_controller.rb b/BrainPortal/app/controllers/users_controller.rb
index 2fad8c49b..945caecca 100644
--- a/BrainPortal/app/controllers/users_controller.rb
+++ b/BrainPortal/app/controllers/users_controller.rb
@@ -54,7 +54,7 @@ def index #:nodoc:
     # Turn the array ordered_real into the final paginated collection
     @users = @users.paginate(:page => @current_page, :per_page => @per_page)
 
-    current_session.save_preferences_for_user(current_user, :users, :per_page)
+    current_session.save_preferences
 
     respond_to do |format|
       format.html # index.html.erb
@@ -271,7 +271,7 @@ def switch #:nodoc:
     myportal.addlog("Admin user '#{current_user.login}' switching to user '#{@user.login}'")
     current_user.addlog("Switching to user '#{@user.login}'")
     @user.addlog("Switched from user '#{current_user.login}'")
-    current_session.clear_data!
+    current_session.clear
     self.current_user = @user
     current_session[:user_id] = @user.id
 
diff --git a/BrainPortal/app/models/cbrain_session.rb b/BrainPortal/app/models/cbrain_session.rb
index ca5a0092e..083c104fe 100644
--- a/BrainPortal/app/models/cbrain_session.rb
+++ b/BrainPortal/app/models/cbrain_session.rb
@@ -20,351 +20,274 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 
-#Model represeting the current session. The current session object can
-#be accessed using the <b><tt>current_session</tt></b> method of the ApplicationController
-#class.
-#
-#This model is meant to act as a wrapper around the session hash.
-#It takes care of updating the values of and performing any logic related
-#to the following attributes of the current session (mainly related
-#to the Userfile index page):
-#* currently active filters.
-#* whether or not pagination is active.
-#* current ordering of the Userfile index.
-#* whether to view current user's files or all files on the system (*admin* only).
+require 'set'
+
+# Model representing a CBRAIN user's Rails session. The currently logged in
+# user's session object can be accessed using the current_session method of
+# ApplicationController (from SessionHelpers).
 #
-#Session attributes can be accessed by calling methods with the attribute name.
-#*Example*: calling +current_session+.+current_filters+ will access <tt>session[:current_filters]</tt>
+# Meant as a wrapper around Rails session hash, this model is mostly used
+# to add additional reporting/monitoring logic, to cleanly support partial
+# updates and to validate certain session attributes.
 #
-#*Note*: this is not a database-backed model.
+# NOTE: This model is not database-backed
 class CbrainSession
 
   Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
 
-  def initialize(session, params, sess_model) #:nodoc:
-    @session       = session    # rails session
-    @session_model = sess_model # active record model that stores the session
-
-    @session[:persistent_userfile_ids] ||= {}
-
-    controller = params[:proxy_destination_controller] || params[:controller]
-    @session[controller.to_sym] ||= {}
-    @session[controller.to_sym]["filter_hash"] ||= {}
-    @session[controller.to_sym]["sort_hash"] ||= {}
+  # Create a new CbrainSession object wrapping +session+ (a Rails session)
+  # backed by +model+, an instance of CbrainSession.session_model (which is
+  # expected to be an ActiveRecord record).
+  def initialize(session, model = nil)
+    @session = session
+    @model   = model
   end
 
-  # Import a user's saved preferences from the db into the session.
-  def load_preferences_for_user(current_user)
-    user_preferences = current_user.meta[:preferences] || {}
-    user_preferences.each { |k, v|  @session[k.to_sym] = v || {}}
-  end
-
-  # Save given preferences from session into the db.
-  def save_preferences_for_user(current_user, cont, *ks)
-    controller = cont.to_sym
-    keys = ks.map(&:to_s)
-    user_preferences = current_user.meta[:preferences].cb_deep_clone || {}
-    user_preferences[controller] ||= {}
-    keys.each do |k|
-      if @session[controller][k] && user_preferences[controller][k] != @session[controller][k]
-        if @session[controller][k].is_a? Hash
-          user_preferences[controller][k] ||= {}
-          user_preferences[controller][k].merge!(@session[controller][k].cb_deep_clone)
-        elsif @session[controller][k].is_a? Array
-          user_preferences[controller][k] ||= []
-          user_preferences[controller][k] |= @session[controller][k].cb_deep_clone
-        else
-          user_preferences[controller][k] = @session[controller][k].cb_deep_clone
-        end
-      end
-    end
-
-    unless user_preferences[controller].blank?
-      current_user.meta[:preferences] = user_preferences
-    end
-  end
-
-  # Mark this session as active in the database.
-  def activate
-    return unless @session_model
-    # @session_model.update_attributes!(:user_id => @session[:user_id], :active => true)
-    @session_model.user_id = @session[:user_id]
-    @session_model.active  = true
-    @session_model.save!
+  # ActiveRecord model class for Rails sessions
+  def self.session_model
+    ActiveRecord::SessionStore::Session
   end
 
-  # Mark this session as inactive in the database.
-  def deactivate
-    return unless @session_model
-    @session_model.active  = false
-    @session_model.save!
+  # Internal CBRAIN session tracking keys. Invisible to the API and end-user,
+  # these keys keep track of the user's connection information.
+  def self.tracking_keys
+    @tracking_keys ||= Set.new([
+      :client_type,
+      :guessed_remote_host,
+      :guessed_remote_ip,
+      :raw_user_agent,
+      :return_to,
+    ].map(&:to_s))
   end
 
-  # Returns the list of currently active users on the system.
-  def self.active_users(options = {})
-    active_sessions = session_class.where(
-      ["sessions.active = 1 AND sessions.user_id IS NOT NULL AND sessions.updated_at > ?", 10.minutes.ago]
-    )
-    user_ids = active_sessions.map(&:user_id).uniq
-    scope = User.where(options)
-    scope.where( :id => user_ids )
+  # Internal CBRAIN session authentication, security, tracking and monitoring
+  # attribute keys. They are invisible to the API and end-user.
+  def self.internal_keys
+    @internal_keys ||= Set.new([
+      :_csrf_token,
+      :cbrain_toggle,
+      :user_id,
+    ].map(&:to_s) + self.tracking_keys.to_a)
   end
 
-  def self.count(options = {}) #:nodoc:
-    scope = session_class.where(options)
-    scope.count
+  # User this session belongs to, from the :user_id attribute
+  def user
+    @user = User.find_by_id(@session[:user_id]) unless
+      @user && @user.id == @session[:user_id]
+    @user
   end
 
-  def self.session_class #:nodoc:
-     ActiveRecord::SessionStore::Session
+  # Load +user+'s preferences (session attributes) in the session from the
+  # user's meta storage.
+  # If +user+ is not specified or nil, load_preferences will try to use the
+  # user bound to the session, if available.
+  def load_preferences(user = nil)
+    user  = self.user unless user.is_a?(User)
+    prefs = (user.meta[:preferences] || {})
+      .map    { |k,v| [k.to_sym, v] }
+      .to_h
+      .reject { |k,v| self.class.internal_keys.include?(k) }
+
+    @session.merge!(prefs)
   end
 
-  def self.all #:nodoc:
-    self.session_class.all
+  # Save this session object's attributes as the +user+'s preferences in the
+  # user's meta storage (opposite of load_preferences).
+  # If +user+ is not specified or nil, save_preferences will try to use the
+  # user bound to the session, if available.
+  def save_preferences(user = nil)
+    user  = self.user unless user.is_a?(User)
+    prefs = @session
+      .reject { |k,v| self.class.internal_keys.include?(k) }
+      .cb_deep_clone
+
+    user.meta[:preferences] = (user.meta[:preferences] || {}).merge(prefs)
   end
 
-  def self.recent_activity(n = 10, options = {}) #:nodoc:
-    self.clean_sessions
-    last_sessions = session_class.where( "sessions.user_id IS NOT NULL" ).order("sessions.updated_at DESC")
-    entries = []
-
-    last_sessions.each do |sess|
-      break if entries.size >= n
-      next  if sess.user_id.blank?
-      user = User.find_by_id(sess.user_id)
-      next unless user
-      sessdata = (sess.data || {}) rescue {}
-      entries << {
-        :user           => user,
-        :active         => sess.active?,
-        :last_access    => sess.updated_at,
-        :remote_ip      => sessdata["guessed_remote_ip"],    # can be nil, must be fetched with string not symbol
-        :remote_host    => sessdata["guessed_remote_host"],  # can be nil, must be fetched with string not symbol
-        :raw_user_agent => sessdata["raw_user_agent"],       # can be nil, must be fetched with string not symbol
-      }
-    end
-
-    entries
-  end
+  # Hash-like interface to session attributes
 
-  # Remove all spurious sessions entries:
-  #   a) older than 1 hour and
-  #   b) with no user_id and
-  #   c) not active
-  # These are usually created simply by any access to the
-  # login page.
-  def self.clean_sessions #:nodoc:
-    self.session_class.where("user_id is null").where([ "updated_at < ?", 1.hour.ago]).destroy_all
-  rescue
-    nil
+  # Delegate [] to @session
+  def [](key) #:nodoc:
+    @session[key]
   end
 
-  # Erase most of the entries in the data
-  # section of the session; this is used when the
-  # user logs out. Some elements are kept
-  # for tracking no matter what, like the
-  # :guessed_remote_host and the :raw_user_agent
-  def clear_data!
-    @session.each do |k,v|
-      next if k.to_s =~ /guessed_remote_ip|guessed_remote_host|raw_user_agent|client_type/
-      @session.delete(k)
-    end
+  # Delegate []= to @session
+  def []=(key, value) #:nodoc:
+    @session[key] = value
   end
 
-  # Update attributes of the session object based on the incoming request parameters
-  # contained in the +params+ hash.
-  def update(params)
-    controller = params[:proxy_destination_controller] || params[:controller]
-    if params[controller]
-      params[controller].each do |k, v|
-        if @session[controller.to_sym][k].nil?
-          if k =~ /_hash/
-            @session[controller.to_sym][k] = {}
-          elsif k =~ /_array/
-            @session[controller.to_sym][k] = []
-          end
-        end
-        if k == "remove" && v.is_a?(Hash)
-          v.each do |list, item|
-            if @session[controller.to_sym][list].respond_to? :delete
-              @session[controller.to_sym][list].delete item
-            else
-              @session[controller.to_sym].delete list
-            end
-          end
-        elsif k =~ /^clear_(.+)/
-          pattern = Regexp.last_match[1].gsub(/\W/, "")
-          if pattern == "all"
-            clear_list = v
-            clear_list = [v] unless v.is_a? Array
-          else
-            clear_list = @session[controller.to_sym].keys.grep(/^#{pattern}/)
-          end
-          clear_list.each do |item|
-            if item == "all"
-              @session[controller.to_sym].clear
-              @session[controller.to_sym]["filter_hash"] ||= {}
-              @session[controller.to_sym]["sort_hash"] ||= {}
-            elsif @session[controller.to_sym][item].respond_to? :clear
-              @session[controller.to_sym][item].clear
-            else
-              @session[controller.to_sym].delete item
-            end
+  # Update sessions attributes from the contents of +hash+. While similiar to
+  # Hash's merge method, this method has a few key differences:
+  #
+  # - Hashes in +hash+ and session attributes are recursively merged:
+  #     @session # { :a => { :b => 1 } }
+  #     update({ :a => { :c => 1 } })
+  #     @session # { :a => { :b => 1, :c => 1 } }
+  #
+  # - update does not accept a block; session attributes are always overwritten
+  #   by their new value in +hash+, if present.
+  #
+  # - nil values are automatically removed from hashes to avoid clutter. This
+  #   cleanly allows removing keys from hashes:
+  #     @session # { :a => { :b => 1 } }
+  #     update({ :a => { :b => nil } })
+  #     @session # { :a => {} }
+  #
+  # - collection (Array, Set) collision handling is based on +collection_mode+,
+  #   which is one of:
+  #
+  #   [:replace]
+  #    Handle collections just like regular values; replace the entire
+  #    collection with the new one in +hash+:
+  #      @session # { :a => [1] }
+  #      update({ :a => [2] }, :replace)
+  #      @session # { :a => [2] }
+  #
+  #   [:append]
+  #    Append the values in +hash+'s collection to the corresponding one in
+  #    the session attributes.
+  #      @session # { :a => [1] }
+  #      update({ :a => [2] }, :append)
+  #      @session # { :a => [1, 2] }
+  #
+  #   [:delete]
+  #    Opposite of append; remove the values in +hash+'s collection from the
+  #    corresponding one in the session attributes.
+  #      @session # { :a => [1] }
+  #      update({ :a => [1, 2] }, :delete)
+  #      @session # { :a => [2] }
+  def update(hash, collection_mode = :replace)
+    (update = lambda do |base, new|
+      base.merge!(new) do |key, old, new|
+        next new unless old.is_a?(new.class) || new.is_a?(old.class)
+
+        case old
+        when Hash
+          update.(old, new)
+        when Set, Array
+          case collection_mode
+          when :replace
+            new
+          when :append
+            old + new
+          when :delete
+            old - new
           end
         else
-          if @session[controller.to_sym][k].is_a? Hash
-            @session[controller.to_sym][k].merge!(sanitize_params(k, v) || {})
-            @session[controller.to_sym][k].delete_if { |pk, pv| pv.blank? }
-          elsif @session[controller.to_sym][k].is_a? Array
-            sanitized_param = sanitize_params(k, v)
-            @session[controller.to_sym][k] |= [sanitized_param] if sanitized_param
-          else
-            @session[controller.to_sym][k] = sanitize_params(k, v)
-          end
+          new
         end
       end
-    end
-  end
-
-  # Returns the params saved for +controller+.
-  def params_for(controller)
-    @session[controller.to_sym] || {}
-  end
 
-  # Find nested values without raising an exception.
-  def param_chain(*keys)
-    return nil if keys.empty?
-    final_key = keys.pop
-    empty_value = nil
-    empty_value = {} if final_key =~ /_hash$/
-    empty_value = [] if final_key =~ /_array$/
-
-    current_hash = @session
-    keys.each do |k|
-      current_hash = current_hash[k]
-      return empty_value unless current_hash.is_a?(Hash)
-    end
-    return empty_value unless current_hash.has_key?(final_key)
-    current_hash[final_key]
+      base.delete_if { |k,v| v.nil? }
+      base
+    end).(
+      @session,
+      hash.reject { |k,v| self.class.internal_keys.include?(k) }
+    )
   end
 
-  # Hash-like access to session attributes.
-  def [](key)
-    @session[key]
+  # Clear out all session attributes bar those used for tracking (IP, host,
+  # user agent, ...). Used when the user logs out.
+  def clear
+    @session.select! { |k,v| self.class.tracking_keys.include?(k) }
   end
 
-  # Hash-like assignment to session attributes.
-  def []=(key, value)
-    return unless @session_model
-    if key == :user_id
-      @session_model.user_id = value
-      @session_model.save
-    end
-    @session[key] = value
+  # Convert all session attributes directly into a regular hash.
+  def to_h
+    @session.to_h
   end
 
-  # The method_missing method has been redefined to allow for simplified access to session parameters.
-  #
-  # *Example*: calling +current_session+.+current_filters+ will access <tt>session[:current_filters]</tt>
-  def method_missing(key, *args)
-    @session[key.to_sym]
-  end
+  # Reporting/monitoring methods
 
-  ###########################################
-  # Peristent Userfile Ids Management Methods
-  ###########################################
-
-  # Clear the list of persistent userfile IDs;
-  # returns the number of userfiles that were there.
-  def persistent_userfile_ids_clear
-    persistent_ids = self[:persistent_userfile_ids] ||= {}
-    original_count = persistent_ids.size
-    self[:persistent_userfile_ids] = {}
-    original_count
-  end
+  # Active/inactive state; used mainly to mark currently active (logged in)
+  # users for reporting purposes, as the sessions records sometimes linger
+  # after the user logs out.
 
-  # Add the IDs in the array +id_list+ to the
-  # list of persistent userfile IDs.
-  # Returns the number of IDs that were actually added.
-  def persistent_userfile_ids_add(id_list)
-    added_count    = 0
-    persistent_ids = self[:persistent_userfile_ids] ||= {}
-    size_limit = 2500
-    if (persistent_ids.size + id_list.size) > size_limit
-      cb_error "You cannot have more than a total of #{size_limit} files selected persistently."
-      return
-    end
-    id_list.each do |id|
-      next if persistent_ids[id]
-      persistent_ids[id] = true
-      added_count += 1
-    end
-    added_count
-  end
+  # Mark this session as active.
+  def activate
+    return unless @model
 
-  # Removed the IDs in the array +id_list+ to the
-  # list of persistent userfile IDs.
-  # Returns the number of IDs that were actually removed.
-  def persistent_userfile_ids_remove(id_list)
-    removed_count  = 0
-    persistent_ids = self[:persistent_userfile_ids] ||= {}
-    id_list.each do |id|
-      next unless persistent_ids[id]
-      persistent_ids.delete(id)
-      removed_count += 1
-    end
-    removed_count
+    @model.user_id = @session[:user_id]
+    @model.active  = true
+    @model.save!
   end
 
-  # Returns an array of the list of persistent userfile IDs.
-  def persistent_userfile_ids_list
-    persistent_ids = self[:persistent_userfile_ids] ||= {}
-    persistent_ids.keys
-  end
+  # Mark this session as inactive.
+  def deactivate
+    return unless @model
 
-  # Returns the persistent userfile IDs as a hash.
-  def persistent_userfile_ids
-    persistent_ids = self[:persistent_userfile_ids] ||= {}
-    persistent_ids
+    @model.active = false
+    @model.save!
   end
 
-  private
-
-  def sanitize_params(k, param) #:nodoc:
-    key = k.to_sym
-
-    if key == :sort_hash
-      param["order"] = sanitize_sort_order(param["order"])
-      param["dir"] = sanitize_sort_dir(param["dir"])
-    end
+  # User model scope of currently (recently) active users.
+  # (active and had activity since +since+).
+  def self.active_users(since: 10.minutes.ago)
+    sessions = session_model.quoted_table_name
+    users    = User.quoted_table_name
 
-    param
+    User
+      .joins("INNER JOIN #{sessions} ON #{sessions}.user_id = #{users}.id")
+      .where("#{sessions}.active = 1")
+      .where(since ? ["#{sessions}.updated_at > ?", since] : {})
   end
 
-  def sanitize_sort_order(order) #:nodoc:
-    table, column = order.strip.split(".")
-    table = table.tableize
-
-    unless ActiveRecord::Base.connection.tables.include?(table)
-      cb_error "Invalid sort table: #{table}."
-    end
+  # Report (as a list of hashes) the +n+ most recently active users and their
+  # IP address, host name and user agent.
+  def self.recent_activity(n = 10)
+    sessions = session_model.quoted_table_name
+    users    = User.quoted_table_name
+
+    session_model
+      .joins("INNER JOIN #{users} ON #{users}.id = #{sessions}.user_id")
+      .order("#{sessions}.updated_at DESC")
+      .limit(n)
+      .map do |session|
+        data = (session.data || {}) rescue {}
+        {
+          :user           => User.find_by_id(session.user_id),
+          :active         => session.active?,
+          :last_access    => session.updated_at,
+          :remote_ip      => data['guessed_remote_ip'],
+          :remote_host    => data['guessed_remote_host'],
+          :raw_user_agent => data['raw_user_agent']
+        }
+      end
+  end
 
-    klass = Class.const_get table.classify
+  # Clean out spurious session entries; entries older than +since+ without
+  # an attached user.
+  def self.clean_sessions(since: 1.hour.ago)
+    session_model
+      .where('user_id IS NULL')
+      .where('updated_at < ?', since)
+      .destroy_all
+  end
 
-    unless klass.column_names.include?(column) ||
-        (klass.respond_to?(:pseudo_sort_columns) && klass.pseudo_sort_columns.include?(column))
-      cb_error "Invalid sort column: #{table}.#{column}"
-    end
+  # Purge all session entries older than +since+, no matter if theres an
+  # attached user or not.
+  def self.purge_sessions(since: 1.hour.ago)
+    session_model
+      .where('updated_at < ?', since)
+      .delete_all
+  end
 
-    "#{table}.#{column}"
+  # Delegate other calls on CbrainSession to session_model, making CbrainSession
+  # behave like Rails's session model.
+  def self.method_missing(method, *args) # :nodoc:
+    session_model.send(method, *args)
   end
 
-  def sanitize_sort_dir(dir) #:nodoc:
-    if dir.to_s.strip.upcase == "DESC"
-      "DESC"
-    else
-      "ASC"
-    end
+  # Deprecated/old API methods
+
+  # Fetch session parameters specific to controller +controller+.
+  # Marked as deprecated as session attributes are no longer necessarily bound
+  # to a controller.
+  def params_for(controller) #:nodoc:
+    controller  = (@session[controller.to_sym] ||= {})
+    controller['filter_hash'] ||= {}
+    controller['sort_hash']   ||= {}
+    controller
   end
 
 end
diff --git a/BrainPortal/app/views/userfiles/_file_menu.html.erb b/BrainPortal/app/views/userfiles/_file_menu.html.erb
index c7acbf005..d3dab34ba 100644
--- a/BrainPortal/app/views/userfiles/_file_menu.html.erb
+++ b/BrainPortal/app/views/userfiles/_file_menu.html.erb
@@ -135,7 +135,11 @@
         <%= hijacker_submit_button("Mark Content As Newer", :url  => url_for(:controller => 'userfiles', :action => 'sync_multiple', :operation => 'all_newer'), :ajax_submit  => false, :method  => :post, :class => "button") %>
     <% end %>
 
-    <% select_label = "Selected Files" + (current_session.persistent_userfile_ids.size != 0 ? " (now: #{current_session.persistent_userfile_ids.size})" : "") %>
+    <%
+      select_label  = "Selected Files"
+      select_label += " (now: #{current_session[:persistent_userfiles].size})" if
+        current_session[:persistent_userfiles].present?
+    %>
     <%= button_with_dropdown_menu(select_label) do %>
       <p class="left_align">
       This panel manages your list of <em>persistently</em> selected files.
@@ -144,10 +148,10 @@
       for all operation buttons (move/copy, submit tasks, etc).
       </p>
       <p>
-      <% if current_session.persistent_userfile_ids.size == 0 %>
+      <% if current_session[:persistent_userfiles].blank? %>
         Currently, no files are selected persistently.
       <% else %>
-        <%= html_colorize("#{pluralize(current_session.persistent_userfile_ids.size,"file")} currently selected persistently.") %>
+        <%= html_colorize("#{pluralize(current_session[:persistent_userfiles].size,"file")} currently selected persistently.") %>
       <% end %>
       </p>
       <p>
diff --git a/BrainPortal/app/views/userfiles/_userfiles_display.html.erb b/BrainPortal/app/views/userfiles/_userfiles_display.html.erb
index 882940485..43b751b14 100644
--- a/BrainPortal/app/views/userfiles/_userfiles_display.html.erb
+++ b/BrainPortal/app/views/userfiles/_userfiles_display.html.erb
@@ -25,9 +25,9 @@
 <%= render :partial => 'shared/active_filters', :locals => { :model => :userfile } %>
 
 <div class="pagination">
-  <% if current_session.persistent_userfile_ids.size > 0 %>
+  <% if current_session[:persistent_userfiles].present? %>
     <div class="pagination_left_side">
-      <blink><%= html_colorize("(#{pluralize(current_session.persistent_userfile_ids.size," file")} persistently selected)") %></blink>
+      <blink><%= html_colorize("(#{pluralize(current_session[:persistent_userfiles].size," file")} persistently selected)") %></blink>
     </div>
   <% end %>
   <div class="page_links">
@@ -73,7 +73,7 @@
 
     t.row do |u|
       {
-        :selected     => current_session.persistent_userfile_ids[u.id.to_s],
+        :selected     => current_session[:persistent_userfiles].try(:include?, u.id.to_s),
         :select_param => 'file_ids[]',
         :select_value => u.id
       } if u.available?
diff --git a/BrainPortal/config/routes.rb b/BrainPortal/config/routes.rb
index 2558d156c..d782dbef4 100644
--- a/BrainPortal/config/routes.rb
+++ b/BrainPortal/config/routes.rb
@@ -157,8 +157,10 @@
   get   '/credits'                => 'portal#credits'
   get   '/about_us'               => 'portal#about_us'
   get   '/login'                  => 'sessions#new'
-  get   '/session_status'         => 'sessions#show'
   get   '/logout'                 => 'sessions#destroy'
+  get   '/session_status'         => 'sessions#show'
+  get   '/session_data'           => 'session_data#show'
+  post  '/session_data'           => 'session_data#update'
   get   '/filter_proxy'           => 'application#filter_proxy'
 
   # Report Maker
diff --git a/BrainPortal/lib/basic_filter_helpers.rb b/BrainPortal/lib/basic_filter_helpers.rb
index 51e6e68b8..7f1a64453 100644
--- a/BrainPortal/lib/basic_filter_helpers.rb
+++ b/BrainPortal/lib/basic_filter_helpers.rb
@@ -148,32 +148,14 @@ def association_filters_for(filtered_scope, header_scope, tab, assoc, options =
   # Set up the current_session variable. Mainly used to set up the filter hash to be
   # used by index actions.
   def update_filters
-    current_controller = params[:proxy_destination_controller] || params[:controller]
-    params[current_controller] ||= {}
-    clear_params       = params.keys.select{ |k| k.to_s =~ /^clear_/}
-    clear_param_key    = clear_params.first
-    clear_param_value  = params[clear_param_key]
-    if clear_param_key
-      params[current_controller][clear_param_key.to_s] = clear_param_value
-    end
-    clear_params.each { |p| params.delete p.to_s }
-    if params[:update_filter]
-      update_filter      = params[:update_filter].to_s
-      parameters = request.query_parameters.clone
-      parameters.delete "update_filter"
-      parameters.delete "proxy_destination_controller"
-      parameters.delete "proxy_destination_action"
-      if update_filter =~ /_hash$/
-        params[current_controller][update_filter] = parameters
-      else
-        params[current_controller] = parameters
-      end
-      params.delete "update_filter"
-      parameters.keys.each { |p|  params.delete p}
-    end
-    current_session.update(params)
-
-    @filter_params = current_session.params_for(params[:proxy_destination_controller] || params[:controller])
+    Rails.logger.warn(
+      'WARNING: BasicFilterHelpers::update_filters has been ' +
+      'stubbed pending a rewrite of the filtering subsystem'
+    )
+
+    controller = params[:proxy_destination_controller] || params[:controller]
+    current_session.update({ :controllers => { controller => params } })
+    @filter_params = current_session.params_for(controller)
   end
 
   ########################################################################
diff --git a/BrainPortal/lib/session_helpers.rb b/BrainPortal/lib/session_helpers.rb
index fefcf02ff..fe6c3b2d9 100644
--- a/BrainPortal/lib/session_helpers.rb
+++ b/BrainPortal/lib/session_helpers.rb
@@ -34,7 +34,7 @@ def self.included(includer) #:nodoc:
 
   # Returns the current session as a CbrainSession object.
   def current_session
-    @cbrain_session ||= CbrainSession.new(session, params, request.env['rack.session.record'] )
+    @cbrain_session ||= CbrainSession.new(session, request.env['rack.session.record'] )
   end
 
   # Returns currently active project.

From 5d02384cc59fb56f3efcfa9a8baf759eaa046618 Mon Sep 17 00:00:00 2001
From: Pierre Rioux <pierre.rioux@mcgill.ca>
Date: Mon, 17 Aug 2015 11:48:21 -0400
Subject: [PATCH 11/85] Fix logfile viewer; improved user index table.

---
 .../app/controllers/portal_controller.rb      |  4 ++--
 BrainPortal/app/models/data_provider.rb       |  6 +++---
 .../app/views/users/_users_table.html.erb     | 20 +++++++++++--------
 .../public/stylesheets/dynamic-table.css      |  3 ---
 4 files changed, 17 insertions(+), 16 deletions(-)

diff --git a/BrainPortal/app/controllers/portal_controller.rb b/BrainPortal/app/controllers/portal_controller.rb
index 1543c6f6d..9a4312a32 100644
--- a/BrainPortal/app/controllers/portal_controller.rb
+++ b/BrainPortal/app/controllers/portal_controller.rb
@@ -142,7 +142,7 @@ def portal_log #:nodoc:
       found_ctrl = nil
       found_ms   = 0
 
-      (log.split("\n",num_lines+10) + [ "\n" ]).each do |line|
+      (log.split("\n") + [ "\n" ]).each do |line|
         next unless line
         next unless line =~ /^Started (\S+) "\/(\w*)/ || ! paragraph.empty?
 
@@ -168,7 +168,7 @@ def portal_log #:nodoc:
       end
       log = filtlogs.join("\n")
     else
-      log.split("\n",num_lines+10).each do |line|
+      log.split("\n").each do |line|
         if line =~ /^User: (\S+)/
           found_user = Regexp.last_match[1]
           @user_counts[found_user] += 1
diff --git a/BrainPortal/app/models/data_provider.rb b/BrainPortal/app/models/data_provider.rb
index 39cb15893..3eafe2bf7 100644
--- a/BrainPortal/app/models/data_provider.rb
+++ b/BrainPortal/app/models/data_provider.rb
@@ -513,8 +513,8 @@ def cache_writehandle(userfile, rel_path = nil)
     sync_to_provider(userfile)
   end
 
-  # This method provides a quick way to set the cache's file
-  # content to an exact copy of +localfile+, a locally accessible file.
+  # This method provides a quick way to set the cache's file content
+  # to an exact copy of +localpath+, a locally accessible file or directory.
   # The syncronization method +sync_to_provider+ will automatically
   # be called after the copy is performed.
   def cache_copy_from_local_file(userfile, localpath)
@@ -545,7 +545,7 @@ def cache_copy_from_local_file(userfile, localpath)
 
   # This method provides a quick way to copy the cache's file
   # to an exact copy +localfile+, a locally accessible file.
-  # The syncronization method +sync_to_cache+ will automatically
+  # The synchronization method +sync_to_cache+ will automatically
   # be called before the copy is performed.
   #
   # Note that if +localpath+ is a path to an existing filesystem
diff --git a/BrainPortal/app/views/users/_users_table.html.erb b/BrainPortal/app/views/users/_users_table.html.erb
index 3e0837893..b74db7e80 100644
--- a/BrainPortal/app/views/users/_users_table.html.erb
+++ b/BrainPortal/app/views/users/_users_table.html.erb
@@ -77,14 +77,18 @@
     ) { |u| u.last_connected_at ? to_localtime(u.last_connected_at, :datetime) : "Unknown" }
 
     t.column("Projects", :groups) do |u|
-      groups = u.available_groups.sort { |a,b| a.name.casecmp(b.name) }
-      html_tool_tip(pluralize(groups.size, "project"), :offset_x => 60) do
-        array_to_table(groups,
-          :table_class     => 'simple',
-          :ratio           => "3:1",
-          :fill_by_columns => true
-        ) { |g,r,c| g.name }
-      end.html_safe if groups.size > 0
+      group_names = u.available_groups.order(:name).raw_first_column(:name).reject { |n| n == u.login }
+      if group_names.size > 1 && group_names.size < 40
+        html_tool_tip(pluralize(group_names.size, "project"), :offset_x => 60) do
+          array_to_table(group_names,
+            :table_class     => 'simple',
+            :ratio           => "3:1",
+            :fill_by_columns => true
+          ) { |name,r,c| name }
+        end.html_safe
+      elsif group_names.size > 1
+        pluralize(group_names.size, "project")
+      end
     end
 
     t.column("Role", :type,
diff --git a/BrainPortal/public/stylesheets/dynamic-table.css b/BrainPortal/public/stylesheets/dynamic-table.css
index fdc7b1401..dd78d1c44 100644
--- a/BrainPortal/public/stylesheets/dynamic-table.css
+++ b/BrainPortal/public/stylesheets/dynamic-table.css
@@ -28,7 +28,6 @@
 .dynamic-table {
   color: #000000;
   display: inline-block;
-  font-family: sans-serif;
 }
 
 .dt-table {
@@ -42,7 +41,6 @@
   background: inherit;
   border: 0;
   color: inherit;
-  font-family: inherit;
   padding: 0.2em 0em 0.2em 0.9em;
   text-align: inherit;
   white-space: nowrap;
@@ -51,7 +49,6 @@
 .dt-body > tr > td {
   border: 0;
   color: inherit;
-  font-family: inherit;
   padding: 0.2em 0.5em 0.2em 0.9em;
   text-align: left;
 }

From c097b10d2f0f7b1dead6a4eb16378ac213c59fef Mon Sep 17 00:00:00 2001
From: Pierre Rioux <pierre.rioux@mcgill.ca>
Date: Mon, 17 Aug 2015 15:32:14 -0400
Subject: [PATCH 12/85] Index table filters grey out empty entries.

---
 .../app/helpers/dynamic_table_helper.rb       | 39 ++++++++++++-------
 .../app/views/shared/_dynamic_table.html.erb  |  2 +-
 .../public/javascripts/dynamic-table.js       | 22 +++++------
 .../public/stylesheets/dynamic-table.css      | 13 +++----
 4 files changed, 41 insertions(+), 35 deletions(-)

diff --git a/BrainPortal/app/helpers/dynamic_table_helper.rb b/BrainPortal/app/helpers/dynamic_table_helper.rb
index b64d95039..d5576ed93 100644
--- a/BrainPortal/app/helpers/dynamic_table_helper.rb
+++ b/BrainPortal/app/helpers/dynamic_table_helper.rb
@@ -201,8 +201,9 @@ def initialize(collection, template, attributes = {}, targets = {})
     #              the value if not present.
     #  [indicator] Special indicator value to be shown next to the label in the
     #              UI. Usually used for the number of table rows matching the
-    #              filter. Note that specifying '0' will disable selection of
-    #              the filter. Defaults to '-'.
+    #              filter. Defaults to '-'.
+    #  [empty]     If specified, the filter will be rendered in a style indicating
+    #              that it would return an empty result set. Defaults to false.
     #  If you supply an Enumerable of arrays or strings instead, they will be
     #  converted to hashes in the following manner:
     #    [1, "A"]    => { :value =>   1, :label => "A", :indicator => '-' }
@@ -267,13 +268,13 @@ def column(label, name = nil, options = {}, &block)
       # Filtering
       filter_target = as_func.call(options[:filter_target] || @targets[:filter])
       filters       = options[:filters].map do |f|
-        if f.is_a?(Enumerable)
+        if f.is_a?(Hash)
+          f
+        elsif f.is_a?(Enumerable)
           val, lbl, ind = f.to_a
           { :value => val,    :label => lbl || val, :indicator => ind || '-' }
-        elsif f.is_a?(String) || f.is_a?(Symbol)
-          { :value => f.to_s, :label => f.to_s,     :indicator => '-'        }
         else
-          f
+          { :value => f.to_s, :label => f.to_s,     :indicator => '-'        }
         end
       end if options[:filters]
 
@@ -528,7 +529,7 @@ def initialize(name, header, cell, options = {})
 
         if filter = options[:filter]
           @filters = filter[:filters].map do |f|
-            Filter.new(f[:value], f[:label], filter[:target], f[:indicator])
+            Filter.new(f[:value], f[:label], filter[:target], f[:indicator] || "-", f[:empty])
           end
         end
       end
@@ -559,8 +560,10 @@ def initialize(name, header, cell, options = {})
         # Target request to perform when this filter is selected
         :target,
         # Indicator value to show for this filter in the filter list next
-        # to the label. '0' will disable selection of the filter.
-        :indicator
+        # to the label.
+        :indicator,
+        # If true, toggle rendering of the filter text to a style indicating an empty result set.
+        :empty
       )
 
       # Whether or not the column is initially visible. The column's visibility
@@ -967,7 +970,9 @@ def dynamic_index_table(collection, options = {}, &block)
       link.match(/href="(.+?)"/)[1] # FIXME there is no filter_add_url...
     end
 
-    table = (@@index_table_class ||= Class.new(DynamicTable) do
+    # We create and cache a subclass of DynamicTable to act as
+    # a compatibility layer for the old 'index_table' framework
+    @@index_table_class ||= Class.new(DynamicTable) do
       attr_accessor :sort_map
       attr_accessor :filter_map
 
@@ -987,7 +992,8 @@ def dynamic_index_table(collection, options = {}, &block)
 
         # If we have index_table-like filters, convert them to DynamicTable's format
         options[:filters].map! do |label,hash|
-          [hash[:filters].first[1], label]
+          empty = hash[:class].presence.to_s.match(/filter_zero/).present? # old HTML class convention
+          { :value => hash[:filters].first[1], :label => label, :empty => empty }
         end if
           options[:filters] && options[:filters].all? do |filter|
             filter[1][:filters].first[1] rescue nil
@@ -1019,12 +1025,15 @@ def dynamic_index_table(collection, options = {}, &block)
       alias_method :paginated, :pagination
       alias_method :paginate,  :pagination
 
-    end).create(collection, self, options) do |table|
+    end
+
+    # Alright, let's create an instance of our backwards-compatible index_table object
+    table = @@index_table_class.create(collection, self, options) do |mytable|
       # Make the table aware of the sorting and filtering mappings
-      table.sort_map   = sort_map
-      table.filter_map = filter_map
+      mytable.sort_map   = sort_map
+      mytable.filter_map = filter_map
 
-      block.call(table)
+      block.call(mytable)
     end
 
     (options.has_key?(:render) && ! options[:render]) ? table : table.render
diff --git a/BrainPortal/app/views/shared/_dynamic_table.html.erb b/BrainPortal/app/views/shared/_dynamic_table.html.erb
index 23ac4ceef..a246d21b4 100644
--- a/BrainPortal/app/views/shared/_dynamic_table.html.erb
+++ b/BrainPortal/app/views/shared/_dynamic_table.html.erb
@@ -115,7 +115,7 @@
               <tbody class="dt-fpop-body">
                 <% column.filters.each do |filter| %>
                   <tr>
-                    <% zero_cls = filter.indicator.strip == '0' ? 'dt-zero' : '' %>
+                    <% zero_cls = filter.empty.present? ? 'dt-zero' : '' %>
                     <td class="dt-fpop-cnt <%= zero_cls %>">
                       <%= filter.indicator %>
                     </td>
diff --git a/BrainPortal/public/javascripts/dynamic-table.js b/BrainPortal/public/javascripts/dynamic-table.js
index fa8553b4e..af57243e7 100644
--- a/BrainPortal/public/javascripts/dynamic-table.js
+++ b/BrainPortal/public/javascripts/dynamic-table.js
@@ -167,8 +167,8 @@
 
     /* sorting, filtering and pagination requests */
     dyntbl
-      .undelegate('.dt-sort-btn, .dt-fpop-txt:not(.dt-zero), .dt-pag-pages > a', 'click.dyn-tbl')
-      .delegate('.dt-sort-btn, .dt-fpop-txt:not(.dt-zero), .dt-pag-pages > a', 'click.dyn-tbl', function (event) {
+      .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();
 
         var url = $(this).attr('href') || $(this).data('url');
@@ -208,7 +208,7 @@
     /* show/hide popups on filter/columns display button clicks */
     dyntbl
       .undelegate('.dt-filter-btn, .dt-col-btn', 'click.dyn-tbl')
-      .delegate('.dt-filter-btn, .dt-col-btn', 'click.dyn-tbl', function () {
+      .delegate(  '.dt-filter-btn, .dt-col-btn', 'click.dyn-tbl', function () {
         table
           .find('.dt-filter-btn, .dt-col-btn')
           .not(this)
@@ -228,7 +228,7 @@
     /* hide popups when their close buttons are clicked */
     dyntbl
       .undelegate('.dt-pop-close-btn', 'click.dyn-tbl')
-      .delegate('.dt-pop-close-btn', 'click.dyn-tbl', function () {
+      .delegate(  '.dt-pop-close-btn', 'click.dyn-tbl', function () {
         var popup = $(this)
           .parent()
           .hide();
@@ -243,7 +243,7 @@
     /* stick the columns display popup in place when shown */
     dyntbl
       .undelegate('.dt-col-csp > .dt-popup', 'show.dyn-tbl')
-      .delegate('.dt-col-csp > .dt-popup', 'show.dyn-tbl', function () {
+      .delegate(  '.dt-col-csp > .dt-popup', 'show.dyn-tbl', function () {
         var popup    = $(this),
             width    = popup.outerWidth(),
             edge_gap = 10,
@@ -256,7 +256,7 @@
         });
       })
       .undelegate('.dt-col-csp > .dt-popup', 'hide.dyn-tbl')
-      .delegate('.dt-col-csp > .dt-popup', 'hide.dyn-tbl', function () {
+      .delegate(  '.dt-col-csp > .dt-popup', 'hide.dyn-tbl', function () {
         $(this)
           .css({ left: '', top: '' })
           .parent()
@@ -268,7 +268,7 @@
     /* show rows as selected if their respective checkbox is checked */
     dyntbl
       .undelegate('td.dt-sel > .dt-sel-check', 'change.dyn-tbl')
-      .delegate('td.dt-sel > .dt-sel-check', 'change.dyn-tbl', function () {
+      .delegate(  'td.dt-sel > .dt-sel-check', 'change.dyn-tbl', function () {
         $(this)
           .closest('tr')
           .toggleClass('dt-selected', $(this).prop('checked'));
@@ -288,7 +288,7 @@
     /* trigger selection checkboxes when the row is clicked */
     dyntbl
       .undelegate('.dt-body > .dt-sel-row', 'click.dyn-tbl')
-      .delegate('.dt-body > .dt-sel-row', 'click.dyn-tbl', function (event) {
+      .delegate(  '.dt-body > .dt-sel-row', 'click.dyn-tbl', function (event) {
         if (!$(this).children('td').is(event.target)) return;
 
         var checkbox = $(this)
@@ -308,7 +308,7 @@
     /* toggle all checkboxes when the header checkbox is clicked */
     dyntbl
       .undelegate('th.dt-sel > .dt-sel-check', 'change.dyn-tbl')
-      .delegate('th.dt-sel > .dt-sel-check', 'change.dyn-tbl', function () {
+      .delegate(  'th.dt-sel > .dt-sel-check', 'change.dyn-tbl', function () {
         var checked = $(this).prop('checked');
 
         if (selection_mode == 'single') return;
@@ -329,7 +329,7 @@
     /* toggle columns when the column is clicked in the column display popup */
     dyntbl
       .undelegate('.dt-cpop-col', 'click.dyn-tbl')
-      .delegate('.dt-cpop-col', 'click.dyn-tbl', function () {
+      .delegate(  '.dt-cpop-col', 'click.dyn-tbl', function () {
         $(this)
           .find('.dt-cpop-icon')
           .toggleClass(icons.column_show)
@@ -356,7 +356,7 @@
     /* filter out filter options if they dont begin with the search input */
     dyntbl
       .undelegate('.dt-fpop-find > input', 'input.dyn-tbl')
-      .delegate('.dt-fpop-find > input', 'input.dyn-tbl', function () {
+      .delegate(  '.dt-fpop-find > input', 'input.dyn-tbl', function () {
         var key = $.trim($(this).val()).toLowerCase();
 
         $(this)
diff --git a/BrainPortal/public/stylesheets/dynamic-table.css b/BrainPortal/public/stylesheets/dynamic-table.css
index dd78d1c44..3a0f3ae2d 100644
--- a/BrainPortal/public/stylesheets/dynamic-table.css
+++ b/BrainPortal/public/stylesheets/dynamic-table.css
@@ -284,23 +284,20 @@ td.dt-sel > .dt-sel-lbl > .dt-sel-icon {
   width: 100%;
 }
 
-.dt-fpop-cnt.dt-zero {
+.dt-fpop-body > tr > .dt-fpop-txt.dt-zero,
+.dt-fpop-body > tr > .dt-fpop-cnt.dt-zero {
   color: #bbbbbb;
 }
 
-.dt-fpop-txt.dt-zero {
-  color: #bbbbbb;
-}
-
-.dt-fpop-txt:not(.dt-zero) {
+.dt-fpop-txt {
   cursor: pointer;
 }
 
-.dt-fpop-txt:not(.dt-zero):hover {
+.dt-fpop-txt:hover {
   background-color: #fff3d3;
 }
 
-.dt-fpop-txt:not(.dt-zero):active {
+.dt-fpop-txt:active {
   background-color: #ffe49a;
 }
 

From 2408e08b13343fd759a0d1b5d6b678a19b905310 Mon Sep 17 00:00:00 2001
From: Pierre Rioux <pierre.rioux@mcgill.ca>
Date: Mon, 17 Aug 2015 16:05:06 -0400
Subject: [PATCH 13/85] Code esthetics following review by Remi.

---
 BrainPortal/app/helpers/dynamic_table_helper.rb      | 8 ++++----
 BrainPortal/app/views/shared/_dynamic_table.html.erb | 6 +++---
 BrainPortal/public/javascripts/dynamic-table.js      | 4 ++--
 BrainPortal/public/stylesheets/dynamic-table.css     | 4 ++--
 4 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/BrainPortal/app/helpers/dynamic_table_helper.rb b/BrainPortal/app/helpers/dynamic_table_helper.rb
index d5576ed93..54cb74a1c 100644
--- a/BrainPortal/app/helpers/dynamic_table_helper.rb
+++ b/BrainPortal/app/helpers/dynamic_table_helper.rb
@@ -1028,12 +1028,12 @@ def dynamic_index_table(collection, options = {}, &block)
     end
 
     # Alright, let's create an instance of our backwards-compatible index_table object
-    table = @@index_table_class.create(collection, self, options) do |mytable|
+    table = @@index_table_class.create(collection, self, options) do |t|
       # Make the table aware of the sorting and filtering mappings
-      mytable.sort_map   = sort_map
-      mytable.filter_map = filter_map
+      t.sort_map   = sort_map
+      t.filter_map = filter_map
 
-      block.call(mytable)
+      block.call(t)
     end
 
     (options.has_key?(:render) && ! options[:render]) ? table : table.render
diff --git a/BrainPortal/app/views/shared/_dynamic_table.html.erb b/BrainPortal/app/views/shared/_dynamic_table.html.erb
index a246d21b4..2f25458ea 100644
--- a/BrainPortal/app/views/shared/_dynamic_table.html.erb
+++ b/BrainPortal/app/views/shared/_dynamic_table.html.erb
@@ -115,15 +115,15 @@
               <tbody class="dt-fpop-body">
                 <% column.filters.each do |filter| %>
                   <tr>
-                    <% zero_cls = filter.empty.present? ? 'dt-zero' : '' %>
-                    <td class="dt-fpop-cnt <%= zero_cls %>">
+                    <% empty_cls = filter.empty ? 'dt-empty' : '' %>
+                    <td class="dt-fpop-cnt <%= empty_cls %>">
                       <%= filter.indicator %>
                     </td>
                     <%
                       filter_url = filter.target.call(column.name, filter)
                       filter_url = url_for(sort_url) unless sort_url.is_a?(String)
                     %>
-                    <td class="dt-fpop-txt <%= zero_cls %>"
+                    <td class="dt-fpop-txt <%= empty_cls %>"
                         data-url="<%= filter_url.html_safe %>"
                         data-column="<%= column.name.to_s %>"
                         data-value="<%= filter.value %>">
diff --git a/BrainPortal/public/javascripts/dynamic-table.js b/BrainPortal/public/javascripts/dynamic-table.js
index af57243e7..895db26a5 100644
--- a/BrainPortal/public/javascripts/dynamic-table.js
+++ b/BrainPortal/public/javascripts/dynamic-table.js
@@ -158,7 +158,7 @@
     /* trigger a sorting request when the header of a sortable column is clicked */
     dyntbl
       .undelegate('.dt-sort > .dt-hdr', 'click.dyn-tbl')
-      .delegate('.dt-sort > .dt-hdr', 'click.dyn-tbl', function () {
+      .delegate(  '.dt-sort > .dt-hdr', 'click.dyn-tbl', function () {
         $(this)
           .siblings('.dt-sort-btn')
           .first()
@@ -168,7 +168,7 @@
     /* sorting, filtering and pagination requests */
     dyntbl
       .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) {
+      .delegate(  '.dt-sort-btn, .dt-fpop-txt, .dt-pag-pages > a', 'click.dyn-tbl', function (event) {
         event.preventDefault();
 
         var url = $(this).attr('href') || $(this).data('url');
diff --git a/BrainPortal/public/stylesheets/dynamic-table.css b/BrainPortal/public/stylesheets/dynamic-table.css
index 3a0f3ae2d..a4f626dbb 100644
--- a/BrainPortal/public/stylesheets/dynamic-table.css
+++ b/BrainPortal/public/stylesheets/dynamic-table.css
@@ -284,8 +284,8 @@ td.dt-sel > .dt-sel-lbl > .dt-sel-icon {
   width: 100%;
 }
 
-.dt-fpop-body > tr > .dt-fpop-txt.dt-zero,
-.dt-fpop-body > tr > .dt-fpop-cnt.dt-zero {
+.dt-fpop-body > tr > .dt-fpop-txt.dt-empty,
+.dt-fpop-body > tr > .dt-fpop-cnt.dt-empty {
   color: #bbbbbb;
 }
 

From 5f75d5dfe5dda571dca073f79490a596e388ca6c Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Wed, 19 Aug 2015 10:48:55 -0400
Subject: [PATCH 14/85] Issue #197 - Missing user count, minor dynamic table
 style changes

This changeset restores the user index's user count that was lost in the
port to dynamic tables, and removes the old pagination partial where it
was located (was missed due to being tucked in a partial instead of
being directly on the page).

This changeset also fixes a few minor style issues in dynamic_table.rb.
---
 .../app/helpers/dynamic_table_helper.rb       | 44 ++++++++++++++-----
 .../app/views/users/_pagination.html.erb      | 34 --------------
 .../app/views/users/_users_table.html.erb     |  3 ++
 .../public/stylesheets/dynamic-table.css      |  3 ++
 4 files changed, 40 insertions(+), 44 deletions(-)
 delete mode 100644 BrainPortal/app/views/users/_pagination.html.erb

diff --git a/BrainPortal/app/helpers/dynamic_table_helper.rb b/BrainPortal/app/helpers/dynamic_table_helper.rb
index 54cb74a1c..3c022d728 100644
--- a/BrainPortal/app/helpers/dynamic_table_helper.rb
+++ b/BrainPortal/app/helpers/dynamic_table_helper.rb
@@ -202,8 +202,9 @@ def initialize(collection, template, attributes = {}, targets = {})
     #  [indicator] Special indicator value to be shown next to the label in the
     #              UI. Usually used for the number of table rows matching the
     #              filter. Defaults to '-'.
-    #  [empty]     If specified, the filter will be rendered in a style indicating
-    #              that it would return an empty result set. Defaults to false.
+    #  [empty]     If specified, the filter will be rendered in a style
+    #              indicating that it would return an empty result set.
+    #              Defaults to false.
     #  If you supply an Enumerable of arrays or strings instead, they will be
     #  converted to hashes in the following manner:
     #    [1, "A"]    => { :value =>   1, :label => "A", :indicator => '-' }
@@ -269,12 +270,27 @@ def column(label, name = nil, options = {}, &block)
       filter_target = as_func.call(options[:filter_target] || @targets[:filter])
       filters       = options[:filters].map do |f|
         if f.is_a?(Hash)
-          f
+          {
+            :value     => f[:value],
+            :label     => f[:label]     || f[:value],
+            :indicator => f[:indicator] || '-',
+            :empty     => !!f[:empty]
+          }
         elsif f.is_a?(Enumerable)
-          val, lbl, ind = f.to_a
-          { :value => val,    :label => lbl || val, :indicator => ind || '-' }
+          value, label, indicator = f.to_a
+          {
+            :value     => value,
+            :label     => label     || value,
+            :indicator => indicator || '-',
+            :empty     => false
+          }
         else
-          { :value => f.to_s, :label => f.to_s,     :indicator => '-'        }
+          {
+            :value     => f.to_s,
+            :label     => f.to_s,
+            :indicator => '-',
+            :empty     => false
+          }
         end
       end if options[:filters]
 
@@ -529,7 +545,13 @@ def initialize(name, header, cell, options = {})
 
         if filter = options[:filter]
           @filters = filter[:filters].map do |f|
-            Filter.new(f[:value], f[:label], filter[:target], f[:indicator] || "-", f[:empty])
+            Filter.new(
+              f[:value],
+              f[:label],
+              filter[:target],
+              f[:indicator],
+              f[:empty]
+            )
           end
         end
       end
@@ -562,7 +584,8 @@ def initialize(name, header, cell, options = {})
         # Indicator value to show for this filter in the filter list next
         # to the label.
         :indicator,
-        # If true, toggle rendering of the filter text to a style indicating an empty result set.
+        # If true, toggle rendering of the filter text to a style indicating an
+        # empty result set.
         :empty
       )
 
@@ -992,8 +1015,9 @@ def dynamic_index_table(collection, options = {}, &block)
 
         # If we have index_table-like filters, convert them to DynamicTable's format
         options[:filters].map! do |label,hash|
-          empty = hash[:class].presence.to_s.match(/filter_zero/).present? # old HTML class convention
-          { :value => hash[:filters].first[1], :label => label, :empty => empty }
+          value = hash[:filters].first[1]
+          empty = hash[:class].to_s =~ /filter_zero/ # old HTML class convention
+          { :value => value, :label => label, :empty => empty }
         end if
           options[:filters] && options[:filters].all? do |filter|
             filter[1][:filters].first[1] rescue nil
diff --git a/BrainPortal/app/views/users/_pagination.html.erb b/BrainPortal/app/views/users/_pagination.html.erb
deleted file mode 100644
index f6dca67d1..000000000
--- a/BrainPortal/app/views/users/_pagination.html.erb
+++ /dev/null
@@ -1,34 +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 <http://www.gnu.org/licenses/>.  
-#
--%>
-
-<div class="pagination_left_side"></div>
-<div class="page_links">
-  <%= will_paginate @users, :container => false %>
-  (<%= pluralize @users.total_entries, "user" %>)
-</div>
-<div class="pagination_right_side">
-  Search by name:
-  <%= ajax_search_box "name_like", users_path(:update_filter => :filter_hash) %>
-</div>
-
diff --git a/BrainPortal/app/views/users/_users_table.html.erb b/BrainPortal/app/views/users/_users_table.html.erb
index b74db7e80..b030c05b7 100644
--- a/BrainPortal/app/views/users/_users_table.html.erb
+++ b/BrainPortal/app/views/users/_users_table.html.erb
@@ -29,6 +29,9 @@
 <%= render :partial => 'shared/active_filters', :locals => { :model => :user } %>
 
 <div class="pagination">
+  <div class="page_links">
+    (<%= pluralize @users.total_entries, "user" %>)
+  </div>
   <div class="pagination_right_side">
     Search by name:
     <%= ajax_search_box "name_like", users_path(:update_filter => :filter_hash) %>
diff --git a/BrainPortal/public/stylesheets/dynamic-table.css b/BrainPortal/public/stylesheets/dynamic-table.css
index a4f626dbb..2a6e55571 100644
--- a/BrainPortal/public/stylesheets/dynamic-table.css
+++ b/BrainPortal/public/stylesheets/dynamic-table.css
@@ -28,6 +28,7 @@
 .dynamic-table {
   color: #000000;
   display: inline-block;
+  font-family: sans-serif;
 }
 
 .dt-table {
@@ -41,6 +42,7 @@
   background: inherit;
   border: 0;
   color: inherit;
+  font-family: inherit;
   padding: 0.2em 0em 0.2em 0.9em;
   text-align: inherit;
   white-space: nowrap;
@@ -49,6 +51,7 @@
 .dt-body > tr > td {
   border: 0;
   color: inherit;
+  font-family: inherit;
   padding: 0.2em 0.5em 0.2em 0.9em;
   text-align: left;
 }

From d333483fe2f44272865fa85d94d63cf6e661b58c Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Wed, 19 Aug 2015 11:12:52 -0400
Subject: [PATCH 15/85] Issue #197 - Locked/unlocked user counts

Added as requested in issue comments. The counts are also links to
filter the table (filter for just locked/unlocked accounts).
---
 BrainPortal/app/controllers/users_controller.rb  |  8 +++++---
 .../app/views/users/_users_table.html.erb        | 16 +++++++++++++++-
 2 files changed, 20 insertions(+), 4 deletions(-)

diff --git a/BrainPortal/app/controllers/users_controller.rb b/BrainPortal/app/controllers/users_controller.rb
index 8e307f375..e5317c154 100644
--- a/BrainPortal/app/controllers/users_controller.rb
+++ b/BrainPortal/app/controllers/users_controller.rb
@@ -44,9 +44,11 @@ def index #:nodoc:
     @filtered_scope = base_filtered_scope @header_scope.includes( [:groups, :site] ).order( sort_order )
     @users          = base_sorted_scope @filtered_scope
 
-    # Precompute file and task counts.
-    @users_file_counts=Userfile.where(:user_id => @users.map(&:id)).group(:user_id).count
-    @users_task_counts=CbrainTask.real_tasks.where(:user_id => @users.map(&:id)).group(:user_id).count
+    # Precompute file, task and locked/unlocked counts.
+    @users_file_counts  = Userfile.where(:user_id => @users.map(&:id)).group(:user_id).count
+    @users_task_counts  = CbrainTask.real_tasks.where(:user_id => @users.map(&:id)).group(:user_id).count
+    @locked_users_count   = @users.where(:account_locked => true).count
+    @unlocked_users_count = @users.count - @locked_users_count
 
     # For Pagination
     unless [:html, :js].include?(request.format.to_sym)
diff --git a/BrainPortal/app/views/users/_users_table.html.erb b/BrainPortal/app/views/users/_users_table.html.erb
index b030c05b7..2cd40d359 100644
--- a/BrainPortal/app/views/users/_users_table.html.erb
+++ b/BrainPortal/app/views/users/_users_table.html.erb
@@ -30,7 +30,21 @@
 
 <div class="pagination">
   <div class="page_links">
-    (<%= pluralize @users.total_entries, "user" %>)
+    (
+      <%= pluralize @users.total_entries, "user" %>
+      <% if @unlocked_users_count > 0 %>,
+        <%=
+          filter_add_link "#{@unlocked_users_count} active",
+            :filters => { :account_locked => 0 }
+        %>
+      <% end %>
+      <% if @locked_users_count > 0 %>,
+        <%=
+          filter_add_link "#{@locked_users_count} locked",
+            :filters => { :account_locked => 1 }
+        %>
+      <% end %>
+    )
   </div>
   <div class="pagination_right_side">
     Search by name:

From 3d33b3d7a0e8c7ac061deae7689f45a811ce0469 Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Wed, 19 Aug 2015 17:54:35 -0400
Subject: [PATCH 16/85] Initial (rough) version of the new view scoping
 mechanism

Much more flexible, documented, featured and documented scoping
system to replace the current basic_filter_helpers.rb and
filter_helpers.rb.

This new system notably features:
- Extended filtering operators; <, <=, >, >=, string matching, etc.
- Flexible association specification (JOINs)
- Support for an arbitrary amount of filters
- Support for both AR models and Ruby collections
- Pagination via will_paginate
- Straightforward (and documented) URL update mechanism
- Custom attributes and selection

See scope_helpers.rb for full documentation.

This changeset also includes an incomplete set of tests
(scope_helpers_spec.rb).
---
 BrainPortal/lib/scope_helpers.rb              | 1545 +++++++++++++++++
 .../spec/modules/scope_helpers_spec.rb        |  622 +++++++
 2 files changed, 2167 insertions(+)
 create mode 100644 BrainPortal/lib/scope_helpers.rb
 create mode 100644 BrainPortal/spec/modules/scope_helpers_spec.rb

diff --git a/BrainPortal/lib/scope_helpers.rb b/BrainPortal/lib/scope_helpers.rb
new file mode 100644
index 000000000..25c71fd8d
--- /dev/null
+++ b/BrainPortal/lib/scope_helpers.rb
@@ -0,0 +1,1545 @@
+
+#
+# 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 <http://www.gnu.org/licenses/>.
+#
+
+# Helpers to apply user-specified scopes on CBRAIN's models or collections for
+# viewing purposes. Scopes are a flexible and safe way to define which filtering
+# and sorting rules to apply on a given collection before display and keep 
+# track of item selection and pagination information.
+#
+# Scopes currently in use are usually stored in Rails' session, and can easily
+# be converted to and from hashes. For example, a scope to filter by an
+# attribute named user_id and sort by name would look like:
+#   scope = Scope.from_hash({
+#     :filters => [
+#       {
+#         :attribute => :user_id,
+#         :value     => 10,
+#       },
+#     ],
+#     :order => [
+#       {
+#         :attribute => :name,
+#         :direction => :asc,
+#       },
+#     ]
+#   })
+# To then apply this scope to a collection or model, use the scope's apply
+# method:
+#   scoped_tools = scope.apply(Tool)
+#
+# Currently active/known scopes are stored in Rails' session as a hash with
+# scope names for keys and scope hash definitions/representations as values:
+#   current_session[:scopes] == {
+#     'userfiles' => { :f => [ ... ], :o => ... },
+#     'tasks'     => { :f => [ ... ], :o => ... },
+#     ...
+#   }
+# To directly add or replace one of the session scopes, convert the scope to a
+# compact hash representation first before adding to
+# +current_session[:scopes]+:
+#   current_session[:scopes]['tasks'] = scope.to_hash(compact: true)
+#
+# Scopes created from hashes and session attributes are automatically sanitized
+# and it is thus safe to pass user-supplied values to create them.
+# Note that scopes stored in Rails' session are in compact hash representation,
+# see +Scope+'s +compact_hash+ method for more information.
+#
+# NOTE: While similar to ActiveRecord's scoping mechanism, the scopes defined in
+# this module mainly target views, by taking concerns such as selection and
+# pagination, and are expected to be 'closer' to the user than ActiveRecord's
+# scopes (which would pose a security risk if they could be directly accessed).
+module ScopeHelpers
+
+  Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
+
+  # ScopeHelpers is intended to be included as a controller extension module,
+  # exposing +scope_from_session+, +default_scope_name+, +update_session_scopes+,
+  # URL parameter methods and +filter_values_for+.
+  def self.included(includer) #:nodoc:
+    includer.class_eval do
+      helper_method(
+        :filter_values_for,
+        :scope_url_params,
+        :filter_url_params,
+        :order_url_params
+      )
+
+      before_filter :update_session_scopes
+    end
+  end
+
+  # Represents a scope to filter and sort a given model or collection
+  # (via +apply+) and hold selection and pagination information. This object is
+  # typically created from an hash representation (see +from_hash+ and
+  # +scope_from_session+).
+  class Scope
+
+    # Filters this scope filters the collection or model with. Instances of
+    # Scope::Filter, each represents a single filtering rule to apply.
+    #
+    # While filters will be applied in order, filters are expected to be
+    # independent from eachother and should thus given the same result no
+    # matter in which order they are applied.
+    attr_accessor :filters
+
+    # Set operation to combine the filter result sets with. Either +:and+ or
+    # +:intersection+ for intersection (each item in the final result set must
+    # match all filters) or +:or+ or +:union+ for union (each item in the final
+    # result set must match at least one filter).
+    #
+    # TODO: Not implemented yet, as +:or+/+:union+ is not implemented for
+    # ActiveRecord models (the query interface does not support them cleanly
+    # as of Rails 3) and slow/awkward for regular Ruby collections.
+    attr_accessor :filter_combination
+
+    # Ordering/sorting rules to sort the collection or model with. Instances of
+    # Scope::Order, each represents a part of the ordering to apply; each rule
+    # is applied in order, and rules beyond the first one sort elements that
+    # were considered equal under the first rule (just like SQL's ORDER BY
+    # clause).
+    #
+    # TODO: 'ORDER BY'-like behavior is not yet implemented for Ruby
+    # collections; only the first Scope::Order instance will be applied to the
+    # collection/model.
+    attr_accessor :order
+
+    # Pagination component to paginate (split into pages of fixed size) the
+    # collection or model with, if required. Instance of Scope::Pagination.
+    #
+    # While a UI concern somewhat detached from sorting and filtering,
+    # pagination is a key UI concept which needs to be applied to the
+    # collection or model before it can be displayed (and thus belongs in Scope)
+    attr_accessor :pagination
+
+    # List of record IDs (models) and collection keys (or indices, if there is
+    # no such thing) selected by the user in the model or collection.
+    #
+    # While a UI concern, keeping selection in scopes allows any component of
+    # the application to access and alter user selection and allows persisting
+    # selection information with scopes in the session or DB.
+    attr_accessor :selection
+
+    # An indifferent hash of extra scoping/filtering/sorting parameters specific
+    # to the Scope instance. These extra parameters can be used to store extra
+    # view-specific options that would otherwise have to be persisted and set
+    # manually.
+    attr_accessor :custom
+
+    # Create a new blank Scope without any filtering or sorting rules. Once
+    # the filter has been created, rules can be subsequently added using the
+    # filters and order attributes.
+    #
+    # To create a scope already initialized with a set of rules, see the
+    # +from_hash+ class method.
+    def initialize
+      @filters   = []
+      @order     = []
+      @selection = []
+      @custom    = HashWithIndifferentAccess.new
+    end
+
+    # Create a deep copy of the Scope +other+, down to each Filter in *filters*
+    # and each Order in *order*. This method allows +dup+ and +clone+ (which
+    # invoke it) to create independent copies which can then be used by
+    # +scope_url_params+ and +url_for+ to create URLs changing arbitrary Scope
+    # elements (see +scope_url_params+).
+    def initialize_copy(other)
+      hash_dup = lambda { |obj| obj.class.from_hash(obj.to_hash) }
+
+      @filters    = other.filters.map(&hash_dup)
+      @order      = other.order.map(&hash_dup)
+      @pagination = hash_dup.(other.pagination) if other.pagination
+      @selection  = other.selection.dup
+      @custom     = other.custom.dup
+    end
+
+    # Apply the set of filtering and sorting rules and pagination from this
+    # scope to a given +collection+, which is either an ActiveRecord model
+    # or a Ruby Enumerable. Once the rules have been applied, the original
+    # collection is returned, scoped with the scope's rules; a scoped
+    # ActiveRecord model if +collection+ was a model or a new Ruby Enumerable
+    # matching the rules if +collection+ was a Ruby Enumerable.
+    def apply(collection)
+      # Apply all filtering rules
+      collection = @filters.inject(collection) do |collection, filter|
+        filter.apply(collection)
+      end
+
+      # Apply sorting rules
+      if (collection <= ActiveRecord::Base rescue nil)
+        collection = @order.inject(collection) do |collection, order|
+          order.apply(collection)
+        end
+      else
+        collection = @order.first.apply(collection) unless @order.empty?
+      end
+
+      # Paginate
+      collection = @pagination.apply(collection) if @pagination
+
+      collection
+    end
+
+    # Create a new Scope described by the contents of +hash+. Each recognized
+    # pair in +hash+ corresponds to a Scope attribute and is expected to
+    # match the format of the attribute (e.g. +:filters+ should be an Enumerable
+    # of filters).
+    #
+    # For attributes containing objects (*filters*, *order*, *pagination*, etc.)
+    # of which the class implements a +from_hash+ method, a hash is also
+    # accepted instead of an instance; the instance will be created using the
+    # method and the provided hash:
+    #   some_filter_hash = { ... }
+    #   Scope.from_hash({
+    #     :filters => [ some_filter_hash ]
+    #   })
+    # corresponds to:
+    #   some_filter_hash = { ... }
+    #   filter = Scope::Filter.from_hash(some_filter_hash)
+    #   Scope.from_hash({
+    #     :filters => [ filter ]
+    #   })
+    #
+    # The following keys are recognized in +hash+:
+    #
+    # [:filters or :f]
+    #  *filters* attribute: an array (or Enumerable) of Scope::Filter instances.
+    #
+    # [:order or :o]
+    #  *order* attribute: an array (or Enumerable) of Scope::Order instances.
+    #
+    # [:pagination or :p]
+    #  *pagination* attribute: a Scope::Pagination instance.
+    #
+    # [:selection or :s]
+    #  *selection* attribute: an array of selected IDs or keys inside the
+    #  collection.
+    #
+    # [:custom or :c]
+    #  *custom* attribute: an arbitrary Ruby hash of custom view options.
+    #
+    # [:filter_combination or :fc]
+    #  *filter_combination* attribute: either +:and+/+:intersection+ or
+    #  +:or+/+:union+ (defaults to +:and+).
+    #
+    # Any missing key will lead to a nil attribute and be handled appriately;
+    # arrays will default to empty and absent components will be ignored.
+    #
+    # Returns the newly created Scope (just like new would)
+    def self.from_hash(hash)
+      # Make sure +hash+ is proper
+      return nil unless hash.is_a?(Hash)
+
+      hash = hash.with_indifferent_access unless
+        hash.is_a?(HashWithIndifferentAccess)
+
+      scope = self.new
+
+      # Filtering and ordering rules
+      scope.filters = (hash[:filters] || hash[:f] || [])
+        .map { |filter| Filter.from_hash(filter) }
+        .compact
+
+      scope.order = (hash[:order] || hash[:o] || [])
+        .map { |order| Order.from_hash(order) }
+        .compact
+
+      # Pagination, selection and other properties
+      scope.pagination = Pagination.from_hash(hash[:pagination] || hash[:p])
+      scope.selection  =  hash[:selection] || hash[:s] || []
+      scope.custom     = (hash[:custom]    || hash[:c] || {}).with_indifferent_access
+      scope.filter_combination = hash[:filter_combination] || hash[:fc] || :and
+
+      scope
+    end
+
+    # Convert this Scope into a hash, doing the exact opposite of +from_hash+
+    # and converting as many object attributes into hashes (using their own
+    # +to_hash+ methods) as possible. The generated hash will have the same
+    # structure as what +from_hash+ accepts. Specifying +compact+ will have
+    # +to_hash+ compact the generated hash just like +compact_hash+ would (see
+    # +compact_hash+).
+    def to_hash(compact: false)
+      hash = {
+        :filters    => @filters.map(&:to_hash),
+        :order      => @order.map(&:to_hash),
+        :pagination => @pagination.try(:to_hash),
+        :selection  => @selection,
+        :custom     => @custom.symbolize_keys,
+        :filter_combination => @filter_combination,
+      }
+
+      compact ? self.class.compact_hash(hash) : hash
+    end
+
+    # Compact +hash+, which is expected to be a Ruby hash matching +from_hash+'s
+    # structure, to try and make +hash+ as compact/small as possible while
+    # respecting +from_hash+'s structure by using the short key versions and
+    # omitting blank/default fields.
+    def self.compact_hash(hash)
+      # Make sure +hash+ is proper
+      return nil unless hash.is_a?(Hash)
+
+      hash = hash.with_indifferent_access unless
+        hash.is_a?(HashWithIndifferentAccess)
+
+      compact = {
+        # Compact filtering rules
+        :f => (hash[:filters] || hash[:f] || [])
+          .map { |filter| Filter.compact_hash(filter) }
+          .reject(&:blank?),
+
+        # Compact ordering rules
+        :o => (hash[:order] || hash[:o] || [])
+          .map { |order| Order.compact_hash(order) }
+          .reject(&:blank?),
+
+        # Compact the pagination component
+        :p => Pagination.compact_hash(hash[:pagination] || hash[:p]),
+
+        # Include other attributes
+        :s  => hash[:s]  || hash[:selection],
+        :c  => hash[:c]  || hash[:custom],
+        :fc => hash[:fc] || hash[:filter_combination],
+      }
+
+      # Delete empty/default values
+      compact.delete_if { |key, value| value.blank? }
+      compact.delete(:fc) if compact[:fc].to_s == 'and'
+
+      compact
+    end
+
+    # Represents a single filtering rule to apply on an ActiveRecord model or
+    # Ruby collection (Enumerable).
+    #
+    # This class covers the following filtering clauses:
+    # - Direct comparison using operators; ==, !=, >, >=, <, <= and 'like' for
+    #   strings.
+    # - Set inclusion/exclusion (x in [a, b, c, d])
+    # - Range matching (between x and y)
+    # - Association filtering for ActiveRecord models
+    #
+    # This class is also intended to be used as a base class for more
+    # specialized filtering cases. See the +type_name+ and +from_hash+ class
+    # methods for more information on how to subclass Filter.
+    class Filter
+      # Name of the collection/model attribute to filter on, as a string or
+      # symbol. Must be present as an attribute in collection/model elements or
+      # the filter will be ignored.
+      #
+      # Note that it can also be an attribute on the matching association
+      # element if an association is specified.
+      attr_accessor :attribute
+
+      # Value(s) to filter against. Either a single value (direct comparison),
+      # a set of values (set inclusion/exclusion) or a pair of values (range
+      # matching), depending on which kind of filtering is to be done.
+      attr_accessor :value
+
+      # Predicate operator to apply to *attribute*'s value and *value* to
+      # check if the collection/model element passes the filter. The possible
+      # operators are:
+      #
+      # [:==, :!=, :>, :>=, :<, :<=]
+      #  Standard comparison operators; a single value in *value* is expected.
+      #
+      # [:in, :out]
+      #  Set inclusion (:in) or exclusion (:out); a set (Enumerable) of values
+      #  in *value* is expected.
+      #  Behaves like Ruby's include? method and SQL's IN clause.
+      #
+      # [:match]
+      #  Case insensitive string inclusion; a single string in *value* is
+      #  expected.
+      #  Behaves like a case-insensitive Ruby include? and SQL's LIKE clause.
+      #  Shortened to just :m in compact Filter hash representations.
+      #
+      # [:range]
+      #  Range match; a pair of values in *value* is expected.
+      #  Given a range [a, b] in *value* and x as *attribute*'s value,
+      #  corresponds to the predicate a <= x <= b.
+      #  Shortened to just :r in compact Filter hash representations.
+      #
+      # Defaults to an equality comparison (:==).
+      attr_accessor :operator
+
+      # Optional ActiveRecord model to join on to the filtered model before
+      # filtering, to allow for *attribute* to refer to attributes on the
+      # joined model.
+      #
+      # By default, a regular Rails join will be used to join the two models.
+      # To specify join columns, make *association* an array with three
+      # elements; the association model, the association model's join attribute
+      # and the original model's join attribute. For example, to join the Users
+      # model to the Userfiles model via the *owner* attribute:
+      #   # Userfiles has :owner, Users has :id
+      #   [ :userfiles, :owner, :id ]
+      #
+      # To avoid any ambiguity between the two models for which model
+      # *attribute* refers to, *attribute* can be prefixed with the association
+      # name: +'userfiles.name'+ (or +:'userfiles.name'+).
+      #
+      # Only meaningful when filtering ActiveRecord models.
+      attr_accessor :association
+
+      # Short type name for this type of specialized filter.
+      # This method is expected to be implemented in Scope::Filter subclasses
+      # to determine which Filter subclass to load when creating a Filter
+      # instance using +from_hash+.
+      # Returns nil in the superclass (Scope::Filter) as a filter hash is
+      # assumed to be a Scope::Filter if no +:type+ key is present
+      # (see +from_hash+).
+      def self.type_name
+        nil
+      end
+
+      # Filter the given +collection+ (an ActiveRecord model or a Ruby
+      # Enumerable) according to the filtering predicate defined by this
+      # object's attributes (see each attribute's documentation for how they
+      # influence filtering).
+      # Returns a filtered subset of +collection+.
+      #
+      # Note that if the filter is not valid (no *operator* or *attribute*),
+      # an exception will be thrown.
+      def apply(collection)
+        raise "no operator to filter with"      unless @operator
+        raise "no attribute to filter on items" unless @attribute
+
+        @value ||= [] if [ :in, :out, :range ].include?(@operator)
+
+        if (collection <= ActiveRecord::Base rescue nil)
+          apply_on_model(collection)
+        else
+          apply_on_collection(collection)
+        end
+      end
+
+      # Check if this Filter object is valid and able to filter a collection or
+      # model; a Filter is valid if it has an *operator* and *attribute*.
+      def valid?
+        return @operator && @attribute
+      end
+
+      # Create a new Filter described by the contents of +hash+. Just like
+      # Scope's +from_hash+ method, each recognized pair in +hash+ corresponds
+      # to a Filter attribute (except for type, see below) and is expected to
+      # match the attribute's format.
+      #
+      # The following keys are recognized in +hash+:
+      #
+      # [:type or :t]
+      #  Type (subclass) of Filter of create from +hash+, as a string or symbol.
+      #  If present, this key's value is expected to match a subclass'
+      #  +type_name+ (or the Ruby class name) and that subclass' +from_hash+
+      #  will be invoked on +hash+ to create the filter instead. If the key does
+      #  not match any subclass' +type_name+, a blank filter will be created.
+      #
+      # [:attribute or :a]
+      #  *attribute* attribute: a symbol or string.
+      #
+      # [:value or :v]
+      #  *value* attribute: a scalar (number, bool, string, symbol, etc.)
+      #  value or an array (or Enumerable) of scalar values.
+      #
+      # [:operator or :o]
+      #  *operator* attribute: one of the possible operators (see the
+      #  *operator* attribute) as a symbol or string (defaults to :==).
+      #
+      # [:association or :j]
+      #  *association* attribute: an ActiveRecord model or an array with an
+      #  ActiveRecord model and the two attributes to perform the join with.
+      #  A string or symbol representing the model or DB table can also be
+      #  supplied instead of the model itself; +from_hash+ will resolve them
+      #  to the actual model.
+      #
+      # Returns the newly created Filter (just like new would)
+      def self.from_hash(hash)
+        # Make sure +hash+ is proper
+        return nil unless hash.is_a?(Hash)
+
+        hash = hash.with_indifferent_access unless
+          hash.is_a?(HashWithIndifferentAccess)
+
+        filter = self.new
+
+        # Handle Filter subclasses (:type key)
+        if type = (hash[:type] || hash[:t])
+          subclass = self.descendants.find { |sub| sub.type_name == type }
+          return subclass ? subclass.from_hash(hash) : filter
+        end
+
+        # *attribute* must be alphanumeric (word-like)
+        attribute = (hash[:attribute] || hash[:a]).to_s.gsub(/[^\w.]/, '')
+        filter.attribute = attribute unless attribute.blank?
+
+        # *operator* must be one of the possible predicate operators
+        operator = (hash[:operator] || hash[:o] || :==).to_s.downcase.to_sym
+        operator = :range if operator == :r
+        operator = :match if operator == :m
+        filter.operator = operator if
+          [ :==, :!=, :>, :>=, :<, :<=, :in, :out, :match, :range ].include?(operator)
+
+        # *value* must be a simple scalar value or a set of simple values,
+        # depending on which *operator* is to be applied
+        value = hash[:value] || hash[:v]
+        value = (value.is_a?(Enumerable) ? value : [value])
+          .map(&:to_s)
+          .reject(&:blank?)
+
+        filter.value = (
+          case operator
+          when :==, :!=, :>, :>=, :<, :<=
+            value.first
+          when :in, :out
+            value unless value.empty?
+          when :match
+            value.first.to_s
+          when :range
+            value[0, 2] if value.length == 2
+          else
+            nil
+          end
+        )
+
+        # *association* must be an ActiveRecord model or an array with the
+        # correct format
+        filter.association = ScopeHelpers.parse_assoc(hash[:association] || hash[:j])
+
+        filter
+      end
+
+      # Convert this Filter into a hash, doing the exact opposite of
+      # +from_hash+. This method behaves almost identically to Scope's +to_hash+
+      # method (and has the same argument +compact+), except for being applied
+      # to a Filter object instead of a Scope.
+      # Note that the *association* attribute will be represented as the name
+      # of its corresponding DB table in the generated hash.
+      #
+      # See Scope's +to_hash+ method for further information.
+      def to_hash(compact: false)
+        hash = {
+          :attribute   => @attribute,
+          :operator    => @operator,
+          :value       => @value,
+          :association => ScopeHelpers.assoc_with_table(@association)
+        }
+
+        compact ? self.class.compact_hash(hash) : hash
+      end
+
+      # Compact +hash+, which is expected to be a Ruby hash matching
+      # +from_hash+'s structure. Behaves similarly to Scope's +compact_hash+
+      # method, except for being applied to a Filter hash representation
+      # instead of a Scope one.
+      def self.compact_hash(hash)
+        Scope.generic_compact_hash(
+          hash,
+          {
+            :type        => :t,
+            :attribute   => :a,
+            :operator    => :o,
+            :value       => :v,
+            :association => :j
+          },
+          values: [
+            [ :operator, :range, :r ],
+            [ :operator, :match, :m ]
+          ],
+          defaults: { :operator => :== }
+        )
+      end
+
+      private
+
+      # Filter the given +model+, an ActiveRecord model.
+      # Internal model-specific implementation of the +apply+ method; see
+      # +apply+ for more information on this method.
+      def apply_on_model(model) #:nodoc:
+        # Resolve and validate *attribute* as an attribute of +model+ (or
+        # *association*).
+        attribute, model = ScopeHelpers.resolve_model_attribute(@attribute, model, @association)
+
+        case @operator
+        # Standard comparison operators can just be used as-is, bar for :== and
+        # when NULLs are involved.
+        when :==, :!=, :>, :>=, :<, :<=
+          operator = (
+            # IS/IS NOT for NULLs (nil)
+            if    @value.nil? && @operator == :== then 'IS'
+            elsif @value.nil? && @operator == :!= then 'IS NOT'
+            # SQL uses a single =
+            elsif @operator == :== then '='
+            # Other cases are as-is
+            else @operator
+            end
+          )
+          return model.where("#{attribute} #{operator} ?", @value)
+
+        # :in corresponds to IN, and :out to NOT IN
+        when :in, :out
+          operator     = (@operator == :in ? 'IN' : 'NOT IN')
+          placeholders = @value.map { '?' }.join(',')
+          return (
+            if @value.present?
+              model.where("#{attribute} #{operator} (#{placeholders})", *@value)
+            elsif @operator == :in
+              model.where('1 = 0')
+            else
+              model.where({})
+            end
+          )
+
+        # :match is more-or-less LIKE
+        when :match
+          pattern = "%#{@value.gsub(/([%_!])/, '!\1')}%"
+          return model.where("#{attribute} LIKE ? ESCAPE '!'", pattern)
+
+        # :range is exactly BETWEEN
+        when :range
+          min, max = @value.sort
+          return model.where("#{attribute} BETWEEN ? AND ?", min, max)
+
+        # Invalid operator?
+        else
+          raise "unknown operator '#{@operator}'"
+        end
+      end
+
+      # Filter the given +collection+, a Ruby Enumerable.
+      # Internal collection-specific implementation of the +apply+ method; see
+      # +apply+ for more information on this method.
+      def apply_on_collection(collection) #:nodoc:
+        # Nothing to filter in an empty collection
+        return collection if collection.empty?
+
+        # Assuming all objects are similar, how is *attribute* accessed? And do
+        # we need to cast/convert *value* before the comparison?
+        # Once known, keep the access and conversion methods as lambdas to make
+        # attribute access as fast as possible.
+        attr_get  = ScopeHelpers.generate_getter(collection.first, @attribute)
+        raise "no way to get '#{@attribute}' out of collection items" unless attr_get
+
+        value     = (@value.is_a?(Enumerable) ? @value.first : @value)
+        attr_cast = ScopeHelpers.generate_cast(value, attr_get.(collection.first))
+        raise "no way to convert '#{value}' to '#{@attribute}' values" unless attr_cast
+
+        case @operator
+        # Standard comparison operators are just invoked directly (send
+        # method) to each item against @value.
+        when :==, :!=, :>, :>=, :<, :<=
+          value = attr_cast.(@value)
+          return collection.select do |item|
+            attr_get.(item).send(@operator, value) rescue nil
+          end
+
+        # :in and :out naturally correspond to the include? method
+        when :in, :out
+          method = (@operator == :in ? :select : :reject)
+          values = @value.map(&attr_cast)
+          return collection.send(method) do |item|
+            values.include?(attr_get.(item)) rescue nil
+          end
+
+        # :match is a case-insensitive :in
+        when :match
+          value = @value.to_s.downcase
+          return collection.select do |item|
+            attr_get.(item).to_s.downcase.include?(value) rescue nil
+          end
+
+        # :range corresponds to min <= value <= max
+        when :range
+          min, max = @value.map(&attr_cast).sort
+          return collection.select do |item|
+            attr = attr_get.(item)
+            (min <= attr && attr <= max) rescue nil
+          end
+
+        # Invalid operator?
+        else
+          raise "unknown operator '#{@operator}'"
+        end
+      end
+    end
+
+    # Represents a single sorting/ordering rule to apply on an ActiveRecord
+    # model or Ruby collection (Enumerable). This class provides basic
+    # ascending/descending ordering, and just like Scope::Filter, is also
+    # intended to be used as a base class for more specialized sorting/ordering
+    # rules. See the +type_name+ and +from_hash+ class methods for more
+    # information on how to subclass Order.
+    class Order
+      # Name of the collection/model attribute to order/sort the
+      # collection/model with, as a string or symbol. Must be present as an
+      # attribute on in collection/model elements and correspond to a comparable
+      # value (anything that supports <, >), or no sorting/orderin will be
+      # performed on the collection/model at all.
+      #
+      # Note that it can also be an attribute on the matching association
+      # element if an association is specified.
+      attr_accessor :attribute
+
+      # SQL-like direction in which to perform the sorting/ordering; either
+      # +:asc+ to sort in ascending order (1, 2, 3, ...) or +:desc+ to sort in
+      # descending order (7, 6, 5, ...).
+      # Defaults to ascending order (:asc).
+      attr_accessor :direction
+
+      # Optional ActiveRecord model to join on to the filtered model before
+      # filtering, to allow for *attribute* to refer to attributes on the
+      # joined model.
+      #
+      # Almost identical to Filter's own *association* attribute; see Filter's
+      # *association* attribute for more information.
+      attr_accessor :association
+
+      # Short type name for this type of specialized ordering rule.
+      # This method has the same role as Filter's type_name method; it is
+      # expected to be implemented in subclasses to determine which subclass
+      # to load when creating an Order instance using +from_hash+
+      # See Filter's +type_name+ for more information.
+      def self.type_name
+        nil
+      end
+
+      # Order the given +collection+ (an ActiveRecord model or a Ruby
+      # Enumerable) by *attribute* in *direction*.
+      # Returns a sorted/ordered version of +collection+.
+      #
+      # Note that if the ordering rule is invalid (no *attribute* or
+      # *direction*), an exception will be thrown.
+      def apply(collection)
+        raise "no direction to sort in" unless @direction
+        raise "no attribute to sort on" unless @attribute
+
+        if (collection <= ActiveRecord::Base rescue nil)
+          apply_on_model(collection)
+        else
+          apply_on_collection(collection)
+        end
+      end
+
+      # Check if this Order object is valid and able to sort/order a collection
+      # or model; an Order is valid if it has a sorting *direction* and
+      # *attribute*.
+      def valid?
+        return @direction && @attribute
+      end
+
+      # Create a new Order described by the contents of +hash+. Works similarly
+      # to Filter's +from_hash+ method, as each recognized pair in +hash+
+      # corresponds to an Order attribute and is expected to match the
+      # attribute's format, bar for +:type+.
+      #
+      # The following keys are recognized in +hash+:
+      #
+      # [:type or :t]
+      #  Type (subclass) of Filter to create from +hash+, as a string or symbol.
+      #  Handled the same way as Filter's own +:type+ key; see Filter's
+      #  +from_hash+ method.
+      #
+      # [:attribute or :a]
+      #  *attribute* attribute: a symbol or string.
+      #
+      # [:direction or :d]
+      #  *direction* attribute: either +:asc+ or +:desc+ (defaults to +:asc+).
+      #
+      # [:association or :j]
+      #  *association* attribute: an ActiveRecord model or an array with an
+      #  ActiveRecord model and the two attributes to perform the join with.
+      #  Handled the same way as Filter's own +:association+ key; see Filter's
+      #  +from_hash+ method.
+      #
+      # Returns the newly created Order (just like new would)
+      def self.from_hash(hash)
+        # Make sure +hash+ is proper
+        return nil unless hash.is_a?(Hash)
+
+        hash = hash.with_indifferent_access unless
+          hash.is_a?(HashWithIndifferentAccess)
+
+        order = self.new
+
+        # Handle Order subclasses (:type key)
+        if type = (hash[:type] || hash[:t])
+          subclass = self.descendants.find { |sub| sub.type_name == type }
+          return subclass ? subclass.from_hash(hash) : order
+        end
+
+        # *attribute* must be alphanumeric (word-like)
+        attribute = (hash[:attribute] || hash[:a]).to_s.gsub(/[^\w.]/, '')
+        order.attribute = attribute unless attribute.blank?
+
+        # *direction* must be either ascending or descending
+        direction   = (hash[:direction] || hash[:d] || :asc).to_s.downcase.to_sym
+        order.direction = direction if [ :asc, :desc ].include?(direction)
+
+        # *association* must be an ActiveRecord model or an array with the
+        # correct format
+        order.association = ScopeHelpers.parse_assoc(hash[:association] || hash[:j])
+
+        order
+      end
+
+      # Convert this Order object into a hash, doing the exact opposite of
+      # +from_hash+. This method behaves almost identically to Scope's +to_hash+
+      # method (and has the same argument +compact+), except for being applied
+      # to a Order object instead of a Scope.
+      #
+      # See Scope's +to_hash+ method for further information.
+      def to_hash(compact: false)
+        hash = {
+          :attribute   => @attribute,
+          :direction   => @direction,
+          :association => ScopeHelpers.assoc_with_table(@association)
+        }
+
+        compact ? self.class.compact_hash(hash) : hash
+      end
+
+      # Compact +hash+, which is expected to be a Ruby hash matching
+      # +from_hash+'s structure. Behaves similarly to Scope's +compact_hash+
+      # method, except for being applied to a Order hash representation instead
+      # of a Scope one.
+      def self.compact_hash(hash)
+        Scope.generic_compact_hash(
+          hash,
+          {
+            :type        => :t,
+            :attribute   => :a,
+            :direction   => :d,
+            :association => :j
+          },
+          defaults: { :direction => :asc }
+        )
+      end
+
+      private
+
+      # Sort/order the given ActiveRecord +model+.
+      # Internal model-specific implementation of the +apply+ method; see
+      # +apply+ for more information on this method.
+      def apply_on_model(model) #:nodoc:
+        # Resolve and validate *attribute* as an attribute of +model+ (or
+        # *association*).
+        attribute, model = ScopeHelpers.resolve_model_attribute(@attribute, model, @association)
+
+        raise "unknown direction '#{@direction}'" unless
+          [ :asc, :desc ].include?(@direction)
+
+        model.order("#{attribute} #{@direction.to_s.upcase}")
+      end
+
+      # Sort/order the given Ruby +collection+.
+      # Internal collection-specific implementation of the +apply+ method; see
+      # +apply+ for more information on this method.
+      def apply_on_collection(collection) #:nodoc:
+        # Nothing to sort in an empty collection.
+        return collection if collection.empty?
+
+        # Assuming all objects are similar, how is *attribute* accessed?
+        # Once known, keep the access method as a lambda to make attribute
+        # access as fast as possible.
+        attr_get = ScopeHelpers.generate_getter(collection.first, @attribute)
+        raise "no way to get '#{@attribute}' out of collection items" unless attr_get
+
+        collection = collection.sort_by(&attr_get)
+        collection.reverse! if @direction == :desc
+        collection
+      end
+    end
+
+    # Represents a pagination component, used to paginate the given collection
+    # (Ruby Enumerable) or ActiveRecord model. This class behaves as a wrapper
+    # around will_paginate to handle most of the heavy work (since most Scope
+    # users expect will_paginate collections).
+    class Pagination
+      # Page number to scope the collection/model to. For example, a collection
+      # of 1000 items paginated with 100 elements per page would be scoped to
+      # items 101-200 for *page* 2.
+      # Defaults to 1.
+      attr_accessor :page
+
+      # Limit (number) of items per collection/model page. For example a
+      # collection of 1050 items with 100 elements per page would result in a
+      # paginated collection of 11 pages, 10 with 100 elements each and one with
+      # only 50. Defaults to will_paginate's default of 30.
+      attr_accessor :per_page
+
+      # Optional total number of items in the collection/model, for when the
+      # collection/model's entry count differs from what should be used when
+      # paginating the collection/model.
+      # Naturally defaults to the size of the collection/model.
+      attr_accessor :total
+
+      # Paginate +collection+, (an ActiveRecord model or a Ruby Enumerable)
+      # with *per_page* elements per page, and return the paginated collection
+      # scoped to the page corresponding to *page*.
+      def apply(collection)
+        collection = collection.to_a unless
+          (collection <= ActiveRecord::Base rescue nil)
+
+        # Clamp @page and @per_page to a sane range
+        page     = [1,  [@page,     99_999].min].max
+        per_page = [25, [@per_page, 1000  ].min].max
+
+        collection.paginate(
+          :page          => page,
+          :per_page      => per_page,
+          :total_entries => @total
+        )
+      end
+
+      # Create a new Pagination object described by the contents of +hash+. Just
+      # like Scope's +from_hash+ method, each recognized pair in +hash+
+      # corresponds to a Pagination attribute and is expected to match the
+      # attribute's format.
+      #
+      # The following keys are recognized in +hash+:
+      #
+      # [:page or :i]
+      #  *page* attribute: an integer.
+      #
+      # [:per_page or :p]
+      #  *per_page* attribute: an integer.
+      #
+      # [:total or :t]
+      #  *total* attribute: an integer.
+      #
+      # Returns the newly created Pagination (just like new would)
+      def self.from_hash(hash)
+        return nil unless hash.is_a?(Hash)
+
+        hash = hash.with_indifferent_access unless
+          hash.is_a?(HashWithIndifferentAccess)
+
+        pagination = self.new
+        pagination.page     = (hash[:i] || hash[:page] || 1).to_i
+        pagination.per_page = (hash[:p] || hash[:per_page]).to_i
+        pagination.total    = (hash[:t] || hash[:total]).to_i
+        pagination
+      end
+
+      # Convert this Pagination object into a hash, doing the exact opposite of
+      # +from_hash+. This method behaves almost identically to Scope's +to_hash+
+      # method (and has the same argument +compact+), except for being applied
+      # to a Pagination object instead of a Scope.
+      #
+      # See Scope's +to_hash+ method for further information.
+      def to_hash(compact: false)
+        hash = {
+          :page     => @page,
+          :per_page => @per_page,
+          :total    => @total
+        }
+
+        compact ? self.class.compact_hash(hash) : hash
+      end
+
+      # Compact +hash+, which is expected to be a Ruby hash matching
+      # +from_hash+'s structure. Behaves similarly to Scope's +compact_hash+
+      # method, except for being applied to a Order hash representation instead
+      # of a Scope one.
+      def self.compact_hash(hash)
+        Scope.generic_compact_hash(
+          hash,
+          {
+            :page     => :i,
+            :per_page => :p,
+            :total    => :t
+          },
+          defaults: { :page => 1 }
+        )
+      end
+    end
+
+    # Utility methods for Scope components (Filter, Order and Pagination)
+
+    # Compact +hash+, an hash representation of a Scope component.
+    # This method is intended only as a generic way to implement a component's
+    # +compact_hash+ method.
+    #
+    # +keys+ is expected to be a mapping of +hash+'s keys to shorter
+    # versions of the same keys:
+    #   {
+    #     :attribute => :a,
+    #     :operator  => :o,
+    #     :value     => :v
+    #   }
+    #
+    # +values+, if given, is expected to be a list of +hash+ values to
+    # shorten in the following format:
+    #   [
+    #     [<key>, <long value>, <short value>],
+    #
+    #     # hash[:operator] would become :r if it was :range
+    #     [:operator,  :range,     :r],
+    #
+    #     # hash[:direction] would become :asc if it was :ascending
+    #     [:direction, :ascending, :asc],
+    #   ]
+    #
+    # +defaults+, if given, is expected to be a mapping of default values
+    # for +hash+ which should be removed when compacting:
+    #   {
+    #     # :asc is the default for :direction, and doesn't need to be included
+    #     # in the compacted hash version
+    #     :direction => :asc
+    #   }
+    def self.generic_compact_hash(hash, keys, values: {}, defaults: {})
+      # Make sure +hash+ is proper
+      return nil unless hash.is_a?(Hash)
+
+      compact = hash.symbolize_keys
+
+      hash = hash.with_indifferent_access unless
+        hash.is_a?(HashWithIndifferentAccess)
+
+      # Shorten attribute values
+      values.each do |key, long, short|
+        compact[key] = short if compact[key] == long
+      end
+
+      # Delete empty/default values
+      compact.delete_if { |key, value| value.blank? }
+      defaults.each do |key, value|
+        compact.delete(key) if compact[key] == value
+      end
+
+      # Compact attribute keys
+      keys.each do |long, short|
+        compact[short] = compact.delete(long) if compact.has_key?(long)
+      end
+
+      compact
+    end
+
+  end
+
+  # Create a new Scope from the hash-based session scope definition named +name+
+  # stored in Rails' session object (+:scopes+ key), invoking Scope's
+  # +from_hash+ method to create the Scope instance. If +name+ is not present in
+  # the session, an empty Scope is created instead. +name+ defaults to the
+  # default scope name; +default_scope_name+.
+  def scope_from_session(name = nil)
+    name ||= default_scope_name
+    scopes = (current_session[:scopes] ||= {})
+    hash   = (scopes[name] ||= {})
+    Scope.from_hash(hash)
+  end
+
+  # Store a +scope+ under the name +name+ in compact hash form in Rails' session
+  # object (+:scopes+ key), invoking the scope's +to_hash+ method to convert
+  # to Scope instance to a hash. If +name+ is already present in the session's
+  # scopes, the old scope is replaced by +scope+. +name+ defaults to the
+  # default scope name; +default_scope_name+
+  def scope_to_session(scope, name = nil)
+    name ||= default_scope_name
+    scopes = (current_session[:scopes] ||= {})
+    scopes[name] = scope.to_hash(compact: true)
+  end
+
+  # Default scope name for the current route. Typically '<controller>#<route>'.
+  # For example, to fetch the default scope from Rails' session explicitly:
+  #   @scope = scope_from_session(default_scope_name)
+  def default_scope_name
+    "#{params[:controller]}##{params[:action]}"
+  end
+
+  # Update the hash-based scope definitions stored in Rails' session (under the
+  # +:scopes+ key) using scope-specific query parameters.
+  # This method, called just before any action (as a before_filter), allows
+  # updating the session's view scopes just before the control is handed to the
+  # controller.
+  #
+  # The following query parameters are recognized by +update_session_scopes+:
+  #
+  # [_scopes]
+  #  Expected to be a hash to be merged in the session's scopes (:scopes) as
+  #  specified by CbrainSession's +update+ method.
+  #
+  # [_cur_scope]
+  #  Expected to be a hash to be merged in the current route's scope
+  #  (current_session[:scopes][+default_scope_name+]). Behaves similarly to
+  #  +_scopes+, as it too uses CbrainSession's +update+ method.
+  #
+  # [_scope_mode]
+  #  Mode to merge array/collections when merging into session scopes using
+  #  +_scopes+ or +_cur_scope+. Corresponds to the collection_mode parameter
+  #  of CbrainSession's +update+ method. Defaults to 'replace'.
+  #
+  # [page, per_page]
+  #  Common pagination parameters to update the current route's default scope
+  #  with. These parameters correspond to the *page* and *per_page* attributes
+  #  of Scope::Pagination, and are handled purely for convenience and
+  #  convention; the same functionality (and more) can be accessed by
+  #  passing a hash to the +_scopes+ parameter instead.
+  #
+  # Note that the scopes in +_cur_scope+ and +_scopes+ can be in
+  # compressed format (see the +compress_scope+ and +decompress_scope+ utility
+  # methods).
+  def update_session_scopes
+    default = default_scope_name
+    mode    = (params['_scope_mode'] || 'replace').to_sym
+
+    # Decompress (if required) and merge _scopes and _cur_scope
+    scopes = (params['_scopes'] || {})
+    scopes.merge!({ default => params['_cur_scope'] }) if params['_cur_scope']
+    scopes = scopes.map do |n, s|
+      return [n, s] if s.is_a?(Hash)
+      [ n, (ScopeHelpers.decompress_scope(s) rescue s) ]
+    end.to_h
+
+    current_session.update({ :scopes => scopes }, mode) unless scopes.blank?
+
+    # Pagination parameters (which override _scopes and _cur_scope)
+    pagination = {}
+    pagination[:i] = params['page']     if params['page']
+    pagination[:p] = params['per_page'] if params['per_page']
+
+    current_session.update({
+      :scopes => { default => { :p => pagination } }
+    }, mode) unless
+      pagination.empty?
+  end
+
+  # View methods
+
+  # Generate URL parameters suitable for +url_for+ to update the session scope
+  # named +name+ to match +scope+ (a Scope instance or a hash representation)
+  # via +update_session_scopes+. For example, to change the first filter of the
+  # 'userfiles' scope:
+  #   @scope = scope_from_session('userfiles')
+  #   # ...
+  #   new_scope = @scope.dup
+  #   new_scope.filters[0].operator = :!=
+  #   query_params = scope_url_params('userfiles', new_scope)
+  # Same as above, using the hash representation of +@scope+:
+  #   @scope = scope_from_session('userfiles')
+  #   # ...
+  #   scope_hash = @scope.to_hash
+  #   scope_hash[:filters][0][:operator] = :!=
+  #   scope_hash = @scope.class.compact_hash(scope_hash)
+  #   query_params = scope_url_params('userfiles', scope_hash)
+  # Unless +compress+ is specified as false, the generated URL parameters will
+  # use the compressed format as specified by +compress_scope+.
+  def scope_url_params(name, scope, compress: true)
+    scope = scope.to_hash if scope.is_a?(Scope)
+    scope = Scope.compact_hash(scope)
+    scope = ScopeHelpers.compress_scope(scope) if compress
+
+    { '_scopes' => { name => scope } }
+  end
+
+  # Generate URL parameters suitable for +url_for+ to update the session scope
+  # named +scope+'s filters (via +update_session_scopes+) via a given
+  # +operation+. +filters+ is expected to be Filter instances or hash
+  # representations (a single filter or an Enumerable), depending on which
+  # +operation+ is to be performed, and +operation+ is expected to be one of:
+  # [+:add+]
+  #  Add one or more +filters+ to the specified scope.
+  # [+:remove+]
+  #  Remove one or more +filters+ from the specified scope.
+  # [+:set+]
+  #  Add one or more +filters+ to the specified scope, replacing existing
+  #  filters filtering on the same attributes as +filters+.
+  # [+:replace+]
+  #  Replace all filters in the specified scope by the ones in +filters+.
+  # [+:clear+]
+  #  Remove all filters in the specified scope (+filters is ignored).
+  #  Equivalent to using +:replace+ with an empty +filters+.
+  #
+  # +scope+ defaults to the current route's scope name (see
+  # +default_scope_name+).
+  #
+  # Note that the generated URL parameters are in compressed format (see
+  # +compress_scope+).
+  def filter_url_params(operation, filters, scope: nil)
+    scope ||= default_scope_name
+    filters = (filters.is_a?(Array) ? filters : [filters]).map do |filter|
+      filter = filter.to_hash if filter.is_a?(Scope::Filter)
+      Scope::Filter.compact_hash(filter)
+    end
+
+    ScopeHelpers.scope_items_url_params(scope, operation, :filters, filters)
+  end
+
+  # Generate URL parameters suitable for +url_for+ to update the session scope
+  # named +scope+'s ordering rules (via +update_session_scopes+) via a given
+  # +operation+. This method behaves just like +filter_url_params+, but operates
+  # on a Scope's ordering rules (Order instances or hash representations)
+  # instead of filters. As such, the same +operation+s are available (:add,
+  # :remove, :set, :replace, :clear) and the +scope+ and +orders+ parameters are
+  # handled the exact same way +filter_url_params+'s +scope+ and +filters+
+  # parameters are handled.
+  def order_url_params(operation, orders, scope: nil)
+    scope ||= default_scope_name
+    orders = (orders.is_a?(Array) ? orders : [orders]).map do |order|
+      order = order.to_hash if order.is_a?(Scope::Order)
+      Scope::Order.compact_hash(order)
+    end
+
+    ScopeHelpers.scope_items_url_params(scope, operation, :order, orders)
+  end
+
+  # Fetch the possible values (and their count) for +attribute+ within
+  # +collection+, which is either a Ruby Enumerable or ActiveRecord model.
+  # As this method is intended as a view helper to create the list of values to
+  # filter a collection/model with, the possible values are returned as a list
+  # of hashes matching +DynamicTable+'s filter format, containing:
+  # [:value]
+  #  Possible value for +attribute+.
+  # [:label]
+  #  String representation of +:value+ (or just +:value+ if unavailable).
+  # [:indicator]
+  #  Count of how many times this specific +:value: was found for +attribute+ in
+  #  +collection+.
+  #
+  # If +label+ is specified, it is expected to be an attribute name as a string
+  # or symbol (like +attribute+), representing which +collection+ attribute to
+  # use as value labels.
+  #
+  # If +association+ is specified, it is expected to be in the same format as
+  # +Scope+::+Filter+'s *association* attribute, and fulfills roughly the same
+  # purpose; allow +attribute+ and +label+ to refer to attributes on the joined
+  # model (only applicable if +collection+ is an ActiveRecord model).
+  def filter_values_for(collection, attribute, label: nil, association: nil)
+    # TODO Unscoped/base scope/total item count.
+
+    if (collection <= ActiveRecord::Base rescue nil)
+      # Resolve and validate the main +attribute+ to fetch the values of
+      attribute, model = ScopeHelpers.resolve_model_attribute(attribute, collection, association)
+
+      # And +label+, if provided
+      if label
+        label, model = ScopeHelpers.resolve_model_attribute(label, model, association)
+      else
+        label = attribute
+      end
+
+      # NOTE: The 'AS' specifier bypasses Rails' uniq on the column names, which
+      # would remove the label column if label happens to have the same value
+      # as attribute.
+      label_alias = model.connection.quote_column_name('label')
+
+      model
+        .where("#{attribute} IS NOT NULL")
+        .order(attribute, label)
+        .group(attribute, label)
+        .raw_rows(attribute, "#{label} AS #{label_alias}", "COUNT(#{attribute})")
+        .reject { |r| r.first.blank? }
+        .map    { |v, l, c| { :value => v, :label => l, :indicator => c } }
+
+    else
+      # Make sure +attribute+ and +label+ can be accessed in
+      # +collection+'s items.
+      attr_get = ScopeHelpers.generate_getter(collection.first, attribute)
+      raise "no way to get '#{attribute}' out of collection items" unless attr_get
+
+      if label == attribute
+        lbl_get = attr_get
+      else
+        lbl_get = ScopeHelpers.generate_getter(collection.first, label || attribute)
+        raise "no way to get '#{label}' out of collection items" unless lbl_get
+      end
+
+      collection
+        .map     { |i| [attr_get.(i), lbl_get.(i)].freeze }
+        .reject  { |v, l| v.blank? }
+        .sort_by { |v, l| v }
+        .inject(Hash.new(0)) { |h, i| h[i] += 1; h }
+        .map { |(v, l), c| { :value => v, :label => l, :indicator => c } }
+    end
+  end
+
+  # Utility/internal methods
+
+  # Compress +scope+, which is expected to be a hash representation of a Scope,
+  # into a string intended to be embedded in a URL. The +decompress_scope+
+  # method can be used to convert the string back into a hash representation.
+  # Note that if +scope+ is a string, it will be returned unchanged (to allow
+  # trying to compress an already compressed scope).
+  # Returns the compressed string.
+  def self.compress_scope(scope)
+    return scope if scope.is_a?(String)
+
+    scope = scope.to_yaml
+    scope = ActiveSupport::Gzip.compress(scope)
+    scope = Base64.encode64(scope)
+    scope
+      .tr('+/', '-_')
+      .sub(/=*$/, '')
+      .gsub(/\s/, '')
+  end
+
+  # Decompress +scope+, which is expected to be a scope string compressed by
+  # +compress_scope+, into the original hash representation that was passed to
+  # +compress_scope+ when compressing.
+  # Note that if +scope+ is a hash, it will be returned unchanged (to allow
+  # trying to decompress an already decompressed scope).
+  # Returns the scope's hash representation.
+  def self.decompress_scope(scope)
+    return scope if scope.is_a?(Hash)
+
+    scope.tr!('-_', '+/')
+    scope = Base64.decode64(scope)
+    scope = ActiveSupport::Gzip.decompress(scope)
+    scope = YAML.load(scope)
+    scope
+  end
+
+  # Generate URL parameters suitable for +url_for+ to update the session scope
+  # named +scope+'s items (ordering or filtering rules). This method is the
+  # internal implementation of +filter_url_params+ (and +order_url_params+).
+  # - +operation+ corresponds exactly to +filter_url_params+'s +operation+
+  # parameter.
+  # - +scope+ corresponds to +filter_url_params+'s +scope+ parameter, minus
+  # the default value.
+  # - +attr+ is expected to be either :filters, to update scope filtering rules,
+  # or :order, for ordering rules. It corresponds to the Scope attribute name
+  # to apply +changes+ on.
+  # - +changes+ corresponds to +filter_url_params+'s +changes+ parameter, and
+  # is expected to be an array of compact hash representations of filters
+  # (Scope::Filter) or ordering rules (Scope::Order).
+  #
+  # Note that unlike most other utility methods, this method is exclusively
+  # intended to be used only to implement +filter_url_params+ and
+  # +order_url_params+ and is most likely unsuitable for anything else.
+  def self.scope_items_url_params(scope, operation, attr, changes) #:nodoc:
+    return if changes.blank? && operation != :clear
+
+    key  = (attr == :filters ? :f : :o)
+    hash = (
+      case operation
+      when :set
+        replaced  = changes.map { |c| c[:a] }
+        changes  += scope_from_session(scope)
+          .send(attr)
+          .reject { |c| replaced.include?(f.attribute) }
+        { key => changes }
+      when :clear
+        { key => [] }
+      else
+        { key => changes }
+      end
+    )
+
+    mode = (
+      case operation
+      when :add    then :append
+      when :remove then :delete
+      else :replace
+      end
+    )
+
+    {
+      '_scope_mode' => mode,
+      '_scopes' => {
+        scope => ScopeHelpers.compress_scope(hash)
+      }
+    }
+  end
+
+  # Generate a getter function (lambda) to directly get the value of +attribute+
+  # inside +item+. This method is mainly intended for when +item+ is a sample
+  # of a large collection and a way to quickly get the value corresponding to
+  # +attribute+ of each item in the collection is required (for example in
+  # +Scope+::+Filter+ and +Scope+::+Order+'s +apply+ methods).
+  # Returns a getter lambda, or nil if no way has been found to fetch
+  # +attribute+ from +item+.
+  def self.generate_getter(item, attribute)
+    # item responds directly to attribute
+    return lambda { |item| item.send(attribute) } if
+      item.respond_to?(attribute.to_s)
+
+    # item is hash-like, and attribute is a key
+    if item.is_a?(Hash)
+      return lambda { |item| item[attribute] } if
+        item.has_key?(attribute)
+
+      string = attribute.to_s
+      return lambda { |item| item[string] } if
+        item.has_key?(string)
+
+      symbol = string.to_sym
+      return lambda { |item| item[symbol] } if
+        item.has_key?(symbol)
+    end
+
+    # item is array-like, and attribute is an index
+    if item.is_a?(Array)
+      index = Integer(attribute) rescue nil
+      return lambda { |item| item[index] } if
+        index && item.length > index
+    end
+
+    # item is not a hash, but still seems to accept keys
+    return lambda { |item| item[attribute] } if
+      item.respond_to?(:[])
+
+    # No idea how to access attribute
+    return nil
+  end
+
+  # Generate a cast/conversion function (lambda), to try and convert a value
+  # of +from+'s type to a value of +to+'s type, for comparison purposes. This
+  # method, just like +generate_getter+, is mainly intended for when +from+
+  # is a sample of a large collection and a way to quickly convert to the
+  # collection's type is required (for example in +Scope+::+Filter+'s +apply+
+  # method).
+  # Note that +from+ and +to+ are expected to be scalars (number, bool, string,
+  # symbol, etc.), not compound values (array, hash, object, set, etc.).
+  # Returns a cast/conversion lambda, or nil if its not possible to convert
+  # +from+ to +to+.
+  def self.generate_cast(from, to)
+    # Same type already? Nil? Nothing to do.
+    return lambda { |v| v } if from.is_a?(to.class) || from.nil? || to.nil?
+
+    case to
+    # to_s (and to_sym) for String-like types
+    when String     then lambda { |v| v.to_s        }
+    when Symbol     then lambda { |v| v.to_s.to_sym }
+
+    # Straight conversions for numeric types
+    when Integer    then lambda { |v| Integer(v) }
+    when Float      then lambda { |v| Float(v)   }
+    when Numeric    then lambda { |v| v.to_f     }
+
+    # Match against known true/false representations for boolean types
+    when TrueClass  then lambda { |v| v.to_s =~ /^(true|t|yes|y|on|1)$/i  }
+    when FalseClass then lambda { |v| v.to_s =~ /^(false|f|no|n|off|0)$/i }
+
+    else nil
+    end
+  end
+
+  # Parse an association (+assoc+) coming from a hash in the context of
+  # a +from_hash+ method. The association is expected to be in the same
+  # format as +Scope+::+Filter+'s *association* attribute: either the
+  # ActiveRecord model itself, a table name, or an array with the model and two
+  # attributes name to perform the association join with
+  # (see +Scope+::+Filter+'s *association* attribute and +from_hash+ method for
+  # more information).
+  def self.parse_assoc(assoc)
+    assoc, assoc_attr, model_attr = assoc
+    return nil if assoc.blank?
+
+    # Convert a table name into an ActiveRecord model class
+    unless (assoc <= ActiveRecord::Base rescue nil)
+      table = assoc.to_s.tableize
+      assoc = ActiveRecord::Base.descendants.find do |m|
+        assoc == m.name || table == m.table_name
+      end
+    end
+
+    # Clean out join attribute names
+    assoc_attr = assoc_attr.to_s.gsub(/[^\w]/, '')
+    model_attr = model_attr.to_s.gsub(/[^\w]/, '')
+
+    return assoc if assoc_attr.blank? || model_attr.blank?
+    [ assoc, assoc_attr, model_attr ]
+  end
+
+  # Create a new association identical to +assoc+ (same format as
+  # +parse_assoc+) but using a table name (as a string) instead of an
+  # ActiveRecord model class.
+  def self.assoc_with_table(assoc)
+    return assoc.table_name if (assoc <= ActiveRecord::Base rescue nil)
+    return assoc unless assoc.is_a?(Enumerable)
+
+    assoc, assoc_attr, model_attr = assoc
+    [ assoc.table_name, assoc_attr, model_attr ]
+  end
+
+  # Join an association (+assoc+) to a +model+, validating all column and
+  # table names. +model+ is expected to be an ActiveRecord model and
+  # +assoc+ is expected to be a model or array in the same format as
+  # +parse_assoc+'s +assoc+ parameter or +Scope+::+Filter+'s *association*
+  # attribute (see +Scope+::+Filter+'s *association* attribute and +from_hash+
+  # method for more information).
+  #
+  # Returns an array containing +model+ joined to +assoc+ and +assoc+'s model
+  # class.
+  def self.join_assoc(model, assoc)
+    # Re-parse the association to ensure its validity
+    assoc, assoc_attr, model_attr = self.parse_assoc(assoc)
+    return [ model, nil ] unless assoc
+
+    # No join columns? Just use a natural join.
+    return [ model.joins(assoc.table_name.to_sym), assoc ] if
+      assoc_attr.blank? || model_attr.blank?
+
+    # Joins columns are specified? Validate them first before joining.
+    raise "unknown association column #{assoc_attr}" unless
+      assoc.attribute_names.include?(assoc_attr)
+
+    raise "unknown model column #{model_attr}" unless
+      model.attribute_names.include?(model_attr)
+
+    # Quote attributes and tables to avoid any nasty surprises
+    assoc_attr  = assoc.connection.quote_column_name(assoc_attr)
+    assoc_table = assoc.quoted_table_name
+    model_attr  = model.connection.quote_column_name(model_attr)
+    model_table = model.quoted_table_name
+
+    return [ model.joins(
+      "INNER JOIN #{assoc_table} ON " \
+      "(#{assoc_table}.#{assoc_attr} = #{model_table}.#{model_attr})"
+    ), assoc ]
+  end
+
+  # Resolve +attribute+ as an attribute of +model+ joined by +association+
+  # (if supplied). In order, +resolve_model_attribute+ joins +association+
+  # to +model+ (if +association+ is valid) then validates that +attribute+
+  # is effectively an attribute of +model+ or +association+, throwing an
+  # exception otherwise.
+  # This internal method is intended as a safe and generic way to fetch
+  # +attribute+ from +model+ (and +association+).
+  # Returns a pair; the fully qualified and quoted attribute name (quoted
+  # table + column name) and +model+.
+  def self.resolve_model_attribute(attribute, model, association)
+    columns = { model.table_name => model.attribute_names }
+
+    # Join up the association's model, if required
+    model, assoc = self.join_assoc(model, association)
+    columns[assoc.table_name] = assoc.attribute_names if assoc
+
+    # Make sure @attribute is a valid column name, or a valid column and
+    # table name.
+    column, table = attribute.to_s.split('.').reverse
+    table ||= model.table_name
+
+    raise "unknown table #{table}" unless
+      columns[table]
+    raise "unknown column #{table}.#{column}" unless
+      columns[table].include?(column)
+
+    # Quote both the table name and column name to avoid issues with
+    # special characters (spaces, for example).
+    column = model.connection.quote_column_name(column)
+    table  = model.connection.quote_table_name(table)
+
+    [ "#{table}.#{column}", model ]
+  end
+
+end
diff --git a/BrainPortal/spec/modules/scope_helpers_spec.rb b/BrainPortal/spec/modules/scope_helpers_spec.rb
new file mode 100644
index 000000000..21483fe5f
--- /dev/null
+++ b/BrainPortal/spec/modules/scope_helpers_spec.rb
@@ -0,0 +1,622 @@
+
+#
+# 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 <http://www.gnu.org/licenses/>.
+#
+
+require 'rails_helper'
+
+describe ScopeHelpers do
+  # TODO
+end
+
+module ScopeHelpers
+  describe Scope do
+    # TODO
+  end
+
+  describe Scope::Filter do
+    let(:filter) { Scope::Filter.from_hash({ :attribute => :full_name, :value => 'A' }) }
+
+    wacky_string = lambda do
+      (1..0x1000)
+        .to_a
+        .shuffle
+        .map { |v| v.chr.encode('utf-8') rescue nil }
+        .compact
+        .join
+    end
+
+    it "should be created blank" do
+      blank = Scope::Filter.new
+      [ :attribute, :value, :operator, :association ].each do |attr|
+        expect(blank.send(attr)).to be_nil
+      end
+    end
+
+    it "should have no type name" do
+      expect(Scope::Filter.type_name).to be_nil
+    end
+
+    it "shouldn't be valid if blank" do
+      expect(Scope::Filter.new.valid?).to be_falsey
+    end
+
+    context "when filtering a model" do
+      let!(:a) { create(:normal_user, :full_name => 'A') }
+      let!(:b) { create(:normal_user, :full_name => 'B') }
+      let!(:c) { create(:normal_user, :full_name => 'B') }
+      let!(:d) { create(:normal_user, :full_name => 'C') }
+
+      before do
+        @expect_each = lambda do |op, tests|
+          filter.operator = op
+          tests.map do |value, expected|
+            filter.value = value
+            expect(filter.apply(NormalUser).to_a).to match_array(expected)
+          end
+        end
+      end
+
+      it "should throw an exception if the filter has no operator" do
+        filter.operator = nil
+        expect { filter.apply(NormalUser) }.to raise_error
+      end
+
+      it "should throw an exception if the filter has no attribute" do
+        filter.attribute = nil
+        expect { filter.apply(NormalUser) }.to raise_error
+      end
+
+      it "should validate the attribute name" do
+        filter.attribute = wacky_string.()
+        expect { filter.apply(NormalUser) }.to raise_error(RuntimeError, /(attribute|column|table)/)
+      end
+
+      it "should support standard operators" do
+        filter.value = b.full_name
+
+        ({
+          :== => [b, c],
+          :!= => [a, d],
+          :>  => [d],
+          :>= => [b, c, d],
+          :<  => [a],
+          :<= => [a, b, c]
+        }).each do |op, result|
+          filter.operator = op
+          expect(filter.apply(NormalUser).to_a).to match_array(result)
+        end
+      end
+
+      it "should support set inclusion/exclusion" do
+        @expect_each.(:in, {
+          []              => [],
+          ['A']           => [a],
+          ['A', 'B', 'K'] => [a, b, c],
+          ['K', 'L', 'M'] => [],
+        })
+
+        @expect_each.(:out, {
+          []              => [a, b, c, d],
+          ['A']           => [b, c, d],
+          ['A', 'B', 'K'] => [d],
+          ['K', 'L', 'M'] => [a, b, c, d],
+        })
+      end
+
+      it "should support string matching" do
+        @expect_each.(:match, {
+          'a' => [a],
+          'k' => [],
+          wacky_string.() => []
+        })
+      end
+
+      it "should support range matching" do
+        @expect_each.(:range, {
+          ['A', 'B'] => [a, b, c],
+          ['B', 'C'] => [b, c, d],
+          ['C', 'A'] => [a, b, c, d],
+          ['C', 'K'] => [d],
+          ['K', 'Z'] => []
+        })
+      end
+
+      context "when using an association" do
+        it "should support associations"
+        it "should allow filtering on association attributes"
+        it "should allow join columns"
+        it "should validate join columns"
+      end
+
+      it "should handle nil values" do
+        filter.value     = nil
+        filter.attribute = :id
+
+        filter.operator  = :==
+        expect(filter.apply(NormalUser).to_a).to match_array([])
+
+        filter.operator  = :!=
+        expect(filter.apply(NormalUser).to_a).to match_array([a, b, c, d])
+      end
+    end
+
+    context "when filtering a collection" do
+      let!(:a) { create(:normal_user, :full_name => 'A') }
+      let!(:b) { create(:normal_user, :full_name => 'B') }
+      let!(:c) { create(:normal_user, :full_name => 'B') }
+      let!(:d) { create(:normal_user, :full_name => 'C') }
+      let!(:collection) { [a, b, c, d] }
+
+      before do
+        @expect_each = lambda do |op, tests|
+          filter.operator = op
+          tests.map do |value, expected|
+            filter.value = value
+            expect(filter.apply(collection)).to match_array(expected)
+          end
+        end
+      end
+
+      it "should throw an exception if the filter has no operator" do
+        filter.operator = nil
+        expect { filter.apply(collection) }.to raise_error
+      end
+
+      it "should throw an exception if the filter has no attribute" do
+        filter.attribute = nil
+        expect { filter.apply(collection) }.to raise_error
+      end
+
+      it "should support hash collections (list of hashes)" do
+        hashes = collection.map { |i| { :full_name => i.full_name } }
+        expect(filter.apply(hashes)).to match_array([{ :full_name => 'A' }])
+      end
+
+      it "should support array collections (list of arrays)" do
+        filter.attribute = 0
+        arrays = collection.map { |i| [i.full_name] }
+        expect(filter.apply(arrays)).to match_array([[ 'A' ]])
+      end
+
+      it "should convert mismatched value types" do
+        filter.value = :A
+        expect(filter.apply(collection)).to match_array([a])
+      end
+
+      it "should support standard operators" do
+        filter.value = b.full_name
+
+        ({
+          :== => [b, c],
+          :!= => [a, d],
+          :>  => [d],
+          :>= => [b, c, d],
+          :<  => [a],
+          :<= => [a, b, c]
+        }).each do |op, result|
+          filter.operator = op
+          expect(filter.apply(collection).to_a).to match_array(result)
+        end
+      end
+
+      it "should support set inclusion/exclusion" do
+        @expect_each.(:in, {
+          []              => [],
+          ['A']           => [a],
+          ['A', 'B', 'K'] => [a, b, c],
+          ['K', 'L', 'M'] => [],
+        })
+
+        @expect_each.(:out, {
+          []              => [a, b, c, d],
+          ['A']           => [b, c, d],
+          ['A', 'B', 'K'] => [d],
+          ['K', 'L', 'M'] => [a, b, c, d],
+        })
+      end
+
+      it "should support string matching" do
+        @expect_each.(:match, {
+          'a' => [a],
+          'k' => [],
+          wacky_string.() => []
+        })
+      end
+
+      it "should support range matching" do
+        @expect_each.(:range, {
+          ['A', 'B'] => [a, b, c],
+          ['B', 'C'] => [b, c, d],
+          ['C', 'A'] => [a, b, c, d],
+          ['C', 'K'] => [d],
+          ['K', 'Z'] => []
+        })
+      end
+    end
+
+    context "when creating from a hash" do
+      it "should be blank from a blank hash" do
+        blank = Scope::Filter.from_hash({})
+        [ :attribute, :value, :association ].each do |attr|
+          expect(blank.send(attr)).to be_nil
+        end
+      end
+
+      it "should accept attribute hash keys" do
+        filter = Scope::Filter.from_hash({
+          :attribute   => 'a',
+          :value       => 'v',
+          :operator    => 'm',
+        })
+
+        expect(filter.attribute).to eq('a')
+        expect(filter.value).to     eq('v')
+        expect(filter.operator).to  eq(:match)
+      end
+
+      it "should accept short attribute hash keys" do
+        filter = Scope::Filter.from_hash({
+          :a => 'a',
+          :v => 'v',
+          :o => 'match',
+        })
+
+        expect(filter.attribute).to eq('a')
+        expect(filter.value).to     eq('v')
+        expect(filter.operator).to  eq(:match)
+      end
+
+      it "should delegate to a subclass if :type is given" do
+        subclass = Class.new(Scope::Filter) do
+          def self.type_name
+            'test'
+          end
+        end
+
+        expect((Scope::Filter.from_hash({
+          :type => 'test'
+        })).class).to eq(subclass)
+      end
+
+      it "should validate :operator against the supported operators" do
+        expect((Scope::Filter.from_hash({
+          :attribute   => 'a',
+          :value       => 'v',
+          :operator    => 'z',
+          :association => 'NormalUser'
+        })).operator).to be_nil
+      end
+
+      it "should allow short operators" do
+        Scope::Filter.from_hash({
+          :a => 'a',
+          :v => 'v',
+          :o => 'match',
+          :j => 'NormalUser'
+        })
+      end
+
+      it "should make :value match the operator" do
+        expect((Scope::Filter.from_hash({
+          :attribute => 'a',
+          :value     => 'v',
+          :operator  => 'in',
+        })).value).to eq(['v'])
+
+        expect(Scope::Filter.from_hash({
+          :attribute => 'a',
+          :value     => 'v',
+          :operator  => 'range',
+        }).value).to be_nil
+
+        expect((Scope::Filter.from_hash({
+          :attribute => 'a',
+          :value     => ['v'],
+          :operator  => '==',
+        })).value).to eq('v')
+      end
+
+      it "should resolve :association if provided" do
+        expect((Scope::Filter.from_hash({
+          :attribute   => 'a',
+          :value       => ['v'],
+          :operator    => '==',
+          :association => 'NormalUser'
+        })).association).to eq(NormalUser)
+
+        expect((Scope::Filter.from_hash({
+          :attribute   => 'a',
+          :value       => ['v'],
+          :operator    => '==',
+          :association => 'users'
+        })).association).to eq(User)
+
+        expect((Scope::Filter.from_hash({
+          :attribute   => 'a',
+          :value       => ['v'],
+          :operator    => '==',
+          :association => ['users', 'id', 'user_id']
+        })).association).to eq([User, 'id', 'user_id'])
+      end
+    end
+
+    context "when converting to hash" do
+      it "should export all attributes" do
+        expect(filter.to_hash).to eq({
+          :attribute   => 'full_name',
+          :value       => 'A',
+          :operator    => :==,
+          :association => nil
+        })
+      end
+
+      context "in compact mode" do
+        it "should export only set attributes" do
+          expect(filter.to_hash(compact: true)).to eq({
+            :a => 'full_name',
+            :v => 'A'
+          })
+        end
+
+        it "should shrink attribute keys" do
+          expect(filter.to_hash(compact: true)).to eq({
+            :a => 'full_name',
+            :v => 'A'
+          })
+        end
+
+        it "should shrink long operators" do
+          filter.operator = :match
+          expect(filter.to_hash(compact: true)).to eq({
+            :a => 'full_name',
+            :v => 'A',
+            :o => :m
+          })
+        end
+
+        it "should remove default values" do
+          expect(filter.to_hash(compact: true)).to eq({
+            :a => 'full_name',
+            :v => 'A'
+          })
+        end
+      end
+    end
+  end
+
+  describe Scope::Order do
+    let(:order) { Scope::Order.from_hash({ :attribute => :full_name }) }
+
+    wacky_string = lambda do
+      (1..0x1000)
+        .to_a
+        .shuffle
+        .map { |v| v.chr.encode('utf-8') rescue nil }
+        .compact
+        .join
+    end
+
+    it "should be created blank" do
+      blank = Scope::Order.new
+      [ :attribute, :direction, :association ].each do |attr|
+        expect(blank.send(attr)).to be_nil
+      end
+    end
+
+    it "should have no type name" do
+      expect(Scope::Order.type_name).to be_nil
+    end
+
+    it "shouldn't be valid if blank" do
+      expect(Scope::Order.new.valid?).to be_falsey
+    end
+
+    context "when ordering a model" do
+      let!(:a) { create(:normal_user, :full_name => 'A') }
+      let!(:b) { create(:normal_user, :full_name => 'C') }
+      let!(:c) { create(:normal_user, :full_name => 'B') }
+      let!(:d) { create(:normal_user, :full_name => 'D') }
+
+      it "should throw an exception if the ordering rule has no direction" do
+        order.direction = nil
+        expect { order.apply(NormalUser) }.to raise_error
+      end
+
+      it "should throw an exception if the ordering rule has no attribute" do
+        order.attribute = nil
+        expect { order.apply(NormalUser) }.to raise_error
+      end
+
+      it "should validate the attribute name" do
+        order.attribute = wacky_string.()
+        expect { order.apply(NormalUser) }.to raise_error(RuntimeError, /(attribute|column|table)/)
+      end
+
+      it "should support sorting/ordering in ascending order" do
+        order.direction = :asc
+        expect(order.apply(NormalUser)).to eq([a, c, b, d])
+      end
+
+      it "should support sorting/ordering in descending order" do
+        order.direction = :desc
+        expect(order.apply(NormalUser)).to eq([d, b, c, a])
+      end
+
+      context "when using an association" do
+        it "should support associations"
+        it "should allow filtering on association attributes"
+        it "should allow join columns"
+        it "should validate join columns"
+      end
+    end
+
+    context "when ordering a collection" do
+      let!(:a) { create(:normal_user, :full_name => 'A') }
+      let!(:b) { create(:normal_user, :full_name => 'C') }
+      let!(:c) { create(:normal_user, :full_name => 'B') }
+      let!(:d) { create(:normal_user, :full_name => 'D') }
+      let!(:collection) { [a, b, c, d] }
+
+      it "should throw an exception if the ordering rule has no direction" do
+        order.direction = nil
+        expect { order.apply(collection) }.to raise_error
+      end
+
+      it "should throw an exception if the ordering rule has no attribute" do
+        order.attribute = nil
+        expect { order.apply(collection) }.to raise_error
+      end
+
+      it "should support hash collections (list of hashes)" do
+        hashes = collection.map { |i| { :full_name => i.full_name } }
+        expect(order.apply(hashes)).to eq([
+          { :full_name => 'A' },
+          { :full_name => 'B' },
+          { :full_name => 'C' },
+          { :full_name => 'D' }
+        ])
+      end
+
+      it "should support array collections (list of arrays)" do
+        order.attribute = 0
+        arrays = collection.map { |i| [i.full_name] }
+        expect(order.apply(arrays)).to eq([
+          [ 'A' ],
+          [ 'B' ],
+          [ 'C' ],
+          [ 'D' ]
+        ])
+      end
+
+      it "should support sorting/ordering in ascending order" do
+        order.direction = :asc
+        expect(order.apply(collection)).to eq([a, c, b, d])
+      end
+
+      it "should support sorting/ordering in descending order" do
+        order.direction = :desc
+        expect(order.apply(collection)).to eq([d, b, c, a])
+      end
+    end
+
+    context "when creating from a hash" do
+      it "should be blank from a blank hash" do
+        blank = Scope::Order.from_hash({})
+        [ :attribute, :association ].each do |attr|
+          expect(blank.send(attr)).to be_nil
+        end
+      end
+
+      it "should accept attribute hash keys" do
+        order = Scope::Order.from_hash({
+          :attribute => 'a',
+          :direction => 'asc'
+        })
+
+        expect(order.attribute).to eq('a')
+        expect(order.direction).to eq(:asc)
+      end
+
+      it "should accept short attribute hash keys" do
+        order = Scope::Order.from_hash({
+          :a => 'a',
+          :d => 'asc'
+        })
+
+        expect(order.attribute).to eq('a')
+        expect(order.direction).to eq(:asc)
+      end
+
+      it "should delegate to a subclass if :type is given" do
+        subclass = Class.new(Scope::Order) do
+          def self.type_name
+            'test'
+          end
+        end
+
+        expect((Scope::Order.from_hash({
+          :type => 'test'
+        })).class).to eq(subclass)
+      end
+
+      it "should only accept :asc and :desc as directions" do
+        expect((Scope::Order.from_hash({
+          :attribute   => 'a',
+          :direction   => 'z',
+          :association => 'NormalUser'
+        })).direction).to be_nil
+      end
+
+      it "should resolve :association if provided" do
+        expect((Scope::Order.from_hash({
+          :attribute   => 'a',
+          :association => 'NormalUser'
+        })).association).to eq(NormalUser)
+
+        expect((Scope::Order.from_hash({
+          :attribute   => 'a',
+          :association => 'users'
+        })).association).to eq(User)
+
+        expect((Scope::Order.from_hash({
+          :attribute   => 'a',
+          :association => ['users', 'id', 'user_id']
+        })).association).to eq([User, 'id', 'user_id'])
+      end
+    end
+
+    context "when converting to hash" do
+      it "should export all attributes" do
+        expect(order.to_hash).to eq({
+          :attribute   => 'full_name',
+          :direction   => :asc,
+          :association => nil
+        })
+      end
+
+      context "in compact mode" do
+        it "should export only set attributes" do
+          expect(order.to_hash(compact: true)).to eq({
+            :a => 'full_name'
+          })
+        end
+
+        it "should shrink attribute keys" do
+          expect(order.to_hash(compact: true)).to eq({
+            :a => 'full_name'
+          })
+        end
+
+        it "should remove default values" do
+          expect(order.to_hash(compact: true)).to eq({
+            :a => 'full_name'
+          })
+        end
+      end
+    end
+  end
+
+  describe Scope::Pagination do
+    # TODO
+  end
+
+  # TODO ...
+end

From 100c507981bd5cc22bd9b22da89c2e5267828c6b Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Thu, 20 Aug 2015 14:51:58 -0400
Subject: [PATCH 17/85] Safe YAML deserialization, string hash keys for Scopes

This changeset switches to YAML.load_safe instead of YAML.load to
avoid security issues. Using strings as keys (required as safe_load
won't load Symbols) is slower, but avoids GC issues with symbols on
Ruby < 2.2.0 and makes from_hash methods more robust.
---
 BrainPortal/lib/scope_helpers.rb              | 368 +++++++++---------
 .../spec/modules/scope_helpers_spec.rb        |  46 +--
 2 files changed, 208 insertions(+), 206 deletions(-)

diff --git a/BrainPortal/lib/scope_helpers.rb b/BrainPortal/lib/scope_helpers.rb
index 25c71fd8d..56dc710a5 100644
--- a/BrainPortal/lib/scope_helpers.rb
+++ b/BrainPortal/lib/scope_helpers.rb
@@ -49,8 +49,8 @@
 # Currently active/known scopes are stored in Rails' session as a hash with
 # scope names for keys and scope hash definitions/representations as values:
 #   current_session[:scopes] == {
-#     'userfiles' => { :f => [ ... ], :o => ... },
-#     'tasks'     => { :f => [ ... ], :o => ... },
+#     'userfiles' => { 'f' => [ ... ], 'o' => ... },
+#     'tasks'     => { 'f' => [ ... ], 'o' => ... },
 #     ...
 #   }
 # To directly add or replace one of the session scopes, convert the scope to a
@@ -78,9 +78,9 @@ def self.included(includer) #:nodoc:
     includer.class_eval do
       helper_method(
         :filter_values_for,
-        :scope_url_params,
-        :filter_url_params,
-        :order_url_params
+        :scope_params,
+        :scope_filter_params,
+        :scope_order_params
       )
 
       before_filter :update_session_scopes
@@ -101,12 +101,12 @@ class Scope
     # matter in which order they are applied.
     attr_accessor :filters
 
-    # Set operation to combine the filter result sets with. Either +:and+ or
-    # +:intersection+ for intersection (each item in the final result set must
-    # match all filters) or +:or+ or +:union+ for union (each item in the final
+    # Set operation to combine the filter result sets with. Either +and+ or
+    # +intersection+ for intersection (each item in the final result set must
+    # match all filters) or +or+ or +union+ for union (each item in the final
     # result set must match at least one filter).
     #
-    # TODO: Not implemented yet, as +:or+/+:union+ is not implemented for
+    # TODO: Not implemented yet, as +or+/+union+ is not implemented for
     # ActiveRecord models (the query interface does not support them cleanly
     # as of Rails 3) and slow/awkward for regular Ruby collections.
     attr_accessor :filter_combination
@@ -160,8 +160,8 @@ def initialize
     # Create a deep copy of the Scope +other+, down to each Filter in *filters*
     # and each Order in *order*. This method allows +dup+ and +clone+ (which
     # invoke it) to create independent copies which can then be used by
-    # +scope_url_params+ and +url_for+ to create URLs changing arbitrary Scope
-    # elements (see +scope_url_params+).
+    # +scope_params+ and +url_for+ to create URLs changing arbitrary Scope
+    # elements (see +scope_params+).
     def initialize_copy(other)
       hash_dup = lambda { |obj| obj.class.from_hash(obj.to_hash) }
 
@@ -201,7 +201,7 @@ def apply(collection)
 
     # Create a new Scope described by the contents of +hash+. Each recognized
     # pair in +hash+ corresponds to a Scope attribute and is expected to
-    # match the format of the attribute (e.g. +:filters+ should be an Enumerable
+    # match the format of the attribute (e.g. +filters+ should be an Enumerable
     # of filters).
     #
     # For attributes containing objects (*filters*, *order*, *pagination*, etc.)
@@ -221,25 +221,25 @@ def apply(collection)
     #
     # The following keys are recognized in +hash+:
     #
-    # [:filters or :f]
+    # [+filters+ or +f+]
     #  *filters* attribute: an array (or Enumerable) of Scope::Filter instances.
     #
-    # [:order or :o]
+    # [+order+ or +o+]
     #  *order* attribute: an array (or Enumerable) of Scope::Order instances.
     #
-    # [:pagination or :p]
+    # [+pagination+ or +p+]
     #  *pagination* attribute: a Scope::Pagination instance.
     #
-    # [:selection or :s]
+    # [+selection+ or +s+]
     #  *selection* attribute: an array of selected IDs or keys inside the
     #  collection.
     #
-    # [:custom or :c]
+    # [+custom+ or +c+]
     #  *custom* attribute: an arbitrary Ruby hash of custom view options.
     #
-    # [:filter_combination or :fc]
-    #  *filter_combination* attribute: either +:and+/+:intersection+ or
-    #  +:or+/+:union+ (defaults to +:and+).
+    # [+filter_combination+ or +fc+]
+    #  *filter_combination* attribute: either +and+/+intersection+ or
+    #  +or+/+union+ (defaults to +and+).
     #
     # Any missing key will lead to a nil attribute and be handled appriately;
     # arrays will default to empty and absent components will be ignored.
@@ -255,19 +255,19 @@ def self.from_hash(hash)
       scope = self.new
 
       # Filtering and ordering rules
-      scope.filters = (hash[:filters] || hash[:f] || [])
+      scope.filters = (hash['filters'] || hash['f'] || [])
         .map { |filter| Filter.from_hash(filter) }
         .compact
 
-      scope.order = (hash[:order] || hash[:o] || [])
+      scope.order = (hash['order'] || hash['o'] || [])
         .map { |order| Order.from_hash(order) }
         .compact
 
       # Pagination, selection and other properties
-      scope.pagination = Pagination.from_hash(hash[:pagination] || hash[:p])
-      scope.selection  =  hash[:selection] || hash[:s] || []
-      scope.custom     = (hash[:custom]    || hash[:c] || {}).with_indifferent_access
-      scope.filter_combination = hash[:filter_combination] || hash[:fc] || :and
+      scope.pagination = Pagination.from_hash(hash['pagination'] || hash['p'])
+      scope.selection  =  hash['selection'] || hash['s'] || []
+      scope.custom     = (hash['custom']    || hash['c'] || {}).with_indifferent_access
+      scope.filter_combination = (hash['filter_combination'] || hash['fc'] || 'and').to_s
 
       scope
     end
@@ -280,12 +280,12 @@ def self.from_hash(hash)
     # +compact_hash+).
     def to_hash(compact: false)
       hash = {
-        :filters    => @filters.map(&:to_hash),
-        :order      => @order.map(&:to_hash),
-        :pagination => @pagination.try(:to_hash),
-        :selection  => @selection,
-        :custom     => @custom.symbolize_keys,
-        :filter_combination => @filter_combination,
+        'filters'    => @filters.map(&:to_hash),
+        'order'      => @order.map(&:to_hash),
+        'pagination' => @pagination.try(:to_hash),
+        'selection'  => @selection,
+        'custom'     => @custom.stringify_keys,
+        'filter_combination' => @filter_combination.to_s,
       }
 
       compact ? self.class.compact_hash(hash) : hash
@@ -304,27 +304,27 @@ def self.compact_hash(hash)
 
       compact = {
         # Compact filtering rules
-        :f => (hash[:filters] || hash[:f] || [])
+        'f' => (hash['filters'] || hash['f'] || [])
           .map { |filter| Filter.compact_hash(filter) }
           .reject(&:blank?),
 
         # Compact ordering rules
-        :o => (hash[:order] || hash[:o] || [])
+        'o' => (hash['order'] || hash['o'] || [])
           .map { |order| Order.compact_hash(order) }
           .reject(&:blank?),
 
         # Compact the pagination component
-        :p => Pagination.compact_hash(hash[:pagination] || hash[:p]),
+        'p' => Pagination.compact_hash(hash['pagination'] || hash['p']),
 
         # Include other attributes
-        :s  => hash[:s]  || hash[:selection],
-        :c  => hash[:c]  || hash[:custom],
-        :fc => hash[:fc] || hash[:filter_combination],
+        's'  => hash['s']  || hash['selection'],
+        'c'  => hash['c']  || hash['custom'],
+        'fc' => (hash['fc'] || hash['filter_combination']).to_s,
       }
 
       # Delete empty/default values
       compact.delete_if { |key, value| value.blank? }
-      compact.delete(:fc) if compact[:fc].to_s == 'and'
+      compact.delete('fc') if compact['fc'].to_s == 'and'
 
       compact
     end
@@ -360,27 +360,27 @@ class Filter
       # check if the collection/model element passes the filter. The possible
       # operators are:
       #
-      # [:==, :!=, :>, :>=, :<, :<=]
+      # [+==+, +!=+, +>+, +>=+, +<+, +<=+]
       #  Standard comparison operators; a single value in *value* is expected.
       #
-      # [:in, :out]
-      #  Set inclusion (:in) or exclusion (:out); a set (Enumerable) of values
+      # [+in+, +out+]
+      #  Set inclusion (in) or exclusion (out); a set (Enumerable) of values
       #  in *value* is expected.
       #  Behaves like Ruby's include? method and SQL's IN clause.
       #
-      # [:match]
+      # [+match+]
       #  Case insensitive string inclusion; a single string in *value* is
       #  expected.
       #  Behaves like a case-insensitive Ruby include? and SQL's LIKE clause.
-      #  Shortened to just :m in compact Filter hash representations.
+      #  Shortened to just +m+ in compact Filter hash representations.
       #
-      # [:range]
+      # [+range+]
       #  Range match; a pair of values in *value* is expected.
       #  Given a range [a, b] in *value* and x as *attribute*'s value,
       #  corresponds to the predicate a <= x <= b.
-      #  Shortened to just :r in compact Filter hash representations.
+      #  Shortened to just +r+ in compact Filter hash representations.
       #
-      # Defaults to an equality comparison (:==).
+      # Defaults to an equality comparison (+==+).
       attr_accessor :operator
 
       # Optional ActiveRecord model to join on to the filtered model before
@@ -407,7 +407,7 @@ class Filter
       # to determine which Filter subclass to load when creating a Filter
       # instance using +from_hash+.
       # Returns nil in the superclass (Scope::Filter) as a filter hash is
-      # assumed to be a Scope::Filter if no +:type+ key is present
+      # assumed to be a Scope::Filter if no +type+ key is present
       # (see +from_hash+).
       def self.type_name
         nil
@@ -425,7 +425,7 @@ def apply(collection)
         raise "no operator to filter with"      unless @operator
         raise "no attribute to filter on items" unless @attribute
 
-        @value ||= [] if [ :in, :out, :range ].include?(@operator)
+        @value ||= [] if [ 'in', 'out', 'range' ].include?(@operator.to_s)
 
         if (collection <= ActiveRecord::Base rescue nil)
           apply_on_model(collection)
@@ -447,25 +447,25 @@ def valid?
       #
       # The following keys are recognized in +hash+:
       #
-      # [:type or :t]
+      # [+type+ or +t+]
       #  Type (subclass) of Filter of create from +hash+, as a string or symbol.
       #  If present, this key's value is expected to match a subclass'
       #  +type_name+ (or the Ruby class name) and that subclass' +from_hash+
       #  will be invoked on +hash+ to create the filter instead. If the key does
       #  not match any subclass' +type_name+, a blank filter will be created.
       #
-      # [:attribute or :a]
+      # [+attribute+ or +a+]
       #  *attribute* attribute: a symbol or string.
       #
-      # [:value or :v]
+      # [+value+ or +v+]
       #  *value* attribute: a scalar (number, bool, string, symbol, etc.)
       #  value or an array (or Enumerable) of scalar values.
       #
-      # [:operator or :o]
+      # [+operator+ or +o+]
       #  *operator* attribute: one of the possible operators (see the
-      #  *operator* attribute) as a symbol or string (defaults to :==).
+      #  *operator* attribute) as a symbol or string (defaults to ==).
       #
-      # [:association or :j]
+      # [+association+ or +j+]
       #  *association* attribute: an ActiveRecord model or an array with an
       #  ActiveRecord model and the two attributes to perform the join with.
       #  A string or symbol representing the model or DB table can also be
@@ -482,39 +482,39 @@ def self.from_hash(hash)
 
         filter = self.new
 
-        # Handle Filter subclasses (:type key)
-        if type = (hash[:type] || hash[:t])
+        # Handle Filter subclasses (type key)
+        if type = (hash['type'] || hash['t'])
           subclass = self.descendants.find { |sub| sub.type_name == type }
           return subclass ? subclass.from_hash(hash) : filter
         end
 
         # *attribute* must be alphanumeric (word-like)
-        attribute = (hash[:attribute] || hash[:a]).to_s.gsub(/[^\w.]/, '')
+        attribute = (hash['attribute'] || hash['a']).to_s.gsub(/[^\w.]/, '')
         filter.attribute = attribute unless attribute.blank?
 
         # *operator* must be one of the possible predicate operators
-        operator = (hash[:operator] || hash[:o] || :==).to_s.downcase.to_sym
-        operator = :range if operator == :r
-        operator = :match if operator == :m
+        operator = (hash['operator'] || hash['o'] || :==).to_s.downcase
+        operator = 'range' if operator == 'r'
+        operator = 'match' if operator == 'm'
         filter.operator = operator if
-          [ :==, :!=, :>, :>=, :<, :<=, :in, :out, :match, :range ].include?(operator)
+          [ '==', '!=', '>', '>=', '<', '<=', 'in', 'out', 'match', 'range' ].include?(operator)
 
         # *value* must be a simple scalar value or a set of simple values,
         # depending on which *operator* is to be applied
-        value = hash[:value] || hash[:v]
+        value = hash['value'] || hash['v']
         value = (value.is_a?(Enumerable) ? value : [value])
           .map(&:to_s)
           .reject(&:blank?)
 
         filter.value = (
-          case operator
-          when :==, :!=, :>, :>=, :<, :<=
+          case operator.to_s
+          when '==', '!=', '>', '>=', '<', '<='
             value.first
-          when :in, :out
+          when 'in', 'out'
             value unless value.empty?
-          when :match
+          when 'match'
             value.first.to_s
-          when :range
+          when 'range'
             value[0, 2] if value.length == 2
           else
             nil
@@ -523,7 +523,7 @@ def self.from_hash(hash)
 
         # *association* must be an ActiveRecord model or an array with the
         # correct format
-        filter.association = ScopeHelpers.parse_assoc(hash[:association] || hash[:j])
+        filter.association = ScopeHelpers.parse_assoc(hash['association'] || hash['j'])
 
         filter
       end
@@ -538,10 +538,10 @@ def self.from_hash(hash)
       # See Scope's +to_hash+ method for further information.
       def to_hash(compact: false)
         hash = {
-          :attribute   => @attribute,
-          :operator    => @operator,
-          :value       => @value,
-          :association => ScopeHelpers.assoc_with_table(@association)
+          'attribute'   => @attribute.to_s,
+          'operator'    => @operator.to_s,
+          'value'       => @value,
+          'association' => ScopeHelpers.assoc_with_table(@association)
         }
 
         compact ? self.class.compact_hash(hash) : hash
@@ -555,17 +555,17 @@ def self.compact_hash(hash)
         Scope.generic_compact_hash(
           hash,
           {
-            :type        => :t,
-            :attribute   => :a,
-            :operator    => :o,
-            :value       => :v,
-            :association => :j
+            'type'        => 't',
+            'attribute'   => 'a',
+            'operator'    => 'o',
+            'value'       => 'v',
+            'association' => 'j'
           },
           values: [
-            [ :operator, :range, :r ],
-            [ :operator, :match, :m ]
+            [ 'operator', 'range', 'r' ],
+            [ 'operator', 'match', 'm' ]
           ],
-          defaults: { :operator => :== }
+          defaults: { 'operator' => '==' }
         )
       end
 
@@ -579,49 +579,49 @@ def apply_on_model(model) #:nodoc:
         # *association*).
         attribute, model = ScopeHelpers.resolve_model_attribute(@attribute, model, @association)
 
-        case @operator
-        # Standard comparison operators can just be used as-is, bar for :== and
+        case (operator = @operator.to_s)
+        # Standard comparison operators can just be used as-is, bar for == and
         # when NULLs are involved.
-        when :==, :!=, :>, :>=, :<, :<=
-          operator = (
+        when '==', '!=', '>', '>=', '<', '<='
+          sql_operator = (
             # IS/IS NOT for NULLs (nil)
-            if    @value.nil? && @operator == :== then 'IS'
-            elsif @value.nil? && @operator == :!= then 'IS NOT'
+            if    @value.nil? && operator == '==' then 'IS'
+            elsif @value.nil? && operator == '!=' then 'IS NOT'
             # SQL uses a single =
-            elsif @operator == :== then '='
+            elsif operator == '==' then '='
             # Other cases are as-is
-            else @operator
+            else operator
             end
           )
-          return model.where("#{attribute} #{operator} ?", @value)
+          return model.where("#{attribute} #{sql_operator} ?", @value)
 
-        # :in corresponds to IN, and :out to NOT IN
-        when :in, :out
-          operator     = (@operator == :in ? 'IN' : 'NOT IN')
+        # in corresponds to IN, and out to NOT IN
+        when 'in', 'out'
+          sql_operator = (operator == 'in' ? 'IN' : 'NOT IN')
           placeholders = @value.map { '?' }.join(',')
           return (
             if @value.present?
-              model.where("#{attribute} #{operator} (#{placeholders})", *@value)
-            elsif @operator == :in
+              model.where("#{attribute} #{sql_operator} (#{placeholders})", *@value)
+            elsif operator == 'in'
               model.where('1 = 0')
             else
               model.where({})
             end
           )
 
-        # :match is more-or-less LIKE
-        when :match
+        # match is more-or-less LIKE
+        when 'match'
           pattern = "%#{@value.gsub(/([%_!])/, '!\1')}%"
           return model.where("#{attribute} LIKE ? ESCAPE '!'", pattern)
 
-        # :range is exactly BETWEEN
-        when :range
+        # range is exactly BETWEEN
+        when 'range'
           min, max = @value.sort
           return model.where("#{attribute} BETWEEN ? AND ?", min, max)
 
         # Invalid operator?
         else
-          raise "unknown operator '#{@operator}'"
+          raise "unknown operator '#{operator}'"
         end
       end
 
@@ -643,32 +643,32 @@ def apply_on_collection(collection) #:nodoc:
         attr_cast = ScopeHelpers.generate_cast(value, attr_get.(collection.first))
         raise "no way to convert '#{value}' to '#{@attribute}' values" unless attr_cast
 
-        case @operator
+        case (operator = @operator.to_s)
         # Standard comparison operators are just invoked directly (send
         # method) to each item against @value.
-        when :==, :!=, :>, :>=, :<, :<=
+        when '==', '!=', '>', '>=', '<', '<='
           value = attr_cast.(@value)
           return collection.select do |item|
-            attr_get.(item).send(@operator, value) rescue nil
+            attr_get.(item).send(operator, value) rescue nil
           end
 
-        # :in and :out naturally correspond to the include? method
-        when :in, :out
-          method = (@operator == :in ? :select : :reject)
+        # in and out naturally correspond to the include? method
+        when 'in', 'out'
+          method = (operator == 'in' ? :select : :reject)
           values = @value.map(&attr_cast)
           return collection.send(method) do |item|
             values.include?(attr_get.(item)) rescue nil
           end
 
-        # :match is a case-insensitive :in
-        when :match
+        # match is a case-insensitive in
+        when 'match'
           value = @value.to_s.downcase
           return collection.select do |item|
             attr_get.(item).to_s.downcase.include?(value) rescue nil
           end
 
-        # :range corresponds to min <= value <= max
-        when :range
+        # range corresponds to min <= value <= max
+        when 'range'
           min, max = @value.map(&attr_cast).sort
           return collection.select do |item|
             attr = attr_get.(item)
@@ -677,7 +677,7 @@ def apply_on_collection(collection) #:nodoc:
 
         # Invalid operator?
         else
-          raise "unknown operator '#{@operator}'"
+          raise "unknown operator '#{operator}'"
         end
       end
     end
@@ -700,9 +700,9 @@ class Order
       attr_accessor :attribute
 
       # SQL-like direction in which to perform the sorting/ordering; either
-      # +:asc+ to sort in ascending order (1, 2, 3, ...) or +:desc+ to sort in
+      # +asc+ to sort in ascending order (1, 2, 3, ...) or +desc+ to sort in
       # descending order (7, 6, 5, ...).
-      # Defaults to ascending order (:asc).
+      # Defaults to ascending order (asc).
       attr_accessor :direction
 
       # Optional ActiveRecord model to join on to the filtered model before
@@ -749,25 +749,25 @@ def valid?
       # Create a new Order described by the contents of +hash+. Works similarly
       # to Filter's +from_hash+ method, as each recognized pair in +hash+
       # corresponds to an Order attribute and is expected to match the
-      # attribute's format, bar for +:type+.
+      # attribute's format, bar for +type+.
       #
       # The following keys are recognized in +hash+:
       #
-      # [:type or :t]
+      # [+type+ or +t+]
       #  Type (subclass) of Filter to create from +hash+, as a string or symbol.
-      #  Handled the same way as Filter's own +:type+ key; see Filter's
+      #  Handled the same way as Filter's own +type+ key; see Filter's
       #  +from_hash+ method.
       #
-      # [:attribute or :a]
+      # [+attribute+ or +a+]
       #  *attribute* attribute: a symbol or string.
       #
-      # [:direction or :d]
-      #  *direction* attribute: either +:asc+ or +:desc+ (defaults to +:asc+).
+      # [+direction+ or +d+]
+      #  *direction* attribute: either +asc+ or +desc+ (defaults to +asc+).
       #
-      # [:association or :j]
+      # [+association+ or +j+]
       #  *association* attribute: an ActiveRecord model or an array with an
       #  ActiveRecord model and the two attributes to perform the join with.
-      #  Handled the same way as Filter's own +:association+ key; see Filter's
+      #  Handled the same way as Filter's own +association+ key; see Filter's
       #  +from_hash+ method.
       #
       # Returns the newly created Order (just like new would)
@@ -780,23 +780,23 @@ def self.from_hash(hash)
 
         order = self.new
 
-        # Handle Order subclasses (:type key)
-        if type = (hash[:type] || hash[:t])
+        # Handle Order subclasses (type key)
+        if type = (hash['type'] || hash['t'])
           subclass = self.descendants.find { |sub| sub.type_name == type }
           return subclass ? subclass.from_hash(hash) : order
         end
 
         # *attribute* must be alphanumeric (word-like)
-        attribute = (hash[:attribute] || hash[:a]).to_s.gsub(/[^\w.]/, '')
+        attribute = (hash['attribute'] || hash['a']).to_s.gsub(/[^\w.]/, '')
         order.attribute = attribute unless attribute.blank?
 
         # *direction* must be either ascending or descending
-        direction   = (hash[:direction] || hash[:d] || :asc).to_s.downcase.to_sym
-        order.direction = direction if [ :asc, :desc ].include?(direction)
+        direction   = (hash['direction'] || hash['d'] || 'asc').to_s.downcase
+        order.direction = direction if [ 'asc', 'desc' ].include?(direction)
 
         # *association* must be an ActiveRecord model or an array with the
         # correct format
-        order.association = ScopeHelpers.parse_assoc(hash[:association] || hash[:j])
+        order.association = ScopeHelpers.parse_assoc(hash['association'] || hash['j'])
 
         order
       end
@@ -809,9 +809,9 @@ def self.from_hash(hash)
       # See Scope's +to_hash+ method for further information.
       def to_hash(compact: false)
         hash = {
-          :attribute   => @attribute,
-          :direction   => @direction,
-          :association => ScopeHelpers.assoc_with_table(@association)
+          'attribute'   => @attribute.to_s,
+          'direction'   => @direction.to_s,
+          'association' => ScopeHelpers.assoc_with_table(@association)
         }
 
         compact ? self.class.compact_hash(hash) : hash
@@ -825,12 +825,12 @@ def self.compact_hash(hash)
         Scope.generic_compact_hash(
           hash,
           {
-            :type        => :t,
-            :attribute   => :a,
-            :direction   => :d,
-            :association => :j
+            'type'        => 't',
+            'attribute'   => 'a',
+            'direction'   => 'd',
+            'association' => 'j'
           },
-          defaults: { :direction => :asc }
+          defaults: { 'direction' => 'asc' }
         )
       end
 
@@ -845,7 +845,7 @@ def apply_on_model(model) #:nodoc:
         attribute, model = ScopeHelpers.resolve_model_attribute(@attribute, model, @association)
 
         raise "unknown direction '#{@direction}'" unless
-          [ :asc, :desc ].include?(@direction)
+          [ 'asc', 'desc' ].include?(@direction.to_s)
 
         model.order("#{attribute} #{@direction.to_s.upcase}")
       end
@@ -864,7 +864,7 @@ def apply_on_collection(collection) #:nodoc:
         raise "no way to get '#{@attribute}' out of collection items" unless attr_get
 
         collection = collection.sort_by(&attr_get)
-        collection.reverse! if @direction == :desc
+        collection.reverse! if @direction.to_s == 'desc'
         collection
       end
     end
@@ -917,13 +917,13 @@ def apply(collection)
       #
       # The following keys are recognized in +hash+:
       #
-      # [:page or :i]
+      # [+page+ or +i+]
       #  *page* attribute: an integer.
       #
-      # [:per_page or :p]
+      # [+per_page+ or +p+]
       #  *per_page* attribute: an integer.
       #
-      # [:total or :t]
+      # [+total+ or +t+]
       #  *total* attribute: an integer.
       #
       # Returns the newly created Pagination (just like new would)
@@ -934,9 +934,9 @@ def self.from_hash(hash)
           hash.is_a?(HashWithIndifferentAccess)
 
         pagination = self.new
-        pagination.page     = (hash[:i] || hash[:page] || 1).to_i
-        pagination.per_page = (hash[:p] || hash[:per_page]).to_i
-        pagination.total    = (hash[:t] || hash[:total]).to_i
+        pagination.page     = (hash['i'] || hash['page'] || 1).to_i
+        pagination.per_page = (hash['p'] || hash['per_page']).to_i
+        pagination.total    = (hash['t'] || hash['total']).to_i
         pagination
       end
 
@@ -948,9 +948,9 @@ def self.from_hash(hash)
       # See Scope's +to_hash+ method for further information.
       def to_hash(compact: false)
         hash = {
-          :page     => @page,
-          :per_page => @per_page,
-          :total    => @total
+          'page'     => @page.to_i,
+          'per_page' => @per_page.to_i,
+          'total'    => @total.to_i
         }
 
         compact ? self.class.compact_hash(hash) : hash
@@ -964,11 +964,11 @@ def self.compact_hash(hash)
         Scope.generic_compact_hash(
           hash,
           {
-            :page     => :i,
-            :per_page => :p,
-            :total    => :t
+            'page'     => 'i',
+            'per_page' => 'p',
+            'total'    => 't'
           },
-          defaults: { :page => 1 }
+          defaults: { 'page' => 1 }
         )
       end
     end
@@ -982,9 +982,9 @@ def self.compact_hash(hash)
     # +keys+ is expected to be a mapping of +hash+'s keys to shorter
     # versions of the same keys:
     #   {
-    #     :attribute => :a,
-    #     :operator  => :o,
-    #     :value     => :v
+    #     'attribute' => 'a',
+    #     'operator'  => 'o',
+    #     'value'     => 'v'
     #   }
     #
     # +values+, if given, is expected to be a list of +hash+ values to
@@ -992,25 +992,25 @@ def self.compact_hash(hash)
     #   [
     #     [<key>, <long value>, <short value>],
     #
-    #     # hash[:operator] would become :r if it was :range
-    #     [:operator,  :range,     :r],
+    #     # hash['operator'] would become 'r' if it was 'range'
+    #     ['operator',  'range',     'r'],
     #
-    #     # hash[:direction] would become :asc if it was :ascending
-    #     [:direction, :ascending, :asc],
+    #     # hash['direction'] would become 'asc' if it was 'ascending'
+    #     ['direction', 'ascending', 'asc'],
     #   ]
     #
     # +defaults+, if given, is expected to be a mapping of default values
     # for +hash+ which should be removed when compacting:
     #   {
-    #     # :asc is the default for :direction, and doesn't need to be included
+    #     # 'asc' is the default for 'direction', and doesn't need to be included
     #     # in the compacted hash version
-    #     :direction => :asc
+    #     'direction' => 'asc'
     #   }
     def self.generic_compact_hash(hash, keys, values: {}, defaults: {})
       # Make sure +hash+ is proper
       return nil unless hash.is_a?(Hash)
 
-      compact = hash.symbolize_keys
+      compact = hash.stringify_keys
 
       hash = hash.with_indifferent_access unless
         hash.is_a?(HashWithIndifferentAccess)
@@ -1100,7 +1100,9 @@ def default_scope_name
   # methods).
   def update_session_scopes
     default = default_scope_name
-    mode    = (params['_scope_mode'] || 'replace').to_sym
+    mode    = params['_scope_mode'].to_sym if
+        [ 'append', 'delete', 'replace' ].include?(params['_scope_mode'])
+    mode  ||= :replace
 
     # Decompress (if required) and merge _scopes and _cur_scope
     scopes = (params['_scopes'] || {})
@@ -1114,11 +1116,11 @@ def update_session_scopes
 
     # Pagination parameters (which override _scopes and _cur_scope)
     pagination = {}
-    pagination[:i] = params['page']     if params['page']
-    pagination[:p] = params['per_page'] if params['per_page']
+    pagination['i'] = params['page']     if params['page']
+    pagination['p'] = params['per_page'] if params['per_page']
 
     current_session.update({
-      :scopes => { default => { :p => pagination } }
+      :scopes => { default => { 'p' => pagination } }
     }, mode) unless
       pagination.empty?
   end
@@ -1132,18 +1134,18 @@ def update_session_scopes
   #   @scope = scope_from_session('userfiles')
   #   # ...
   #   new_scope = @scope.dup
-  #   new_scope.filters[0].operator = :!=
-  #   query_params = scope_url_params('userfiles', new_scope)
+  #   new_scope.filters[0].operator = '!='
+  #   query_params = scope_params('userfiles', new_scope)
   # Same as above, using the hash representation of +@scope+:
   #   @scope = scope_from_session('userfiles')
   #   # ...
   #   scope_hash = @scope.to_hash
-  #   scope_hash[:filters][0][:operator] = :!=
+  #   scope_hash['filters'][0]['operator'] = '!='
   #   scope_hash = @scope.class.compact_hash(scope_hash)
-  #   query_params = scope_url_params('userfiles', scope_hash)
+  #   query_params = scope_params('userfiles', scope_hash)
   # Unless +compress+ is specified as false, the generated URL parameters will
   # use the compressed format as specified by +compress_scope+.
-  def scope_url_params(name, scope, compress: true)
+  def scope_params(name, scope, compress: true)
     scope = scope.to_hash if scope.is_a?(Scope)
     scope = Scope.compact_hash(scope)
     scope = ScopeHelpers.compress_scope(scope) if compress
@@ -1174,7 +1176,7 @@ def scope_url_params(name, scope, compress: true)
   #
   # Note that the generated URL parameters are in compressed format (see
   # +compress_scope+).
-  def filter_url_params(operation, filters, scope: nil)
+  def scope_filter_params(operation, filters, scope: nil)
     scope ||= default_scope_name
     filters = (filters.is_a?(Array) ? filters : [filters]).map do |filter|
       filter = filter.to_hash if filter.is_a?(Scope::Filter)
@@ -1186,13 +1188,13 @@ def filter_url_params(operation, filters, scope: nil)
 
   # Generate URL parameters suitable for +url_for+ to update the session scope
   # named +scope+'s ordering rules (via +update_session_scopes+) via a given
-  # +operation+. This method behaves just like +filter_url_params+, but operates
-  # on a Scope's ordering rules (Order instances or hash representations)
+  # +operation+. This method behaves just like +scope_filter_params+, but
+  # operates on a Scope's ordering rules (Order instances or hash representations)
   # instead of filters. As such, the same +operation+s are available (:add,
   # :remove, :set, :replace, :clear) and the +scope+ and +orders+ parameters are
-  # handled the exact same way +filter_url_params+'s +scope+ and +filters+
+  # handled the exact same way +scope_filter_params+'s +scope+ and +filters+
   # parameters are handled.
-  def order_url_params(operation, orders, scope: nil)
+  def scope_order_params(operation, orders, scope: nil)
     scope ||= default_scope_name
     orders = (orders.is_a?(Array) ? orders : [orders]).map do |order|
       order = order.to_hash if order.is_a?(Scope::Order)
@@ -1304,35 +1306,35 @@ def self.decompress_scope(scope)
     scope.tr!('-_', '+/')
     scope = Base64.decode64(scope)
     scope = ActiveSupport::Gzip.decompress(scope)
-    scope = YAML.load(scope)
+    scope = YAML.safe_load(scope)
     scope
   end
 
   # Generate URL parameters suitable for +url_for+ to update the session scope
   # named +scope+'s items (ordering or filtering rules). This method is the
-  # internal implementation of +filter_url_params+ (and +order_url_params+).
-  # - +operation+ corresponds exactly to +filter_url_params+'s +operation+
+  # internal implementation of +scope_filter_params+ (and +scope_order_params+).
+  # - +operation+ corresponds exactly to +scope_filter_params+'s +operation+
   # parameter.
-  # - +scope+ corresponds to +filter_url_params+'s +scope+ parameter, minus
+  # - +scope+ corresponds to +scope_filter_params+'s +scope+ parameter, minus
   # the default value.
   # - +attr+ is expected to be either :filters, to update scope filtering rules,
   # or :order, for ordering rules. It corresponds to the Scope attribute name
   # to apply +changes+ on.
-  # - +changes+ corresponds to +filter_url_params+'s +changes+ parameter, and
+  # - +changes+ corresponds to +scope_filter_params+'s +changes+ parameter, and
   # is expected to be an array of compact hash representations of filters
   # (Scope::Filter) or ordering rules (Scope::Order).
   #
   # Note that unlike most other utility methods, this method is exclusively
-  # intended to be used only to implement +filter_url_params+ and
-  # +order_url_params+ and is most likely unsuitable for anything else.
+  # intended to be used only to implement +scope_filter_params+ and
+  # +scope_order_params+ and is most likely unsuitable for anything else.
   def self.scope_items_url_params(scope, operation, attr, changes) #:nodoc:
     return if changes.blank? && operation != :clear
 
-    key  = (attr == :filters ? :f : :o)
+    key  = (attr == :filters ? 'f' : 'o')
     hash = (
       case operation
       when :set
-        replaced  = changes.map { |c| c[:a] }
+        replaced  = changes.map { |c| c['a'] }
         changes  += scope_from_session(scope)
           .send(attr)
           .reject { |c| replaced.include?(f.attribute) }
diff --git a/BrainPortal/spec/modules/scope_helpers_spec.rb b/BrainPortal/spec/modules/scope_helpers_spec.rb
index 21483fe5f..db4706e85 100644
--- a/BrainPortal/spec/modules/scope_helpers_spec.rb
+++ b/BrainPortal/spec/modules/scope_helpers_spec.rb
@@ -269,7 +269,7 @@ module ScopeHelpers
 
         expect(filter.attribute).to eq('a')
         expect(filter.value).to     eq('v')
-        expect(filter.operator).to  eq(:match)
+        expect(filter.operator).to  eq('match')
       end
 
       it "should accept short attribute hash keys" do
@@ -281,7 +281,7 @@ module ScopeHelpers
 
         expect(filter.attribute).to eq('a')
         expect(filter.value).to     eq('v')
-        expect(filter.operator).to  eq(:match)
+        expect(filter.operator).to  eq('match')
       end
 
       it "should delegate to a subclass if :type is given" do
@@ -361,41 +361,41 @@ def self.type_name
     context "when converting to hash" do
       it "should export all attributes" do
         expect(filter.to_hash).to eq({
-          :attribute   => 'full_name',
-          :value       => 'A',
-          :operator    => :==,
-          :association => nil
+          'attribute'   => 'full_name',
+          'value'       => 'A',
+          'operator'    => '==',
+          'association' => nil
         })
       end
 
       context "in compact mode" do
         it "should export only set attributes" do
           expect(filter.to_hash(compact: true)).to eq({
-            :a => 'full_name',
-            :v => 'A'
+            'a' => 'full_name',
+            'v' => 'A'
           })
         end
 
         it "should shrink attribute keys" do
           expect(filter.to_hash(compact: true)).to eq({
-            :a => 'full_name',
-            :v => 'A'
+            'a' => 'full_name',
+            'v' => 'A'
           })
         end
 
         it "should shrink long operators" do
           filter.operator = :match
           expect(filter.to_hash(compact: true)).to eq({
-            :a => 'full_name',
-            :v => 'A',
-            :o => :m
+            'a' => 'full_name',
+            'v' => 'A',
+            'o' => 'm'
           })
         end
 
         it "should remove default values" do
           expect(filter.to_hash(compact: true)).to eq({
-            :a => 'full_name',
-            :v => 'A'
+            'a' => 'full_name',
+            'v' => 'A'
           })
         end
       end
@@ -532,7 +532,7 @@ def self.type_name
         })
 
         expect(order.attribute).to eq('a')
-        expect(order.direction).to eq(:asc)
+        expect(order.direction).to eq('asc')
       end
 
       it "should accept short attribute hash keys" do
@@ -542,7 +542,7 @@ def self.type_name
         })
 
         expect(order.attribute).to eq('a')
-        expect(order.direction).to eq(:asc)
+        expect(order.direction).to eq('asc')
       end
 
       it "should delegate to a subclass if :type is given" do
@@ -586,28 +586,28 @@ def self.type_name
     context "when converting to hash" do
       it "should export all attributes" do
         expect(order.to_hash).to eq({
-          :attribute   => 'full_name',
-          :direction   => :asc,
-          :association => nil
+          'attribute'   => 'full_name',
+          'direction'   => 'asc',
+          'association' => nil
         })
       end
 
       context "in compact mode" do
         it "should export only set attributes" do
           expect(order.to_hash(compact: true)).to eq({
-            :a => 'full_name'
+            'a' => 'full_name'
           })
         end
 
         it "should shrink attribute keys" do
           expect(order.to_hash(compact: true)).to eq({
-            :a => 'full_name'
+            'a' => 'full_name'
           })
         end
 
         it "should remove default values" do
           expect(order.to_hash(compact: true)).to eq({
-            :a => 'full_name'
+            'a' => 'full_name'
           })
         end
       end

From 76f66779392df622f5ca888a2ce050c6471e290e Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Thu, 20 Aug 2015 18:05:46 -0400
Subject: [PATCH 18/85] Issue #175 - Add time counter since last refresh

The time counter implemented in this changeset is present for all users
in the top right corner, right next to 'Logged in as ...'. It is updated
every 20 seconds and reset when navigating in CBRAIN and when AJAX
requests are performed (new_content event).
---
 .../views/layouts/_section_account.html.erb   | 32 +++++++++++++++++++
 BrainPortal/public/stylesheets/cbrain.css     |  6 ++++
 2 files changed, 38 insertions(+)

diff --git a/BrainPortal/app/views/layouts/_section_account.html.erb b/BrainPortal/app/views/layouts/_section_account.html.erb
index 4ab63b112..989662564 100644
--- a/BrainPortal/app/views/layouts/_section_account.html.erb
+++ b/BrainPortal/app/views/layouts/_section_account.html.erb
@@ -61,6 +61,38 @@
 
   <span class="loggedas">
     <% if current_user %>
+      <span class="last_updated">
+        (last updated <span class="elapsed">0m</span> ago)
+        <script>
+          (function () {
+            "use strict";
+
+            var last_update = new Date();
+            setInterval(function () {
+              var diff = Math.floor((new Date() - last_update) / (60 * 1000)),
+                  part = undefined,
+                  text = [];
+
+              part = Math.round(diff % 60);
+              diff = Math.floor(diff / 60);
+              text.unshift(part + 'm');
+
+              part = Math.round(diff % 24);
+              diff = Math.floor(diff / 24);
+              if (part) text.unshift(part + 'h');
+
+              if (diff) text.unshift(diff + 'd');
+
+              $('span.last_updated > span.elapsed').text(text.join(' '));
+            }, 20 * 1000);
+
+            $(document).delegate('*', 'new_content', function () {
+              last_update = new Date();
+            });
+          })();
+        </script>
+      </span>
+
       Logged in as <%= current_user.full_name %>
       <%= link_to "Sign out", "/logout" %>
     <% else %>
diff --git a/BrainPortal/public/stylesheets/cbrain.css b/BrainPortal/public/stylesheets/cbrain.css
index 15158eab8..9b98ece17 100644
--- a/BrainPortal/public/stylesheets/cbrain.css
+++ b/BrainPortal/public/stylesheets/cbrain.css
@@ -925,6 +925,12 @@ pre {
   margin-right: 0.5em;
 }
 
+.last_updated {
+  margin-right: 0.6em;
+  color: #83b4d1;
+  font-weight: bold;
+}
+
 
 
 /* % ######################################################### */

From ae450150e4767317062513ca0027778616d78684 Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Fri, 21 Aug 2015 16:35:13 -0400
Subject: [PATCH 19/85] Split up view/controller helpers, renamed controller
 helpers

Most view helpers (scope_*_params, notably) now belongs in
app/views/scope_helper.rb instead of lib/. ScopeHelpers has been renamed
to ViewScopes (as to avoid confusing the view helper module and the
controller one).

This changeset also adds a new view helper, pretty_scope_filter, to
generate a pretty string representation of a filter.

NOTE: ViewScopes isnt exactly a nice name either...
---
 .../app/controllers/application_controller.rb |   2 +-
 BrainPortal/app/helpers/scope_helper.rb       | 357 ++++++++++++++++++
 .../lib/{scope_helpers.rb => view_scopes.rb}  | 285 +++-----------
 ...pe_helpers_spec.rb => view_scopes_spec.rb} |   4 +-
 4 files changed, 407 insertions(+), 241 deletions(-)
 create mode 100644 BrainPortal/app/helpers/scope_helper.rb
 rename BrainPortal/lib/{scope_helpers.rb => view_scopes.rb} (83%)
 rename BrainPortal/spec/modules/{scope_helpers_spec.rb => view_scopes_spec.rb} (99%)

diff --git a/BrainPortal/app/controllers/application_controller.rb b/BrainPortal/app/controllers/application_controller.rb
index b02ee0741..20ba6d9e5 100644
--- a/BrainPortal/app/controllers/application_controller.rb
+++ b/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
diff --git a/BrainPortal/app/helpers/scope_helper.rb b/BrainPortal/app/helpers/scope_helper.rb
new file mode 100644
index 000000000..d0740622e
--- /dev/null
+++ b/BrainPortal/app/helpers/scope_helper.rb
@@ -0,0 +1,357 @@
+
+#
+# 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 <http://www.gnu.org/licenses/>.
+#
+
+# Complement of the ViewScopes controller module containing view helpers to
+# create, update and display Scope elements.
+#
+# See the ViewScopes module (lib/scope_helpers.rb) for more information on
+# view scopes.
+module ScopeHelper
+
+  Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
+
+  # Generate URL parameters suitable for +url_for+ to update the session scope
+  # named +name+ to match +scope+ (a Scope instance or a hash representation)
+  # via +update_session_scopes+. For example, to change the first filter of the
+  # 'userfiles' scope:
+  #   @scope = scope_from_session('userfiles')
+  #   # ...
+  #   new_scope = @scope.dup
+  #   new_scope.filters[0].operator = '!='
+  #   query_params = scope_params('userfiles', new_scope)
+  # Same as above, using the hash representation of +@scope+:
+  #   @scope = scope_from_session('userfiles')
+  #   # ...
+  #   scope_hash = @scope.to_hash
+  #   scope_hash['filters'][0]['operator'] = '!='
+  #   scope_hash = @scope.class.compact_hash(scope_hash)
+  #   query_params = scope_params('userfiles', scope_hash)
+  # Unless +compress+ is specified as false, the generated URL parameters will
+  # use the compressed format as specified by +compress_scope+.
+  def scope_params(name, scope, compress: true)
+    scope = scope.to_hash if scope.is_a?(Scope)
+    scope = Scope.compact_hash(scope)
+    scope = ViewScopes.compress_scope(scope) if compress
+
+    { '_scopes' => { name => scope } }
+  end
+
+  # Generate URL parameters suitable for +url_for+ to update the session scope
+  # named +scope+'s filters (via +update_session_scopes+) via a given
+  # +operation+. +filters+ is expected to be Filter instances or hash
+  # representations (a single filter or an Enumerable), depending on which
+  # +operation+ is to be performed, and +operation+ is expected to be one of:
+  # [+:add+]
+  #  Add one or more +filters+ to the specified scope.
+  # [+:remove+]
+  #  Remove one or more +filters+ from the specified scope.
+  # [+:set+]
+  #  Add one or more +filters+ to the specified scope, replacing existing
+  #  filters filtering on the same attributes as +filters+.
+  # [+:replace+]
+  #  Replace all filters in the specified scope by the ones in +filters+.
+  # [+:clear+]
+  #  Remove all filters in the specified scope (+filters is ignored).
+  #  Equivalent to using +:replace+ with an empty +filters+.
+  #
+  # +scope+ defaults to the current route's scope name (see
+  # +default_scope_name+).
+  #
+  # Note that the generated URL parameters are in compressed format (see
+  # +compress_scope+).
+  def scope_filter_params(operation, filters, scope: nil)
+    scope ||= default_scope_name
+    filters = (filters.is_a?(Array) ? filters : [filters]).map do |filter|
+      filter = filter.to_hash if filter.is_a?(Scope::Filter)
+      Scope::Filter.compact_hash(filter)
+    end
+
+    ScopeHelper.scope_items_url_params(scope, operation, :filters, filters)
+  end
+
+  # Generate URL parameters suitable for +url_for+ to update the session scope
+  # named +scope+'s ordering rules (via +update_session_scopes+) via a given
+  # +operation+. This method behaves just like +scope_filter_params+, but
+  # operates on a Scope's ordering rules (Order instances or hash representations)
+  # instead of filters. As such, the same +operation+s are available (:add,
+  # :remove, :set, :replace, :clear) and the +scope+ and +orders+ parameters are
+  # handled the exact same way +scope_filter_params+'s +scope+ and +filters+
+  # parameters are handled.
+  def scope_order_params(operation, orders, scope: nil)
+    scope ||= default_scope_name
+    orders = (orders.is_a?(Array) ? orders : [orders]).map do |order|
+      order = order.to_hash if order.is_a?(Scope::Order)
+      Scope::Order.compact_hash(order)
+    end
+
+    ScopeHelper.scope_items_url_params(scope, operation, :order, orders)
+  end
+
+  # Generate URL parameters suitable for +url_for+ to update the session
+  # scope named +scope+'s custom attributes with +custom+ (expected to be
+  # a hash of attributes to merge in) using CbrainSession's +update+ method.
+  #
+  # +scope+ defaults to the current route's scope name (see
+  # +default_scope_name+).
+  #
+  # Note that as with +scope_filter_params+ and +scope_order_params+, the
+  # generated URL parameters are compressed using +compress_scope+.
+  def scope_custom_params(custom, scope: nil)
+    scope ||= default_scope_name
+
+    { '_scopes' => { scope => ViewScopes.compress_scope({
+      'c' => custom
+    }) } }
+  end
+
+  # Generate a pretty string representation of +filter+, optionally using
+  # +model+ (as the model +filter+ is applied to) to resolve associations
+  # to names (instead of IDs). For example, a filter for +:user_id == 1+
+  # could have a string representation of 'User: admin' while one for
+  # +:status in ['A', 'B', 'C']+ could have 'Status: one of A, B or C'.
+  #
+  # TODO Ruby collections
+  #
+  # Note that this method is rather inflexible on how the representations
+  # are generated and relies on internal mappings for certain known
+  # attributes, values and associations.
+  def pretty_scope_filter(filter, model: nil)
+    # UI names for certain associations.
+    association_names = {
+      'group'    => 'project',
+      'bourreau' => 'server'
+    }
+
+    # Explanatory flag (boolean attributes) value names to use instead of
+    # '<attribute>: true' or '<attribute>: false'.
+    flag_names = {
+      'critical' => ['Critical', 'Not critical'],
+      'read'     => ['Read',     'Unread'],
+      'locked'   => ['Locked',   'Unlocked']
+    }
+
+    # Model methods/attributes to use as representation of a model record
+    naming_methods = {
+      :user => :login
+    }
+
+    attribute = filter.attribute.to_s
+    operator  = filter.operator.to_s
+    values    = Array(filter.value)
+
+    # Known flags are expected to never be association attributes, and the
+    # possible values are fully represented in flag_names. If +filter+'s
+    # attribute is in flag_names, the corresponding flag value name is
+    # the filter's representation.
+    if flag = flag_names[attribute]
+      return values.first ? flag.first : flag.last
+    end
+
+    # Is +filter+'s attribute an association attribute? If so, resolve it
+    # and use it to fetch nicer representations for +filter+'s attribute
+    # and values.
+    if model
+      model = model.to_s.classify.constantize unless
+        (model <= ActiveRecord::Base rescue nil)
+      association = model.reflect_on_all_associations(:belongs_to)
+        .find { |a| a.foreign_key == attribute }
+
+      if association
+        attribute = association.name.to_s
+        attribute = association_names[attribute] if
+          association_names[attribute]
+
+        name_method = (
+          naming_methods[association.foreign_key.to_sym] ||
+          naming_methods[association.name.to_sym] ||
+          :name
+        )
+        values.map! do |value|
+          record = association.klass.find_by_id(value)
+          record ? record.send(name_method) : value
+        end
+      end
+    end
+
+    # The type attribute has a special meaning; it usually corresponds to the
+    # ActiveRecord class name.
+    values.map! { |value| value.constantize.pretty_type rescue value } if
+      attribute == 'type'
+
+    # Convert the values to a textual representation, depending on which
+    # operator they will be used with; single values are as-is, but
+    # sets are converted to 'A, B or C' and ranges to 'A and B'.
+    values = (
+      if ['in', 'out'].include?(operator)
+        values.map! { |v| v.to_s =~ /[,\s]/ ? "'#{v}'" : v.to_s }
+        last = values.pop
+        values.empty? ? last : "#{values.join(', ')} or #{last}"
+      elsif operator == 'range'
+        min, max = values.sort
+        "#{min} and #{max}"
+      else
+        values.first.to_s
+      end
+    )
+
+    # Have a nice textual representation of the operator
+    operator = ({
+      '=='    => '',
+      '!='    => 'not ',
+      '>'     => 'over ',
+      '>='    => 'over ',
+      '<'     => 'under ',
+      '<='    => 'under ',
+      'in'    => 'one of ',
+      'out'   => 'anything except ',
+      'match' => '~',
+      'range' => 'between '
+    })[filter.operator.to_s]
+
+    "#{attribute.humanize}: #{operator}#{values}"
+  end
+
+  # Fetch the possible values (and their count) for +attribute+ within
+  # +collection+, which is either a Ruby Enumerable or ActiveRecord model.
+  # As this method is intended as a view helper to create the list of values to
+  # filter a collection/model with, the possible values are returned as a list
+  # of hashes matching +DynamicTable+'s filter format, containing:
+  # [:value]
+  #  Possible value for +attribute+.
+  # [:label]
+  #  String representation of +:value+ (or just +:value+ if unavailable).
+  # [:indicator]
+  #  Count of how many times this specific +:value: was found for +attribute+ in
+  #  +collection+.
+  #
+  # If +label+ is specified, it is expected to be an attribute name as a string
+  # or symbol (like +attribute+), representing which +collection+ attribute to
+  # use as value labels.
+  #
+  # If +association+ is specified, it is expected to be in the same format as
+  # +Scope+::+Filter+'s *association* attribute, and fulfills roughly the same
+  # purpose; allow +attribute+ and +label+ to refer to attributes on the joined
+  # model (only applicable if +collection+ is an ActiveRecord model).
+  def filter_values_for(collection, attribute, label: nil, association: nil)
+    # TODO Unscoped/base scope/total item count.
+
+    if (collection <= ActiveRecord::Base rescue nil)
+      # Resolve and validate the main +attribute+ to fetch the values of
+      attribute, model = ViewScopes.resolve_model_attribute(attribute, collection, association)
+
+      # And +label+, if provided
+      if label
+        label, model = ViewScopes.resolve_model_attribute(label, model, association)
+      else
+        label = attribute
+      end
+
+      # NOTE: The 'AS' specifier bypasses Rails' uniq on the column names, which
+      # would remove the label column if label happens to have the same value
+      # as attribute.
+      label_alias = model.connection.quote_column_name('label')
+
+      model
+        .where("#{attribute} IS NOT NULL")
+        .order(attribute, label)
+        .group(attribute, label)
+        .raw_rows(attribute, "#{label} AS #{label_alias}", "COUNT(#{attribute})")
+        .reject { |r| r.first.blank? }
+        .map    { |v, l, c| { :value => v, :label => l, :indicator => c } }
+
+    else
+      # Make sure +attribute+ and +label+ can be accessed in
+      # +collection+'s items.
+      attr_get = ViewScopes.generate_getter(collection.first, attribute)
+      raise "no way to get '#{attribute}' out of collection items" unless attr_get
+
+      if label == attribute
+        lbl_get = attr_get
+      else
+        lbl_get = ViewScopes.generate_getter(collection.first, label || attribute)
+        raise "no way to get '#{label}' out of collection items" unless lbl_get
+      end
+
+      collection
+        .map     { |i| [attr_get.(i), lbl_get.(i)].freeze }
+        .reject  { |v, l| v.blank? }
+        .sort_by { |v, l| v }
+        .inject(Hash.new(0)) { |h, i| h[i] += 1; h }
+        .map { |(v, l), c| { :value => v, :label => l, :indicator => c } }
+    end
+  end
+
+  # Utility/internal methods
+
+  # Generate URL parameters suitable for +url_for+ to update the session scope
+  # named +scope+'s items (ordering or filtering rules). This method is the
+  # internal implementation of +scope_filter_params+ (and +scope_order_params+).
+  # - +operation+ corresponds exactly to +scope_filter_params+'s +operation+
+  # parameter.
+  # - +scope+ corresponds to +scope_filter_params+'s +scope+ parameter, minus
+  # the default value.
+  # - +attr+ is expected to be either :filters, to update scope filtering rules,
+  # or :order, for ordering rules. It corresponds to the Scope attribute name
+  # to apply +changes+ on.
+  # - +changes+ corresponds to +scope_filter_params+'s +changes+ parameter, and
+  # is expected to be an array of compact hash representations of filters
+  # (Scope::Filter) or ordering rules (Scope::Order).
+  #
+  # Note that unlike most other utility methods, this method is exclusively
+  # intended to be used only to implement +scope_filter_params+ and
+  # +scope_order_params+ and is most likely unsuitable for anything else.
+  def self.scope_items_url_params(scope, operation, attr, changes) #:nodoc:
+    return if changes.blank? && operation != :clear
+
+    key  = (attr == :filters ? 'f' : 'o')
+    hash = (
+      case operation
+      when :set
+        replaced  = changes.map { |c| c['a'] }
+        changes  += scope_from_session(scope)
+          .send(attr)
+          .reject { |c| replaced.include?(f.attribute) }
+        { key => changes }
+      when :clear
+        { key => [] }
+      else
+        { key => changes }
+      end
+    )
+
+    mode = (
+      case operation
+      when :add    then :append
+      when :remove then :delete
+      else :replace
+      end
+    )
+
+    {
+      '_scope_mode' => mode,
+      '_scopes' => {
+        scope => ViewScopes.compress_scope(hash)
+      }
+    }
+  end
+
+end
diff --git a/BrainPortal/lib/scope_helpers.rb b/BrainPortal/lib/view_scopes.rb
similarity index 83%
rename from BrainPortal/lib/scope_helpers.rb
rename to BrainPortal/lib/view_scopes.rb
index 56dc710a5..e47f2eb64 100644
--- a/BrainPortal/lib/scope_helpers.rb
+++ b/BrainPortal/lib/view_scopes.rb
@@ -67,23 +67,17 @@
 # this module mainly target views, by taking concerns such as selection and
 # pagination, and are expected to be 'closer' to the user than ActiveRecord's
 # scopes (which would pose a security risk if they could be directly accessed).
-module ScopeHelpers
+module ViewScopes
 
   Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
 
-  # ScopeHelpers is intended to be included as a controller extension module,
-  # exposing +scope_from_session+, +default_scope_name+, +update_session_scopes+,
-  # URL parameter methods and +filter_values_for+.
+  # ViewScopes is intended to be included as a controller extension module,
+  # exposing +scope_from_session+, +scope_to_session+ and +default_scope_name+.
   def self.included(includer) #:nodoc:
     includer.class_eval do
-      helper_method(
-        :filter_values_for,
-        :scope_params,
-        :scope_filter_params,
-        :scope_order_params
-      )
-
-      before_filter :update_session_scopes
+      helper_method(:default_scope_name)
+
+      before_filter(:update_session_scopes)
     end
   end
 
@@ -172,13 +166,16 @@ def initialize_copy(other)
       @custom     = other.custom.dup
     end
 
-    # Apply the set of filtering and sorting rules and pagination from this
-    # scope to a given +collection+, which is either an ActiveRecord model
-    # or a Ruby Enumerable. Once the rules have been applied, the original
-    # collection is returned, scoped with the scope's rules; a scoped
-    # ActiveRecord model if +collection+ was a model or a new Ruby Enumerable
-    # matching the rules if +collection+ was a Ruby Enumerable.
-    def apply(collection)
+    # Apply the set of filtering and sorting rules from this scope to a given
+    # +collection+, which is either an ActiveRecord model or a Ruby Enumerable.
+    # Once the rules have been applied, the original collection is returned,
+    # scoped with the scope's rules; a scoped ActiveRecord model if +collection+
+    # was a model or a new Ruby Enumerable matching the rules if +collection+
+    # was a Ruby Enumerable.
+    #
+    # Note that pagination is not applied by default; specify +paginate+ to
+    # paginate +collection+.
+    def apply(collection, paginate: false)
       # Apply all filtering rules
       collection = @filters.inject(collection) do |collection, filter|
         filter.apply(collection)
@@ -194,7 +191,7 @@ def apply(collection)
       end
 
       # Paginate
-      collection = @pagination.apply(collection) if @pagination
+      collection = @pagination.apply(collection) if paginate && @pagination
 
       collection
     end
@@ -493,18 +490,30 @@ def self.from_hash(hash)
         filter.attribute = attribute unless attribute.blank?
 
         # *operator* must be one of the possible predicate operators
+        possible_operators = [
+          '==', '!=', '>', '>=', '<', '<=',
+          'in', 'out', 'match', 'range'
+        ]
+
         operator = (hash['operator'] || hash['o'] || :==).to_s.downcase
         operator = 'range' if operator == 'r'
         operator = 'match' if operator == 'm'
-        filter.operator = operator if
-          [ '==', '!=', '>', '>=', '<', '<=', 'in', 'out', 'match', 'range' ].include?(operator)
+        filter.operator = operator if possible_operators.include?(operator)
 
         # *value* must be a simple scalar value or a set of simple values,
         # depending on which *operator* is to be applied
+        scalars = [
+          Numeric,
+          String, Symbol,
+          Date, DateTime,
+          TrueClass, FalseClass,
+          NilClass
+        ]
+
         value = hash['value'] || hash['v']
-        value = (value.is_a?(Enumerable) ? value : [value])
-          .map(&:to_s)
-          .reject(&:blank?)
+        value = (value.is_a?(Enumerable) ? value : [value]).select do |v|
+          scalars.any? { |c| v.is_a?(c) }
+        end
 
         filter.value = (
           case operator.to_s
@@ -523,7 +532,7 @@ def self.from_hash(hash)
 
         # *association* must be an ActiveRecord model or an array with the
         # correct format
-        filter.association = ScopeHelpers.parse_assoc(hash['association'] || hash['j'])
+        filter.association = ViewScopes.parse_assoc(hash['association'] || hash['j'])
 
         filter
       end
@@ -541,7 +550,7 @@ def to_hash(compact: false)
           'attribute'   => @attribute.to_s,
           'operator'    => @operator.to_s,
           'value'       => @value,
-          'association' => ScopeHelpers.assoc_with_table(@association)
+          'association' => ViewScopes.assoc_with_table(@association)
         }
 
         compact ? self.class.compact_hash(hash) : hash
@@ -577,7 +586,7 @@ def self.compact_hash(hash)
       def apply_on_model(model) #:nodoc:
         # Resolve and validate *attribute* as an attribute of +model+ (or
         # *association*).
-        attribute, model = ScopeHelpers.resolve_model_attribute(@attribute, model, @association)
+        attribute, model = ViewScopes.resolve_model_attribute(@attribute, model, @association)
 
         case (operator = @operator.to_s)
         # Standard comparison operators can just be used as-is, bar for == and
@@ -636,11 +645,11 @@ def apply_on_collection(collection) #:nodoc:
         # we need to cast/convert *value* before the comparison?
         # Once known, keep the access and conversion methods as lambdas to make
         # attribute access as fast as possible.
-        attr_get  = ScopeHelpers.generate_getter(collection.first, @attribute)
+        attr_get  = ViewScopes.generate_getter(collection.first, @attribute)
         raise "no way to get '#{@attribute}' out of collection items" unless attr_get
 
         value     = (@value.is_a?(Enumerable) ? @value.first : @value)
-        attr_cast = ScopeHelpers.generate_cast(value, attr_get.(collection.first))
+        attr_cast = ViewScopes.generate_cast(value, attr_get.(collection.first))
         raise "no way to convert '#{value}' to '#{@attribute}' values" unless attr_cast
 
         case (operator = @operator.to_s)
@@ -796,7 +805,7 @@ def self.from_hash(hash)
 
         # *association* must be an ActiveRecord model or an array with the
         # correct format
-        order.association = ScopeHelpers.parse_assoc(hash['association'] || hash['j'])
+        order.association = ViewScopes.parse_assoc(hash['association'] || hash['j'])
 
         order
       end
@@ -811,7 +820,7 @@ def to_hash(compact: false)
         hash = {
           'attribute'   => @attribute.to_s,
           'direction'   => @direction.to_s,
-          'association' => ScopeHelpers.assoc_with_table(@association)
+          'association' => ViewScopes.assoc_with_table(@association)
         }
 
         compact ? self.class.compact_hash(hash) : hash
@@ -842,7 +851,7 @@ def self.compact_hash(hash)
       def apply_on_model(model) #:nodoc:
         # Resolve and validate *attribute* as an attribute of +model+ (or
         # *association*).
-        attribute, model = ScopeHelpers.resolve_model_attribute(@attribute, model, @association)
+        attribute, model = ViewScopes.resolve_model_attribute(@attribute, model, @association)
 
         raise "unknown direction '#{@direction}'" unless
           [ 'asc', 'desc' ].include?(@direction.to_s)
@@ -860,7 +869,7 @@ def apply_on_collection(collection) #:nodoc:
         # Assuming all objects are similar, how is *attribute* accessed?
         # Once known, keep the access method as a lambda to make attribute
         # access as fast as possible.
-        attr_get = ScopeHelpers.generate_getter(collection.first, @attribute)
+        attr_get = ViewScopes.generate_getter(collection.first, @attribute)
         raise "no way to get '#{@attribute}' out of collection items" unless attr_get
 
         collection = collection.sort_by(&attr_get)
@@ -1109,7 +1118,7 @@ def update_session_scopes
     scopes.merge!({ default => params['_cur_scope'] }) if params['_cur_scope']
     scopes = scopes.map do |n, s|
       return [n, s] if s.is_a?(Hash)
-      [ n, (ScopeHelpers.decompress_scope(s) rescue s) ]
+      [ n, (ViewScopes.decompress_scope(s) rescue s) ]
     end.to_h
 
     current_session.update({ :scopes => scopes }, mode) unless scopes.blank?
@@ -1125,155 +1134,6 @@ def update_session_scopes
       pagination.empty?
   end
 
-  # View methods
-
-  # Generate URL parameters suitable for +url_for+ to update the session scope
-  # named +name+ to match +scope+ (a Scope instance or a hash representation)
-  # via +update_session_scopes+. For example, to change the first filter of the
-  # 'userfiles' scope:
-  #   @scope = scope_from_session('userfiles')
-  #   # ...
-  #   new_scope = @scope.dup
-  #   new_scope.filters[0].operator = '!='
-  #   query_params = scope_params('userfiles', new_scope)
-  # Same as above, using the hash representation of +@scope+:
-  #   @scope = scope_from_session('userfiles')
-  #   # ...
-  #   scope_hash = @scope.to_hash
-  #   scope_hash['filters'][0]['operator'] = '!='
-  #   scope_hash = @scope.class.compact_hash(scope_hash)
-  #   query_params = scope_params('userfiles', scope_hash)
-  # Unless +compress+ is specified as false, the generated URL parameters will
-  # use the compressed format as specified by +compress_scope+.
-  def scope_params(name, scope, compress: true)
-    scope = scope.to_hash if scope.is_a?(Scope)
-    scope = Scope.compact_hash(scope)
-    scope = ScopeHelpers.compress_scope(scope) if compress
-
-    { '_scopes' => { name => scope } }
-  end
-
-  # Generate URL parameters suitable for +url_for+ to update the session scope
-  # named +scope+'s filters (via +update_session_scopes+) via a given
-  # +operation+. +filters+ is expected to be Filter instances or hash
-  # representations (a single filter or an Enumerable), depending on which
-  # +operation+ is to be performed, and +operation+ is expected to be one of:
-  # [+:add+]
-  #  Add one or more +filters+ to the specified scope.
-  # [+:remove+]
-  #  Remove one or more +filters+ from the specified scope.
-  # [+:set+]
-  #  Add one or more +filters+ to the specified scope, replacing existing
-  #  filters filtering on the same attributes as +filters+.
-  # [+:replace+]
-  #  Replace all filters in the specified scope by the ones in +filters+.
-  # [+:clear+]
-  #  Remove all filters in the specified scope (+filters is ignored).
-  #  Equivalent to using +:replace+ with an empty +filters+.
-  #
-  # +scope+ defaults to the current route's scope name (see
-  # +default_scope_name+).
-  #
-  # Note that the generated URL parameters are in compressed format (see
-  # +compress_scope+).
-  def scope_filter_params(operation, filters, scope: nil)
-    scope ||= default_scope_name
-    filters = (filters.is_a?(Array) ? filters : [filters]).map do |filter|
-      filter = filter.to_hash if filter.is_a?(Scope::Filter)
-      Scope::Filter.compact_hash(filter)
-    end
-
-    ScopeHelpers.scope_items_url_params(scope, operation, :filters, filters)
-  end
-
-  # Generate URL parameters suitable for +url_for+ to update the session scope
-  # named +scope+'s ordering rules (via +update_session_scopes+) via a given
-  # +operation+. This method behaves just like +scope_filter_params+, but
-  # operates on a Scope's ordering rules (Order instances or hash representations)
-  # instead of filters. As such, the same +operation+s are available (:add,
-  # :remove, :set, :replace, :clear) and the +scope+ and +orders+ parameters are
-  # handled the exact same way +scope_filter_params+'s +scope+ and +filters+
-  # parameters are handled.
-  def scope_order_params(operation, orders, scope: nil)
-    scope ||= default_scope_name
-    orders = (orders.is_a?(Array) ? orders : [orders]).map do |order|
-      order = order.to_hash if order.is_a?(Scope::Order)
-      Scope::Order.compact_hash(order)
-    end
-
-    ScopeHelpers.scope_items_url_params(scope, operation, :order, orders)
-  end
-
-  # Fetch the possible values (and their count) for +attribute+ within
-  # +collection+, which is either a Ruby Enumerable or ActiveRecord model.
-  # As this method is intended as a view helper to create the list of values to
-  # filter a collection/model with, the possible values are returned as a list
-  # of hashes matching +DynamicTable+'s filter format, containing:
-  # [:value]
-  #  Possible value for +attribute+.
-  # [:label]
-  #  String representation of +:value+ (or just +:value+ if unavailable).
-  # [:indicator]
-  #  Count of how many times this specific +:value: was found for +attribute+ in
-  #  +collection+.
-  #
-  # If +label+ is specified, it is expected to be an attribute name as a string
-  # or symbol (like +attribute+), representing which +collection+ attribute to
-  # use as value labels.
-  #
-  # If +association+ is specified, it is expected to be in the same format as
-  # +Scope+::+Filter+'s *association* attribute, and fulfills roughly the same
-  # purpose; allow +attribute+ and +label+ to refer to attributes on the joined
-  # model (only applicable if +collection+ is an ActiveRecord model).
-  def filter_values_for(collection, attribute, label: nil, association: nil)
-    # TODO Unscoped/base scope/total item count.
-
-    if (collection <= ActiveRecord::Base rescue nil)
-      # Resolve and validate the main +attribute+ to fetch the values of
-      attribute, model = ScopeHelpers.resolve_model_attribute(attribute, collection, association)
-
-      # And +label+, if provided
-      if label
-        label, model = ScopeHelpers.resolve_model_attribute(label, model, association)
-      else
-        label = attribute
-      end
-
-      # NOTE: The 'AS' specifier bypasses Rails' uniq on the column names, which
-      # would remove the label column if label happens to have the same value
-      # as attribute.
-      label_alias = model.connection.quote_column_name('label')
-
-      model
-        .where("#{attribute} IS NOT NULL")
-        .order(attribute, label)
-        .group(attribute, label)
-        .raw_rows(attribute, "#{label} AS #{label_alias}", "COUNT(#{attribute})")
-        .reject { |r| r.first.blank? }
-        .map    { |v, l, c| { :value => v, :label => l, :indicator => c } }
-
-    else
-      # Make sure +attribute+ and +label+ can be accessed in
-      # +collection+'s items.
-      attr_get = ScopeHelpers.generate_getter(collection.first, attribute)
-      raise "no way to get '#{attribute}' out of collection items" unless attr_get
-
-      if label == attribute
-        lbl_get = attr_get
-      else
-        lbl_get = ScopeHelpers.generate_getter(collection.first, label || attribute)
-        raise "no way to get '#{label}' out of collection items" unless lbl_get
-      end
-
-      collection
-        .map     { |i| [attr_get.(i), lbl_get.(i)].freeze }
-        .reject  { |v, l| v.blank? }
-        .sort_by { |v, l| v }
-        .inject(Hash.new(0)) { |h, i| h[i] += 1; h }
-        .map { |(v, l), c| { :value => v, :label => l, :indicator => c } }
-    end
-  end
-
   # Utility/internal methods
 
   # Compress +scope+, which is expected to be a hash representation of a Scope,
@@ -1310,58 +1170,6 @@ def self.decompress_scope(scope)
     scope
   end
 
-  # Generate URL parameters suitable for +url_for+ to update the session scope
-  # named +scope+'s items (ordering or filtering rules). This method is the
-  # internal implementation of +scope_filter_params+ (and +scope_order_params+).
-  # - +operation+ corresponds exactly to +scope_filter_params+'s +operation+
-  # parameter.
-  # - +scope+ corresponds to +scope_filter_params+'s +scope+ parameter, minus
-  # the default value.
-  # - +attr+ is expected to be either :filters, to update scope filtering rules,
-  # or :order, for ordering rules. It corresponds to the Scope attribute name
-  # to apply +changes+ on.
-  # - +changes+ corresponds to +scope_filter_params+'s +changes+ parameter, and
-  # is expected to be an array of compact hash representations of filters
-  # (Scope::Filter) or ordering rules (Scope::Order).
-  #
-  # Note that unlike most other utility methods, this method is exclusively
-  # intended to be used only to implement +scope_filter_params+ and
-  # +scope_order_params+ and is most likely unsuitable for anything else.
-  def self.scope_items_url_params(scope, operation, attr, changes) #:nodoc:
-    return if changes.blank? && operation != :clear
-
-    key  = (attr == :filters ? 'f' : 'o')
-    hash = (
-      case operation
-      when :set
-        replaced  = changes.map { |c| c['a'] }
-        changes  += scope_from_session(scope)
-          .send(attr)
-          .reject { |c| replaced.include?(f.attribute) }
-        { key => changes }
-      when :clear
-        { key => [] }
-      else
-        { key => changes }
-      end
-    )
-
-    mode = (
-      case operation
-      when :add    then :append
-      when :remove then :delete
-      else :replace
-      end
-    )
-
-    {
-      '_scope_mode' => mode,
-      '_scopes' => {
-        scope => ScopeHelpers.compress_scope(hash)
-      }
-    }
-  end
-
   # Generate a getter function (lambda) to directly get the value of +attribute+
   # inside +item+. This method is mainly intended for when +item+ is a sample
   # of a large collection and a way to quickly get the value corresponding to
@@ -1487,8 +1295,9 @@ def self.join_assoc(model, assoc)
     assoc, assoc_attr, model_attr = self.parse_assoc(assoc)
     return [ model, nil ] unless assoc
 
-    # No join columns? Just use a natural join.
-    return [ model.joins(assoc.table_name.to_sym), assoc ] if
+    # No join columns? There should be a relation with a similar name on
+    # the model.
+    return [ model.joins(assoc.table_name.singularize.to_sym), assoc ] if
       assoc_attr.blank? || model_attr.blank?
 
     # Joins columns are specified? Validate them first before joining.
diff --git a/BrainPortal/spec/modules/scope_helpers_spec.rb b/BrainPortal/spec/modules/view_scopes_spec.rb
similarity index 99%
rename from BrainPortal/spec/modules/scope_helpers_spec.rb
rename to BrainPortal/spec/modules/view_scopes_spec.rb
index db4706e85..59f0be2f5 100644
--- a/BrainPortal/spec/modules/scope_helpers_spec.rb
+++ b/BrainPortal/spec/modules/view_scopes_spec.rb
@@ -22,11 +22,11 @@
 
 require 'rails_helper'
 
-describe ScopeHelpers do
+describe ViewScopes do
   # TODO
 end
 
-module ScopeHelpers
+module ViewScopes
   describe Scope do
     # TODO
   end

From b267a2e8a3729ae1661819c9a65576f3cf24bc63 Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Fri, 21 Aug 2015 18:35:21 -0400
Subject: [PATCH 20/85] Issue #184 - CbrainTask properties and untouchable
 params as directives

The new directives are named 'task_properties' and 'untouchable_params',
as suggested in the issue description, and support toggling the property
(task_properties :some_property) and specifying a value (task_properties
:some_property => 1). They are fully compatible with the current API, as
they just define the corresponding API method when called.
---
 BrainPortal/app/models/portal_task.rb | 29 +++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/BrainPortal/app/models/portal_task.rb b/BrainPortal/app/models/portal_task.rb
index 7c77bdb28..6fd752a83 100644
--- a/BrainPortal/app/models/portal_task.rb
+++ b/BrainPortal/app/models/portal_task.rb
@@ -304,7 +304,36 @@ def unpresetable_params_attributes
     {}
   end
 
+  ######################################################
+  # Task properties directives
+  ######################################################
 
+  # Directive version of +self.properties+. +*args+ is
+  # expected to be a list of task properties to enable.
+  #   class SomeTask < PortalTask
+  #     task_properties :a, :b, :c
+  #   end
+  # is equivalent to
+  #   class SomeTask < PortalTask
+  #     def self.properties
+  #       { :a => true, :b => true, :c => true }
+  #     end
+  #   end
+  # See +self.properties+ for a list of available
+  # task properties.
+  def self.task_properties(*args)
+    properties = args.pop if args.last.is_a?(Hash)
+    properties = properties.reverse_merge(args.map { |p| [p, true] }.to_h)
+    define_singleton_method(:properties) { properties }
+  end
+
+  # Directive version of +self.untouchable_params_attributes+.
+  # Similar in behaviour to +self.task_properties+.
+  def self.untouchable_params(*args)
+    params = args.pop if args.last.is_a?(Hash)
+    params = params.reverse_merge(args.map { |p| [p, true] }.to_h)
+    define_method(:untouchable_params_attributes) { params }
+  end
 
   ######################################################
   # Wrappers around official API

From 25fd1bce5141369cd659b4760d747b0699e5c83d Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Mon, 24 Aug 2015 10:49:08 -0400
Subject: [PATCH 21/85] Issue #188 - Directive for unpresetable parameters

The new directive is named unpresetable_params, and redefines
untouchable_params_attributes, just like the two other property
directives. This changeset also refactors directive definition into a
lambda.
---
 BrainPortal/app/models/portal_task.rb | 40 +++++++++++++++++----------
 1 file changed, 25 insertions(+), 15 deletions(-)

diff --git a/BrainPortal/app/models/portal_task.rb b/BrainPortal/app/models/portal_task.rb
index 6fd752a83..a9b918a12 100644
--- a/BrainPortal/app/models/portal_task.rb
+++ b/BrainPortal/app/models/portal_task.rb
@@ -308,9 +308,15 @@ def unpresetable_params_attributes
   # Task properties directives
   ######################################################
 
-  # Directive version of +self.properties+. +*args+ is
-  # expected to be a list of task properties to enable.
+  # Create a property directive named +name+ for property method +method+
+  # (property methods are methods expected to return property hashes, such
+  # as +untouchable_params_attributes+ and +unpresetable_params_attributes+).
+  # If +instance_method+ is given, an instance method is created for the
+  # property instead of a class method.
+  #
   #   class SomeTask < PortalTask
+  #     property_directive.(:task_properties, :properties)
+  #     # ...
   #     task_properties :a, :b, :c
   #   end
   # is equivalent to
@@ -319,22 +325,26 @@ def unpresetable_params_attributes
   #       { :a => true, :b => true, :c => true }
   #     end
   #   end
-  # See +self.properties+ for a list of available
-  # task properties.
-  def self.task_properties(*args)
-    properties = args.pop if args.last.is_a?(Hash)
-    properties = properties.reverse_merge(args.map { |p| [p, true] }.to_h)
-    define_singleton_method(:properties) { properties }
-  end
+  property_directive = lambda do |name, method, instance_method: false|
+    define_singleton_method(name) do |*args|
+      props = args.pop if args.last.is_a?(Hash)
+      props = props.reverse_merge(args.map { |p| [p, true] }.to_h)
 
-  # Directive version of +self.untouchable_params_attributes+.
-  # Similar in behaviour to +self.task_properties+.
-  def self.untouchable_params(*args)
-    params = args.pop if args.last.is_a?(Hash)
-    params = params.reverse_merge(args.map { |p| [p, true] }.to_h)
-    define_method(:untouchable_params_attributes) { params }
+      if instance_method
+        define_method(method) { props }
+      else
+        define_singleton_method(method) { props }
+      end
+    end
   end
 
+  # Directive versions of +self.properties+, +untouchable_params_attributes+ and
+  # +unpresetable_params_attributes+. See +property_directive+ for more
+  # information on how they are used.
+  property_directive.(:task_properties,     :properties)
+  property_directive.(:untouchable_params,  :untouchable_params_attributes,  instance_method: true)
+  property_directive.(:unpresetable_params, :unpresetable_params_attributes, instance_method: true)
+
   ######################################################
   # Wrappers around official API
   # These are not to be called by subtasks nor

From 97d8c876f3b07b4800eb87b62fbacc59e7b512ce Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Mon, 24 Aug 2015 16:23:40 -0400
Subject: [PATCH 22/85] Issue #199 - Broken 'switch to batch view' link

Caused by an overly general handler in cbrain.js (.pagination a)
catching links in pagination_left_side and pagination_right_side. This
caused the request to be sent twice, leading to the odd observed
behavior.

This changeset also removes another unused _pagination partial.
---
 .../app/views/tasks/_pagination.html.erb      | 42 -------------------
 BrainPortal/public/javascripts/cbrain.js      |  2 +-
 2 files changed, 1 insertion(+), 43 deletions(-)
 delete mode 100644 BrainPortal/app/views/tasks/_pagination.html.erb

diff --git a/BrainPortal/app/views/tasks/_pagination.html.erb b/BrainPortal/app/views/tasks/_pagination.html.erb
deleted file mode 100644
index f6691927d..000000000
--- a/BrainPortal/app/views/tasks/_pagination.html.erb
+++ /dev/null
@@ -1,42 +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 <http://www.gnu.org/licenses/>.  
-#
--%>
-
-<div class="pagination_left_side">
-  <% if @filter_params["sort_hash"]["order"] == 'cbrain_tasks.batch' %>
-    <strong>Currently in Batch View</strong>
-  <% end %>  
-</div>
-<div class="page_links">
-  <%= will_paginate @paginated_list, :container => false %>
-  (<%= pluralize @total_tasks, "task" %>)
-</div>
-<div class="pagination_right_side">
-  <% if @total_space_known > 0 %>
-  Total task space used: <%= colored_pretty_size(@total_space_known) %>
-  <% end %>
-  <% if @total_space_unkn  > 0 %>
-  (<%= pluralize @total_space_unkn, "task" %> without space estimates)
-  <% end %>
-</div>
-
diff --git a/BrainPortal/public/javascripts/cbrain.js b/BrainPortal/public/javascripts/cbrain.js
index 8e4effce7..7cf8bf5d3 100644
--- a/BrainPortal/public/javascripts/cbrain.js
+++ b/BrainPortal/public/javascripts/cbrain.js
@@ -517,7 +517,7 @@
       return page;
     }
     
-    $(document).delegate(".pagination a", "click", function() {
+    $(document).delegate(".page_links > a", "click", function() {
       var link = $(this);
       var url = link.attr("href");
       var page_param = get_page_parameter(url);

From 583950ae257865fd000f6456d2dd3456dcbad504 Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Fri, 28 Aug 2015 14:22:59 -0400
Subject: [PATCH 23/85] Added IRB enhancement gem Pry

Along with debugger mode (pry-byebug) and extended documentation
(pry-doc). Use `binding.pry` anywhere in the code to invoke a Pry
console when hit.
---
 BrainPortal/Gemfile | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/BrainPortal/Gemfile b/BrainPortal/Gemfile
index 6ccecd58f..6f4a92892 100644
--- a/BrainPortal/Gemfile
+++ b/BrainPortal/Gemfile
@@ -40,6 +40,9 @@ group :development do
   gem "wirble"
   gem "looksee"
   gem "hirb"
+  gem "pry"
+  gem "pry-byebug"
+  gem "pry-doc"
 end
 
 group :test do

From 04683a9b4783297580d6639e3a845d114eb6de53 Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Fri, 28 Aug 2015 14:31:39 -0400
Subject: [PATCH 24/85] Various bugfixes and small enhancements for Scopes

- name attribute for Scope (avoids scope_from_session calls)
- Helpers can now take Scope instances instead of names
- Fixed some incorrect documentation (and examples)
- Reworked CbrainSession's update method (now named apply_changes) to
  better match what is required.
- to_hash and compact_hash no longer return HashWithIndifferentAccess
  instances.
- Pagination attributes now default to nil instead of 0
- Parameter _pag_scope_name for the scope to update with page/per_page
- Missing to_hash in scope_items_url_params
---
 BrainPortal/app/helpers/scope_helper.rb  |  72 ++++++-----
 BrainPortal/app/models/cbrain_session.rb | 150 +++++++++++++++--------
 BrainPortal/lib/view_scopes.rb           | 127 +++++++++++--------
 3 files changed, 216 insertions(+), 133 deletions(-)

diff --git a/BrainPortal/app/helpers/scope_helper.rb b/BrainPortal/app/helpers/scope_helper.rb
index d0740622e..67e3102a3 100644
--- a/BrainPortal/app/helpers/scope_helper.rb
+++ b/BrainPortal/app/helpers/scope_helper.rb
@@ -29,6 +29,9 @@ module ScopeHelper
 
   Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
 
+  # Internal alias to ease access to ViewScopes::Scope and its inner classes.
+  Scope = ViewScopes::Scope
+
   # Generate URL parameters suitable for +url_for+ to update the session scope
   # named +name+ to match +scope+ (a Scope instance or a hash representation)
   # via +update_session_scopes+. For example, to change the first filter of the
@@ -43,7 +46,6 @@ module ScopeHelper
   #   # ...
   #   scope_hash = @scope.to_hash
   #   scope_hash['filters'][0]['operator'] = '!='
-  #   scope_hash = @scope.class.compact_hash(scope_hash)
   #   query_params = scope_params('userfiles', scope_hash)
   # Unless +compress+ is specified as false, the generated URL parameters will
   # use the compressed format as specified by +compress_scope+.
@@ -56,10 +58,10 @@ def scope_params(name, scope, compress: true)
   end
 
   # Generate URL parameters suitable for +url_for+ to update the session scope
-  # named +scope+'s filters (via +update_session_scopes+) via a given
-  # +operation+. +filters+ is expected to be Filter instances or hash
-  # representations (a single filter or an Enumerable), depending on which
-  # +operation+ is to be performed, and +operation+ is expected to be one of:
+  # +scope+'s filters (via +update_session_scopes+) via a given +operation+.
+  # +filters+ is expected to be Filter instances or hash representations (a
+  # single filter or an Enumerable), depending on which +operation+ is to be
+  # performed, and +operation+ is expected to be one of:
   # [+:add+]
   #  Add one or more +filters+ to the specified scope.
   # [+:remove+]
@@ -73,52 +75,59 @@ def scope_params(name, scope, compress: true)
   #  Remove all filters in the specified scope (+filters is ignored).
   #  Equivalent to using +:replace+ with an empty +filters+.
   #
-  # +scope+ defaults to the current route's scope name (see
-  # +default_scope_name+).
+  # +scope+ is expected to be either the name of a session scope to be fetched
+  # using +scope_from_session+ or a Scope object with a valid *name* attribute.
+  # Falls back on +default_scope_name+ if nil.
   #
   # Note that the generated URL parameters are in compressed format (see
   # +compress_scope+).
-  def scope_filter_params(operation, filters, scope: nil)
-    scope ||= default_scope_name
+  def scope_filter_params(scope, operation, filters)
+    scope = scope_from_session(scope || default_scope_name) unless
+      scope.is_a?(Scope)
+
     filters = (filters.is_a?(Array) ? filters : [filters]).map do |filter|
       filter = filter.to_hash if filter.is_a?(Scope::Filter)
       Scope::Filter.compact_hash(filter)
     end
 
-    ScopeHelper.scope_items_url_params(scope, operation, :filters, filters)
+    scope_items_url_params(scope, operation, :filters, filters)
   end
 
   # Generate URL parameters suitable for +url_for+ to update the session scope
-  # named +scope+'s ordering rules (via +update_session_scopes+) via a given
+  # +scope+'s ordering rules (via +update_session_scopes+) via a given
   # +operation+. This method behaves just like +scope_filter_params+, but
   # operates on a Scope's ordering rules (Order instances or hash representations)
   # instead of filters. As such, the same +operation+s are available (:add,
   # :remove, :set, :replace, :clear) and the +scope+ and +orders+ parameters are
   # handled the exact same way +scope_filter_params+'s +scope+ and +filters+
   # parameters are handled.
-  def scope_order_params(operation, orders, scope: nil)
-    scope ||= default_scope_name
+  def scope_order_params(scope, operation, orders)
+    scope = scope_from_session(scope || default_scope_name) unless
+      scope.is_a?(Scope)
+
     orders = (orders.is_a?(Array) ? orders : [orders]).map do |order|
       order = order.to_hash if order.is_a?(Scope::Order)
       Scope::Order.compact_hash(order)
     end
 
-    ScopeHelper.scope_items_url_params(scope, operation, :order, orders)
+    scope_items_url_params(scope, operation, :order, orders)
   end
 
   # Generate URL parameters suitable for +url_for+ to update the session
-  # scope named +scope+'s custom attributes with +custom+ (expected to be
-  # a hash of attributes to merge in) using CbrainSession's +update+ method.
+  # +scope+ custom attributes with +custom+ (expected to be a hash of attributes
+  # to merge in) using CbrainSession's +apply_changes+ method.
   #
-  # +scope+ defaults to the current route's scope name (see
-  # +default_scope_name+).
+  # +scope+ is expected to be either the name of a session scope to be fetched
+  # using +scope_from_session+ or a Scope object with a valid *name* attribute.
+  # Falls back on +default_scope_name+ if nil.
   #
   # Note that as with +scope_filter_params+ and +scope_order_params+, the
   # generated URL parameters are compressed using +compress_scope+.
-  def scope_custom_params(custom, scope: nil)
-    scope ||= default_scope_name
+  def scope_custom_params(scope, custom)
+    name   = scope.name if scope.is_a?(Scope)
+    name ||= scope || default_scope_name
 
-    { '_scopes' => { scope => ViewScopes.compress_scope({
+    { '_scopes' => { name => ViewScopes.compress_scope({
       'c' => custom
     }) } }
   end
@@ -129,8 +138,6 @@ def scope_custom_params(custom, scope: nil)
   # could have a string representation of 'User: admin' while one for
   # +:status in ['A', 'B', 'C']+ could have 'Status: one of A, B or C'.
   #
-  # TODO Ruby collections
-  #
   # Note that this method is rather inflexible on how the representations
   # are generated and relies on internal mappings for certain known
   # attributes, values and associations.
@@ -302,13 +309,13 @@ def filter_values_for(collection, attribute, label: nil, association: nil)
 
   # Utility/internal methods
 
-  # Generate URL parameters suitable for +url_for+ to update the session scope
-  # named +scope+'s items (ordering or filtering rules). This method is the
-  # internal implementation of +scope_filter_params+ (and +scope_order_params+).
+  # Generate URL parameters suitable for +url_for+ to update the session +scope+
+  # items (ordering or filtering rules). This method is the internal
+  # implementation of +scope_filter_params+ (and +scope_order_params+).
   # - +operation+ corresponds exactly to +scope_filter_params+'s +operation+
   # parameter.
-  # - +scope+ corresponds to +scope_filter_params+'s +scope+ parameter, minus
-  # the default value.
+  # - +scope+ is a Scope object corresponding to +scope_filter_params+'s +scope+
+  # parameter.
   # - +attr+ is expected to be either :filters, to update scope filtering rules,
   # or :order, for ordering rules. It corresponds to the Scope attribute name
   # to apply +changes+ on.
@@ -319,7 +326,7 @@ def filter_values_for(collection, attribute, label: nil, association: nil)
   # Note that unlike most other utility methods, this method is exclusively
   # intended to be used only to implement +scope_filter_params+ and
   # +scope_order_params+ and is most likely unsuitable for anything else.
-  def self.scope_items_url_params(scope, operation, attr, changes) #:nodoc:
+  def scope_items_url_params(scope, operation, attr, changes) #:nodoc:
     return if changes.blank? && operation != :clear
 
     key  = (attr == :filters ? 'f' : 'o')
@@ -327,9 +334,10 @@ def self.scope_items_url_params(scope, operation, attr, changes) #:nodoc:
       case operation
       when :set
         replaced  = changes.map { |c| c['a'] }
-        changes  += scope_from_session(scope)
+        changes  += scope
           .send(attr)
-          .reject { |c| replaced.include?(f.attribute) }
+          .reject { |c| replaced.include?(c.attribute) }
+          .map    { |c| c.to_hash(compact: true) }
         { key => changes }
       when :clear
         { key => [] }
@@ -349,7 +357,7 @@ def self.scope_items_url_params(scope, operation, attr, changes) #:nodoc:
     {
       '_scope_mode' => mode,
       '_scopes' => {
-        scope => ViewScopes.compress_scope(hash)
+        scope.name => ViewScopes.compress_scope(hash)
       }
     }
   end
diff --git a/BrainPortal/app/models/cbrain_session.rb b/BrainPortal/app/models/cbrain_session.rb
index 083c104fe..609627240 100644
--- a/BrainPortal/app/models/cbrain_session.rb
+++ b/BrainPortal/app/models/cbrain_session.rb
@@ -116,74 +116,128 @@ def []=(key, value) #:nodoc:
     @session[key] = value
   end
 
-  # Update sessions attributes from the contents of +hash+. While similiar to
-  # Hash's merge method, this method has a few key differences:
+  # Update sessions attributes from the contents of +changes+. +changes+ is
+  # expected to be either a +hash+ of attributes to update, a +mode+ and a
+  # +hash+ (pair) or a list of those to be applied in order:
+  #   apply_changes({ ... }) # Single hash
+  #   apply_changes([:delete, { ... }]) # Pair
+  #   apply_changes([{ ... }, { ... }]) # List of hashes
+  #   apply_changes([[:append, { ... }], [:delete, { ... }]]) # List of pairs
+  #
+  # While similiar to Hash's merge method, this method has a few key
+  # differences:
   #
   # - Hashes in +hash+ and session attributes are recursively merged:
   #     @session # { :a => { :b => 1 } }
   #     update({ :a => { :c => 1 } })
   #     @session # { :a => { :b => 1, :c => 1 } }
   #
-  # - update does not accept a block; session attributes are always overwritten
-  #   by their new value in +hash+, if present.
-  #
   # - nil values are automatically removed from hashes to avoid clutter. This
   #   cleanly allows removing keys from hashes:
   #     @session # { :a => { :b => 1 } }
   #     update({ :a => { :b => nil } })
   #     @session # { :a => {} }
   #
-  # - collection (Array, Set) collision handling is based on +collection_mode+,
-  #   which is one of:
+  # - update does not accept a block; session attributes are always overwritten
+  #   by their new value in +hash+, if present.
   #
-  #   [:replace]
-  #    Handle collections just like regular values; replace the entire
-  #    collection with the new one in +hash+:
-  #      @session # { :a => [1] }
-  #      update({ :a => [2] }, :replace)
-  #      @session # { :a => [2] }
+  # +mode+ determines what kind of update should be performed. The possible
+  # +mode+s are:
   #
-  #   [:append]
-  #    Append the values in +hash+'s collection to the corresponding one in
-  #    the session attributes.
-  #      @session # { :a => [1] }
-  #      update({ :a => [2] }, :append)
-  #      @session # { :a => [1, 2] }
+  # [:replace]
+  #  Replace colliding values in session attributes from the ones in +hash+,
+  #  regardless of their type (default mode).
   #
-  #   [:delete]
-  #    Opposite of append; remove the values in +hash+'s collection from the
-  #    corresponding one in the session attributes.
-  #      @session # { :a => [1] }
-  #      update({ :a => [1, 2] }, :delete)
-  #      @session # { :a => [2] }
-  def update(hash, collection_mode = :replace)
-    (update = lambda do |base, new|
+  # [:append]
+  #  Replace colliding values, as in +:replace+, except when at least one of
+  #  them is a collection (Array or Set), in which case the resulting value
+  #  is the union of both collections (or the collection and the element).
+  #
+  # [:delete]
+  #  Remove any non-colliding value present in +hash+ from session
+  #  attributes, except for collections (Array or Set), from which the elements
+  #  in +changes+ are substracted.
+  #
+  # While oddly specified, this method is hopefully intuitive to use and allow
+  # a wide range of operations from just an input hash and a mode switch.
+  # For example:
+  #   # Adding a key to the session
+  #   @session # { :a => 1 }
+  #   apply_changes({ :b => 2 })
+  #   @session # { :a => 1, :b => 2 }
+  #
+  #   # Adding an element to an array in the session
+  #   @session # { :a => { :c => [1] } }
+  #   apply_changes([:append, { :a => { :c => [2] } }])
+  #   @session # { :a => { :c => [1, 2] } }
+  #
+  #   # Removing keys from the session
+  #   @session # { :a => { :c => 1, :d => 2 } }
+  #   apply_changes([:delete, { :a => { :c => nil, :d => 2 } }])
+  #   @session # { :a => {} }
+  def apply_changes(changes)
+    # At least one of +vars+ is one of +classes+
+    any_of = lambda do |vars, classes|
+      vars.any? { |v| classes.any? { |c| v.is_a?(c) } }
+    end
+    # Every element of +vars+ is one of +classes+
+    all_of = lambda do |vars, classes|
+      vars.all? { |v| classes.any? { |c| v.is_a?(c) } }
+    end
+
+    # Apply the changes +new+ to +base+ (respecting +mode+) recursively.
+    apply = lambda do |base, new, mode|
+      # Avoid adding new keys when merging in delete mode
+      new.select! { |k,v| base.has_key?(k) } if mode == :delete
+
       base.merge!(new) do |key, old, new|
-        next new unless old.is_a?(new.class) || new.is_a?(old.class)
-
-        case old
-        when Hash
-          update.(old, new)
-        when Set, Array
-          case collection_mode
-          when :replace
-            new
-          when :append
-            old + new
-          when :delete
-            old - new
-          end
-        else
-          new
+        # Recursively merge hashes with the same key
+        next apply.(old, new, mode) if old.is_a?(Hash) && new.is_a?(Hash)
+
+        # Unless one of the values is a collection, the old value is replaced
+        # by the new one (or nil, when deleting).
+        next (mode == :delete ? nil : new) unless (
+          all_of.([new, old], [Set, Array, NilClass]) &&
+          any_of.([new, old], [Set, Array]) &&
+          [:append, :delete].include?(mode)
+        )
+
+        # Ensure both values exist before trying to merge them
+        old ||= new.class.new
+        new ||= old.class.new
+        new   = new.to_a if old.is_a?(Array)
+
+        # Merge both collections
+        case mode
+        when :append then old + new
+        when :delete then old - new
         end
       end
 
-      base.delete_if { |k,v| v.nil? }
+      # Clear out nil values to avoid cluttering
+      base.reject! { |k,v| v.nil? }
       base
-    end).(
-      @session,
-      hash.reject { |k,v| self.class.internal_keys.include?(k) }
-    )
+    end
+
+    # Is +obj+ a symbol-hash pair? ([Symbol, Hash])
+    is_pair = lambda do |obj|
+      obj.is_a?(Array) &&
+      obj.size == 2 &&
+      obj.first.is_a?(Symbol) &&
+      obj.last.is_a?(Hash)
+    end
+
+    # Push each changeset through the update lambda (removing internal_keys
+    # beforehand).
+    changes = [changes] if is_pair.(changes)
+    changes = [[:replace, changes]] if changes.is_a?(Hash)
+    changes.each do |mode, change|
+      apply.(
+        @session,
+        change.reject { |k,v| self.class.internal_keys.include?(k) },
+        mode || :replace
+      )
+    end
   end
 
   # Clear out all session attributes bar those used for tracking (IP, host,
diff --git a/BrainPortal/lib/view_scopes.rb b/BrainPortal/lib/view_scopes.rb
index e47f2eb64..d49be4190 100644
--- a/BrainPortal/lib/view_scopes.rb
+++ b/BrainPortal/lib/view_scopes.rb
@@ -48,15 +48,15 @@
 #
 # Currently active/known scopes are stored in Rails' session as a hash with
 # scope names for keys and scope hash definitions/representations as values:
-#   current_session[:scopes] == {
+#   current_session['scopes'] == {
 #     'userfiles' => { 'f' => [ ... ], 'o' => ... },
 #     'tasks'     => { 'f' => [ ... ], 'o' => ... },
 #     ...
 #   }
 # To directly add or replace one of the session scopes, convert the scope to a
 # compact hash representation first before adding to
-# +current_session[:scopes]+:
-#   current_session[:scopes]['tasks'] = scope.to_hash(compact: true)
+# +current_session['scopes']+:
+#   current_session['scopes']['tasks'] = scope.to_hash(compact: true)
 #
 # Scopes created from hashes and session attributes are automatically sanitized
 # and it is thus safe to pass user-supplied values to create them.
@@ -75,7 +75,11 @@ module ViewScopes
   # exposing +scope_from_session+, +scope_to_session+ and +default_scope_name+.
   def self.included(includer) #:nodoc:
     includer.class_eval do
-      helper_method(:default_scope_name)
+      helper_method(
+        :default_scope_name,
+        :scope_from_session,
+        :scope_to_session
+      )
 
       before_filter(:update_session_scopes)
     end
@@ -87,6 +91,16 @@ def self.included(includer) #:nodoc:
   # +scope_from_session+).
   class Scope
 
+    # Name of this scope in Rails' session. This attribute is transient, not
+    # present in any hash representation and is only used to keep track of
+    # which session scope hash representation it was generated from. It notably
+    # allows keeping track of the active session scope in a controller without
+    # having to carry the name around.
+    #
+    # Note that this attribute is entirely optional and does not influence the
+    # operation of Scope's methods in any way.
+    attr_accessor :name
+
     # Filters this scope filters the collection or model with. Instances of
     # Scope::Filter, each represents a single filtering rule to apply.
     #
@@ -281,7 +295,7 @@ def to_hash(compact: false)
         'order'      => @order.map(&:to_hash),
         'pagination' => @pagination.try(:to_hash),
         'selection'  => @selection,
-        'custom'     => @custom.stringify_keys,
+        'custom'     => @custom.stringify_keys.to_h,
         'filter_combination' => @filter_combination.to_s,
       }
 
@@ -314,8 +328,8 @@ def self.compact_hash(hash)
         'p' => Pagination.compact_hash(hash['pagination'] || hash['p']),
 
         # Include other attributes
-        's'  => hash['s']  || hash['selection'],
-        'c'  => hash['c']  || hash['custom'],
+        's'  =>  hash['s']  || hash['selection'],
+        'c'  => (hash['c']  || hash['custom']).stringify_keys.to_h,
         'fc' => (hash['fc'] || hash['filter_combination']).to_s,
       }
 
@@ -909,8 +923,8 @@ def apply(collection)
           (collection <= ActiveRecord::Base rescue nil)
 
         # Clamp @page and @per_page to a sane range
-        page     = [1,  [@page,     99_999].min].max
-        per_page = [25, [@per_page, 1000  ].min].max
+        page     = [1,  [@page.to_i,     99_999].min].max
+        per_page = [25, [@per_page.to_i, 1000  ].min].max
 
         collection.paginate(
           :page          => page,
@@ -943,9 +957,9 @@ def self.from_hash(hash)
           hash.is_a?(HashWithIndifferentAccess)
 
         pagination = self.new
-        pagination.page     = (hash['i'] || hash['page'] || 1).to_i
-        pagination.per_page = (hash['p'] || hash['per_page']).to_i
-        pagination.total    = (hash['t'] || hash['total']).to_i
+        pagination.page     = Integer(hash['i'] || hash['page'] || 1) rescue nil
+        pagination.per_page = Integer(hash['p'] || hash['per_page'])  rescue nil
+        pagination.total    = Integer(hash['t'] || hash['total'])     rescue nil
         pagination
       end
 
@@ -957,9 +971,9 @@ def self.from_hash(hash)
       # See Scope's +to_hash+ method for further information.
       def to_hash(compact: false)
         hash = {
-          'page'     => @page.to_i,
-          'per_page' => @per_page.to_i,
-          'total'    => @total.to_i
+          'page'     => (@page.to_i     if @page),
+          'per_page' => (@per_page.to_i if @per_page),
+          'total'    => (@total.to_i    if @total)
         }
 
         compact ? self.class.compact_hash(hash) : hash
@@ -1019,7 +1033,7 @@ def self.generic_compact_hash(hash, keys, values: {}, defaults: {})
       # Make sure +hash+ is proper
       return nil unless hash.is_a?(Hash)
 
-      compact = hash.stringify_keys
+      compact = hash.stringify_keys.to_h
 
       hash = hash.with_indifferent_access unless
         hash.is_a?(HashWithIndifferentAccess)
@@ -1046,25 +1060,27 @@ def self.generic_compact_hash(hash, keys, values: {}, defaults: {})
   end
 
   # Create a new Scope from the hash-based session scope definition named +name+
-  # stored in Rails' session object (+:scopes+ key), invoking Scope's
+  # stored in Rails' session object (+scopes+ key), invoking Scope's
   # +from_hash+ method to create the Scope instance. If +name+ is not present in
   # the session, an empty Scope is created instead. +name+ defaults to the
   # default scope name; +default_scope_name+.
   def scope_from_session(name = nil)
-    name ||= default_scope_name
-    scopes = (current_session[:scopes] ||= {})
-    hash   = (scopes[name] ||= {})
-    Scope.from_hash(hash)
+    name   ||= default_scope_name
+    scopes   = (current_session['scopes'] ||= {})
+    hash     = (scopes[name] ||= {})
+
+    Scope.from_hash(hash).tap { |s| s.name = name }
   end
 
   # Store a +scope+ under the name +name+ in compact hash form in Rails' session
-  # object (+:scopes+ key), invoking the scope's +to_hash+ method to convert
+  # object (+scopes+ key), invoking the scope's +to_hash+ method to convert
   # to Scope instance to a hash. If +name+ is already present in the session's
-  # scopes, the old scope is replaced by +scope+. +name+ defaults to the
-  # default scope name; +default_scope_name+
+  # scopes, the old scope is replaced by +scope+. +name+ defaults to the scope's
+  # *name* attribute or (if unset) to the default scope name
+  # (+default_scope_name+).
   def scope_to_session(scope, name = nil)
-    name ||= default_scope_name
-    scopes = (current_session[:scopes] ||= {})
+    name   ||= scope.name || default_scope_name
+    scopes   = (current_session['scopes'] ||= {})
     scopes[name] = scope.to_hash(compact: true)
   end
 
@@ -1076,7 +1092,7 @@ def default_scope_name
   end
 
   # Update the hash-based scope definitions stored in Rails' session (under the
-  # +:scopes+ key) using scope-specific query parameters.
+  # +scopes+ key) using scope-specific query parameters.
   # This method, called just before any action (as a before_filter), allows
   # updating the session's view scopes just before the control is handed to the
   # controller.
@@ -1084,53 +1100,58 @@ def default_scope_name
   # The following query parameters are recognized by +update_session_scopes+:
   #
   # [_scopes]
-  #  Expected to be a hash to be merged in the session's scopes (:scopes) as
-  #  specified by CbrainSession's +update+ method.
+  #  Expected to be a hash of changes to be merged in the session's scopes as
+  #  specified by CbrainSession's +apply_changes+ method.
   #
-  # [_cur_scope]
-  #  Expected to be a hash to be merged in the current route's scope
-  #  (current_session[:scopes][+default_scope_name+]). Behaves similarly to
-  #  +_scopes+, as it too uses CbrainSession's +update+ method.
+  # [_default_scope]
+  #  Expected to be a hash to be merged in the current route's default scope
+  #  (current_session['scopes'][+default_scope_name+]). Behaves similarly to
+  #  +_scopes+, as it too uses CbrainSession's +apply_changes+ method.
   #
   # [_scope_mode]
-  #  Mode to merge array/collections when merging into session scopes using
-  #  +_scopes+ or +_cur_scope+. Corresponds to the collection_mode parameter
-  #  of CbrainSession's +update+ method. Defaults to 'replace'.
+  #  Merging mode to employ when merging into session scopes using +_scopes+ or
+  #  +_default_scope+. Corresponds to the mode parameter of CbrainSession's
+  #  +apply_changes+ method. Defaults to 'replace'.
   #
-  # [page, per_page]
-  #  Common pagination parameters to update the current route's default scope
+  # [page, per-page/per_page]
+  #  Common pagination parameters to update the scope named _pag_scope_name
   #  with. These parameters correspond to the *page* and *per_page* attributes
   #  of Scope::Pagination, and are handled purely for convenience and
   #  convention; the same functionality (and more) can be accessed by
   #  passing a hash to the +_scopes+ parameter instead.
   #
-  # Note that the scopes in +_cur_scope+ and +_scopes+ can be in
+  # [_pag_scope_name]
+  #  Name of the scope to update with the page and per-page/per_page parameters.
+  #  Defaults to the current route's default scope name (+default_scope_name+).
+  #
+  # Note that the scopes in +_default_scope+ and +_scopes+ can be in
   # compressed format (see the +compress_scope+ and +decompress_scope+ utility
   # methods).
   def update_session_scopes
-    default = default_scope_name
-    mode    = params['_scope_mode'].to_sym if
+    mode   = params['_scope_mode'].to_sym if
         [ 'append', 'delete', 'replace' ].include?(params['_scope_mode'])
-    mode  ||= :replace
+    mode ||= :replace
 
-    # Decompress (if required) and merge _scopes and _cur_scope
-    scopes = (params['_scopes'] || {})
-    scopes.merge!({ default => params['_cur_scope'] }) if params['_cur_scope']
+    # Decompress (if required) and merge _scopes and _default_scope
+    scopes = (params['_scopes'] || {}).deep_dup
+    scopes.merge!({ default_scope_name => params['_default_scope'] }) if
+      params['_default_scope']
     scopes = scopes.map do |n, s|
       return [n, s] if s.is_a?(Hash)
       [ n, (ViewScopes.decompress_scope(s) rescue s) ]
     end.to_h
 
-    current_session.update({ :scopes => scopes }, mode) unless scopes.blank?
+    current_session.apply_changes([mode, { 'scopes' => scopes }]) unless scopes.blank?
 
-    # Pagination parameters (which override _scopes and _cur_scope)
+    # Pagination parameters (which override _scopes and _default_scope)
     pagination = {}
     pagination['i'] = params['page']     if params['page']
+    pagination['p'] = params['per-page'] if params['per-page']
     pagination['p'] = params['per_page'] if params['per_page']
 
-    current_session.update({
-      :scopes => { default => { 'p' => pagination } }
-    }, mode) unless
+    current_session.apply_changes({ 'scopes' => {
+      (params['_pag_scope_name'] || default_scope_name) => { 'p' => pagination }
+    } }) unless
       pagination.empty?
   end
 
@@ -1149,9 +1170,9 @@ def self.compress_scope(scope)
     scope = ActiveSupport::Gzip.compress(scope)
     scope = Base64.encode64(scope)
     scope
-      .tr('+/', '-_')
-      .sub(/=*$/, '')
-      .gsub(/\s/, '')
+      .tr('+/',  '-_')
+      .gsub(/=+$/, '')
+      .gsub(/\s/,  '')
   end
 
   # Decompress +scope+, which is expected to be a scope string compressed by

From 56aa2962e6549be67780697ebb92508c0e074c80 Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Fri, 28 Aug 2015 14:43:22 -0400
Subject: [PATCH 25/85] Scope-backed dynamic_table helper

The new helper, dynamic_scoped_table, is similar in behavior to
dynamic_index_table; it extends dynamic_table with native integration
for the new scope-based filtering mechanism; the options `order_map`
and `filter_map` can be used to specify which Order and Filter instances
to use for sorting and filtering links while `scope` corresponds to the
currently active scope to fetch the current sorting order and target
scope name from.

This changeset also include a few bugfixes for dynamic table's ERB
template.
---
 .../app/helpers/dynamic_table_helper.rb       | 153 ++++++++++++++++++
 .../app/views/shared/_dynamic_table.html.erb  |  17 +-
 2 files changed, 162 insertions(+), 8 deletions(-)

diff --git a/BrainPortal/app/helpers/dynamic_table_helper.rb b/BrainPortal/app/helpers/dynamic_table_helper.rb
index 3c022d728..057c116db 100644
--- a/BrainPortal/app/helpers/dynamic_table_helper.rb
+++ b/BrainPortal/app/helpers/dynamic_table_helper.rb
@@ -1063,4 +1063,157 @@ def dynamic_index_table(collection, options = {}, &block)
     (options.has_key?(:render) && ! options[:render]) ? table : table.render
   end
 
+  # Specialization of +dynamic_table+ (and DynamicTable) to make creating
+  # tables using the view scopes mechanism (see the ViewScopes module) easier
+  # by supplying sort_targer and filter_target lambda functions using Scope
+  # filtering and ordering rules.
+  # This method's parameters are the same as +dynamic_table+'s, with the
+  # following additional options:
+  #
+  # [scope]
+  #  Session scope to use for filtering, sorting and pagination targets. Either
+  #  a Scope object with a valid *name* attribute or the name of a scope to
+  #  fetch from scope_from_session. Defaults to the instance variable @scope
+  #  (if it exists and is a Scope with a valid name) or the route's default
+  #  scope (see default_scope_name).
+  #
+  # [order_map]
+  #  Mapping (hash) of column names to ViewScopes::Scope::Order objects (or
+  #  their hash representations). These objects will be used with
+  #  scope_order_params to create sorting links updating the scope named
+  #  scope_name. Columns default to an Order object sorting on the column name
+  #  (the object's attribute is the column name). Note that the Order object's
+  #  direction is automatically set to the opposite of the current value or
+  #  :asc if empty.
+  #
+  # [filter_map]
+  #  Similarly to order_map, filter_map is a mapping of column names to
+  #  ViewScopes::Scope::Filter objects (or hash representations). It is handled
+  #  the same way as order_map, except for acting on filtering rules instead of
+  #  ordering ones, using scope_filter_params to create links. Note that the
+  #  Filter object's value is automatically set to the selected filter's value.
+  #
+  # This method customizes:
+  # * sort_target and filter_target using scope_*_params
+  # * fetching the sorting order and column
+  # * scope name used for pagination-related requests
+  def dynamic_scoped_table(collection, options = {}, &block)
+    scope = options[:scope] || @scope || default_scope_name
+    scope = scope_from_session(scope) unless scope.is_a?(ViewScopes::Scope)
+    order_map  = (options[:order_map]  || {}).with_indifferent_access
+    filter_map = (options[:filter_map] || {}).with_indifferent_access
+
+    # Fetch (order_map) or create an Order object for column +column+
+    column_order = lambda do |column|
+      order = order_map[column] || { :attribute => column }
+      order = ViewScopes::Scope::Order.from_hash(order) unless
+        order.is_a?(ViewScopes::Scope::Order)
+      order
+    end
+
+    # Fetch (filter_map) or create a Filter object for column +column+
+    column_filter = lambda do |column|
+      filter = filter_map[column] || { :attribute => column }
+      filter = ViewScopes::Scope::Filter.from_hash(filter) unless
+        filter.is_a?(ViewScopes::Scope::Filter)
+      filter
+    end
+
+    # The sorting target is +scope_order_params+ with the corresponding
+    # column Order object for sorting/ordering.
+    options[:sort_target] ||= lambda do |column, direction|
+      order = column_order.(column)
+      order.direction = (direction.to_s == 'asc' ? 'desc' : 'asc')
+
+      ({
+        :controller => params[:controller],
+        :action     => params[:action],
+      }).merge(scope_order_params(scope, :replace, order))
+    end
+
+    # And the filtering target is +scope_filter_params+ with the corresponding
+    # column Filter object for filtering.
+    options[:filter_target] ||= lambda do |column, table_filter|
+      filter = column_filter.(column)
+      filter.value = table_filter.value
+
+      ({
+        :controller => params[:controller],
+        :action     => params[:action],
+        :page            => 1,
+        :_pag_scope_name => scope.name
+      }).merge(scope_filter_params(scope, :set, filter))
+    end
+
+    # Create and cache a subclass of DynamicTable customized to handle the
+    # Scopes API directly.
+    @@scoped_table_class ||= Class.new(DynamicTable) do
+      attr_accessor :scope
+      attr_accessor :column_order
+      attr_accessor :column_filter
+
+      define_method(:column) do |label, name = nil, options = {}, &block| #:nodoc:
+        # If the column is sortable and its order set as :auto, use the
+        # currently active Scope's matching ordering rule's direction rather
+        # than the params[<column>][:sort_order] default.
+        sortable = [:sortable, :sort_target, :sort_order].any? { |k| options[k] }
+        is_auto  = ! options[:sort_order] || options[:sort_order] == :auto
+        if ! @scope.order.empty? && sortable && is_auto
+          name  = (name || label.to_s.underscore).to_sym
+          order = @scope.order.find { |o| o.attribute == @column_order.(name).attribute }
+          options[:sort_order] = order.try(:direction) || :none
+        end
+
+        super(label, name, options, &block)
+      end
+
+      define_method(:pagination) do |location = nil, options = {}| #:nodoc:
+        # If options are given without a location...
+        if options.blank? && ! [:top, :bottom, :both].include?(location)
+          options  = location || {}
+          location = nil
+        end
+
+        # Pre-set some HTML attributes for the per-page input
+        (options[:input_html] ||= {}).reverse_merge!({
+          :name        => 'per_page',
+          :class       => 'search_box',
+          :'data-type' => 'script',
+          :'data-url'  =>  @template.instance_eval do
+            url_for(
+              :controller => params[:controller],
+              :action     => params[:action],
+              :_pag_scope_name => @scope.name
+            )
+          end
+        })
+
+        # Ensure the correct scope is used when updating pagination-related
+        # attributes.
+        (options[:params] ||= {}).reverse_merge!({
+          :_pag_scope_name => @scope.name
+        })
+
+        super(location, options)
+      end
+
+      alias_method :paginated, :pagination
+      alias_method :paginate,  :pagination
+
+    end
+
+    # Create the Scope-based dynamic table instance and bind the scope and
+    # Filter/Order column lambda functions before handing it to the caller's
+    # block.
+    table = @@scoped_table_class.create(collection, self, options) do |t|
+      t.scope         = scope
+      t.column_order  = column_order
+      t.column_filter = column_filter
+
+      block.call(t)
+    end
+
+    (options.has_key?(:render) && ! options[:render]) ? table : table.render
+  end
+
 end
diff --git a/BrainPortal/app/views/shared/_dynamic_table.html.erb b/BrainPortal/app/views/shared/_dynamic_table.html.erb
index 2f25458ea..fab1e63e3 100644
--- a/BrainPortal/app/views/shared/_dynamic_table.html.erb
+++ b/BrainPortal/app/views/shared/_dynamic_table.html.erb
@@ -87,10 +87,10 @@
             sort_url     = column.sort_target.call(column.name, sort_order)
             sort_url     = url_for(sort_url) unless sort_url.is_a?(String)
             sort_icon    = ({
-              :asc  => "ui-icon-carat-1-n",
-              :desc => "ui-icon-carat-1-s",
-              :none => "ui-icon-carat-2-n-s"
-            })[sort_order]
+              'asc'  => "ui-icon-carat-1-n",
+              'desc' => "ui-icon-carat-1-s",
+              'none' => "ui-icon-carat-2-n-s"
+            })[sort_order.to_s]
           %>
           <span class="dt-sort-btn ui-icon <%= sort_icon %>"
                 data-url="<%= sort_url.html_safe %>"
@@ -121,7 +121,7 @@
                     </td>
                     <%
                       filter_url = filter.target.call(column.name, filter)
-                      filter_url = url_for(sort_url) unless sort_url.is_a?(String)
+                      filter_url = url_for(filter_url) unless filter_url.is_a?(String)
                     %>
                     <td class="dt-fpop-txt <%= empty_cls %>"
                         data-url="<%= filter_url.html_safe %>"
@@ -203,15 +203,16 @@
 <%# Template for the pagination component of a dynamic table %>
 <% templates[:pagination] = Proc.new do %>
   <%
-    pagination           = table.components[:pagination]
-    input_attr           = pagination.input_html
+    pagination = table.components[:pagination]
+    options    = pagination.options.reverse_merge({ :container => false })
+    input_attr = pagination.input_html
     input_attr[:type]  ||= 'text'
     input_attr[:name]  ||= 'per-page'
     input_attr[:value] ||= pagination.collection.per_page
   %>
   <div class="dt-pagination">
     <div class="dt-pag-pages">
-      <%= will_paginate pagination.collection, :container => false %>
+      <%= will_paginate(pagination.collection, options) %>
     </div>
     <div class="dt-pag-cnt">
       <input <%= input_attr.to_html_attributes.html_safe %> />

From ca536817461c9e902ecb113105a17df45da656f2 Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Mon, 31 Aug 2015 11:19:22 -0400
Subject: [PATCH 26/85] Issue #201 - Broken tag filtering

Fixed by manually converting filters and using a custom target in
_userfiles_display.

This changeset also contains a few fixes for dynamic_table:
- Minimum with for filter tooltips to avoid line breaks
- Incorrect column label when using Enumerable filters
- Incorrect check for filter urls in the ERB template
---
 BrainPortal/app/helpers/dynamic_table_helper.rb   |  8 ++++----
 .../app/views/shared/_dynamic_table.html.erb      |  2 +-
 .../views/userfiles/_userfiles_display.html.erb   | 15 ++++++++++++++-
 BrainPortal/public/stylesheets/dynamic-table.css  |  1 +
 4 files changed, 20 insertions(+), 6 deletions(-)

diff --git a/BrainPortal/app/helpers/dynamic_table_helper.rb b/BrainPortal/app/helpers/dynamic_table_helper.rb
index 3c022d728..dd4465947 100644
--- a/BrainPortal/app/helpers/dynamic_table_helper.rb
+++ b/BrainPortal/app/helpers/dynamic_table_helper.rb
@@ -277,11 +277,11 @@ def column(label, name = nil, options = {}, &block)
             :empty     => !!f[:empty]
           }
         elsif f.is_a?(Enumerable)
-          value, label, indicator = f.to_a
+          val, lbl, ind = f.to_a
           {
-            :value     => value,
-            :label     => label     || value,
-            :indicator => indicator || '-',
+            :value     => val,
+            :label     => lbl || val,
+            :indicator => ind || '-',
             :empty     => false
           }
         else
diff --git a/BrainPortal/app/views/shared/_dynamic_table.html.erb b/BrainPortal/app/views/shared/_dynamic_table.html.erb
index 2f25458ea..277ffeae0 100644
--- a/BrainPortal/app/views/shared/_dynamic_table.html.erb
+++ b/BrainPortal/app/views/shared/_dynamic_table.html.erb
@@ -121,7 +121,7 @@
                     </td>
                     <%
                       filter_url = filter.target.call(column.name, filter)
-                      filter_url = url_for(sort_url) unless sort_url.is_a?(String)
+                      filter_url = url_for(filter_url) unless filter_url.is_a?(String)
                     %>
                     <td class="dt-fpop-txt <%= empty_cls %>"
                         data-url="<%= filter_url.html_safe %>"
diff --git a/BrainPortal/app/views/userfiles/_userfiles_display.html.erb b/BrainPortal/app/views/userfiles/_userfiles_display.html.erb
index b48283547..86a60f7ce 100644
--- a/BrainPortal/app/views/userfiles/_userfiles_display.html.erb
+++ b/BrainPortal/app/views/userfiles/_userfiles_display.html.erb
@@ -159,7 +159,20 @@
 
   <%
     t.column("Tags", :tags,
-      :filters => @tag_filters
+      :filters => @tag_filters.map do |label, filter|
+        {
+          :label => label,
+          :value => filter[:value],
+          :empty => filter[:class].to_s =~ /filter_zero/
+        }
+      end,
+      :filter_target => lambda do |column, filter|
+        filter_add_link('', {
+          :parameter => :filter_tags_array,
+          :value     => filter.value,
+          :class     => ""
+        }).match(/href="(.+?)"/)[1]
+      end
     ) do |u|
       u.get_tags_for_user(current_user)
         .collect { |t| h(t.name) }
diff --git a/BrainPortal/public/stylesheets/dynamic-table.css b/BrainPortal/public/stylesheets/dynamic-table.css
index 2a6e55571..aa253974d 100644
--- a/BrainPortal/public/stylesheets/dynamic-table.css
+++ b/BrainPortal/public/stylesheets/dynamic-table.css
@@ -138,6 +138,7 @@
   border: 0.3em solid #0471b4;
   display: none;
   left: 0;
+  min-width: 120px;
   position: absolute;
   text-align: left;
   top: 2.7em;

From 11c6412facf36b197ab04fc2ba0d2f61587f90ab Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Mon, 31 Aug 2015 17:34:22 -0400
Subject: [PATCH 27/85] Scope/Order subclassing fixes/improvements

Improved subclassing support for scope_*_params (incl.
scope_items_url_params), compact_hash and from_hash.

This changeset also includes a small fix for the scope
compression/decompression functions.
---
 BrainPortal/app/helpers/scope_helper.rb | 41 ++++++++---------
 BrainPortal/lib/view_scopes.rb          | 59 ++++++++++++++++++++++---
 2 files changed, 73 insertions(+), 27 deletions(-)

diff --git a/BrainPortal/app/helpers/scope_helper.rb b/BrainPortal/app/helpers/scope_helper.rb
index 67e3102a3..c88c5bdc5 100644
--- a/BrainPortal/app/helpers/scope_helper.rb
+++ b/BrainPortal/app/helpers/scope_helper.rb
@@ -68,7 +68,8 @@ def scope_params(name, scope, compress: true)
   #  Remove one or more +filters+ from the specified scope.
   # [+:set+]
   #  Add one or more +filters+ to the specified scope, replacing existing
-  #  filters filtering on the same attributes as +filters+.
+  #  filters filtering on the same attributes as +filters+ (requires all filters
+  #  in +filters+ to have valid *attribute* values).
   # [+:replace+]
   #  Replace all filters in the specified scope by the ones in +filters+.
   # [+:clear+]
@@ -86,9 +87,8 @@ def scope_filter_params(scope, operation, filters)
       scope.is_a?(Scope)
 
     filters = (filters.is_a?(Array) ? filters : [filters]).map do |filter|
-      filter = filter.to_hash if filter.is_a?(Scope::Filter)
-      Scope::Filter.compact_hash(filter)
-    end
+      filter.is_a?(Scope::Filter) ? filter : Scope::Filter.from_hash(filter)
+    end if filters
 
     scope_items_url_params(scope, operation, :filters, filters)
   end
@@ -106,9 +106,8 @@ def scope_order_params(scope, operation, orders)
       scope.is_a?(Scope)
 
     orders = (orders.is_a?(Array) ? orders : [orders]).map do |order|
-      order = order.to_hash if order.is_a?(Scope::Order)
-      Scope::Order.compact_hash(order)
-    end
+      order.is_a?(Scope::Order) ? order : Scope::Order.from_hash(order)
+    end if orders
 
     scope_items_url_params(scope, operation, :order, orders)
   end
@@ -161,6 +160,10 @@ def pretty_scope_filter(filter, model: nil)
       :user => :login
     }
 
+    # In the best case, +filter+ has its own +to_s+ to generate a nice string
+    # representation directly.
+    return filter.to_s if filter.class.public_instance_methods(false).include?(:to_s)
+
     attribute = filter.attribute.to_s
     operator  = filter.operator.to_s
     values    = Array(filter.value)
@@ -320,8 +323,8 @@ def filter_values_for(collection, attribute, label: nil, association: nil)
   # or :order, for ordering rules. It corresponds to the Scope attribute name
   # to apply +changes+ on.
   # - +changes+ corresponds to +scope_filter_params+'s +changes+ parameter, and
-  # is expected to be an array of compact hash representations of filters
-  # (Scope::Filter) or ordering rules (Scope::Order).
+  # is expected to be an array of filter objects (Scope::Filter) or ordering
+  # rules (Scope::Order).
   #
   # Note that unlike most other utility methods, this method is exclusively
   # intended to be used only to implement +scope_filter_params+ and
@@ -329,20 +332,16 @@ def filter_values_for(collection, attribute, label: nil, association: nil)
   def scope_items_url_params(scope, operation, attr, changes) #:nodoc:
     return if changes.blank? && operation != :clear
 
-    key  = (attr == :filters ? 'f' : 'o')
-    hash = (
+    key   = (attr == :filters ? 'f' : 'o')
+    items = (
       case operation
       when :set
-        replaced  = changes.map { |c| c['a'] }
-        changes  += scope
-          .send(attr)
-          .reject { |c| replaced.include?(c.attribute) }
-          .map    { |c| c.to_hash(compact: true) }
-        { key => changes }
+        replaced = changes.map { |c| c.attribute }
+        changes + scope.send(attr).reject { |c| replaced.include?(c.attribute) }
       when :clear
-        { key => [] }
+        []
       else
-        { key => changes }
+        changes
       end
     )
 
@@ -357,7 +356,9 @@ def scope_items_url_params(scope, operation, attr, changes) #:nodoc:
     {
       '_scope_mode' => mode,
       '_scopes' => {
-        scope.name => ViewScopes.compress_scope(hash)
+        scope.name => ViewScopes.compress_scope({
+          key => items.map { |i| i.to_hash(compact: true) }
+        })
       }
     }
   end
diff --git a/BrainPortal/lib/view_scopes.rb b/BrainPortal/lib/view_scopes.rb
index d49be4190..d76537b52 100644
--- a/BrainPortal/lib/view_scopes.rb
+++ b/BrainPortal/lib/view_scopes.rb
@@ -351,8 +351,16 @@ def self.compact_hash(hash)
     # - Association filtering for ActiveRecord models
     #
     # This class is also intended to be used as a base class for more
-    # specialized filtering cases. See the +type_name+ and +from_hash+ class
-    # methods for more information on how to subclass Filter.
+    # specialized filtering cases. To subclass Filter, the following methods
+    # will most likely need to be re-implemented in the subclass to match the
+    # specialized filter's needs, as their behavior is specific to this generic
+    # filter:
+    # - +self.type_name+
+    # - +apply+
+    # - +valid?+
+    # - +self.from_hash+
+    # - +to_hash+
+    # - +self.compact_hash+
     class Filter
       # Name of the collection/model attribute to filter on, as a string or
       # symbol. Must be present as an attribute in collection/model elements or
@@ -496,7 +504,8 @@ def self.from_hash(hash)
         # Handle Filter subclasses (type key)
         if type = (hash['type'] || hash['t'])
           subclass = self.descendants.find { |sub| sub.type_name == type }
-          return subclass ? subclass.from_hash(hash) : filter
+          return subclass && subclass.respond_to?(:from_hash) ?
+            subclass.from_hash(hash) : filter
         end
 
         # *attribute* must be alphanumeric (word-like)
@@ -574,7 +583,20 @@ def to_hash(compact: false)
       # +from_hash+'s structure. Behaves similarly to Scope's +compact_hash+
       # method, except for being applied to a Filter hash representation
       # instead of a Scope one.
+      #
+      # Note that if +hash+ contains a +type+ (or +t+) key and a valid subclass
+      # exists, this method will invoke the subclass' own +compact_hash+ (if it
+      # exists) to compact +hash+.
       def self.compact_hash(hash)
+        return nil unless hash.is_a?(Hash)
+
+        # Handle Filter subclasses (type key)
+        if type = (hash['type'] || hash[:type] || hash['t'] || hash[:t])
+          subclass = self.descendants.find { |sub| sub.type_name == type }
+          return subclass.compact_hash(hash) if
+            subclass && subclass.respond_to?(:compact_hash)
+        end
+
         Scope.generic_compact_hash(
           hash,
           {
@@ -709,8 +731,17 @@ def apply_on_collection(collection) #:nodoc:
     # model or Ruby collection (Enumerable). This class provides basic
     # ascending/descending ordering, and just like Scope::Filter, is also
     # intended to be used as a base class for more specialized sorting/ordering
-    # rules. See the +type_name+ and +from_hash+ class methods for more
-    # information on how to subclass Order.
+    # rules.
+    #
+    # To subclass Order, the following methods will most likely need to be
+    # re-implemented in the subclass to match the specialized ordering rule's
+    # needs, as their behavior is specific to this simple ordering rule:
+    # - +self.type_name+
+    # - +apply+
+    # - +valid?+
+    # - +self.from_hash+
+    # - +to_hash+
+    # - +self.compact_hash+
     class Order
       # Name of the collection/model attribute to order/sort the
       # collection/model with, as a string or symbol. Must be present as an
@@ -806,7 +837,8 @@ def self.from_hash(hash)
         # Handle Order subclasses (type key)
         if type = (hash['type'] || hash['t'])
           subclass = self.descendants.find { |sub| sub.type_name == type }
-          return subclass ? subclass.from_hash(hash) : order
+          return subclass && subclass.respond_to?(:from_hash) ?
+            subclass.from_hash(hash) : order
         end
 
         # *attribute* must be alphanumeric (word-like)
@@ -844,7 +876,20 @@ def to_hash(compact: false)
       # +from_hash+'s structure. Behaves similarly to Scope's +compact_hash+
       # method, except for being applied to a Order hash representation instead
       # of a Scope one.
+      #
+      # Note that if +hash+ contains a +type+ (or +t+) key and a valid subclass
+      # exists, this method will invoke the subclass' own +compact_hash+ (if it
+      # exists) to compact +hash+.
       def self.compact_hash(hash)
+        return nil unless hash.is_a?(Hash)
+
+        # Handle Order subclasses (type key)
+        if type = (hash['type'] || hash[:type] || hash['t'] || hash[:t])
+          subclass = self.descendants.find { |sub| sub.type_name == type }
+          return subclass.compact_hash(hash) if
+            subclass && subclass.respond_to?(:compact_hash)
+        end
+
         Scope.generic_compact_hash(
           hash,
           {
@@ -1166,7 +1211,7 @@ def update_session_scopes
   def self.compress_scope(scope)
     return scope if scope.is_a?(String)
 
-    scope = scope.to_yaml
+    scope = scope.deep_dup.to_yaml
     scope = ActiveSupport::Gzip.compress(scope)
     scope = Base64.encode64(scope)
     scope

From 6335dd389d6ff7abd7f70dc50564cc70951c7d06 Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Tue, 1 Sep 2015 10:38:13 -0400
Subject: [PATCH 28/85] Issue #183 - Improve 'trigger error recovery' button

The button now displays a proper label depending on the task's status.
The messages are exactly the ones suggested in the issue description.

This changeset also bars update and destroy from being available as API
methods, as they are not implemented as such yet.
---
 BrainPortal/app/controllers/tasks_controller.rb |  2 +-
 BrainPortal/app/views/tasks/show.html.erb       | 11 ++++++++++-
 2 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/BrainPortal/app/controllers/tasks_controller.rb b/BrainPortal/app/controllers/tasks_controller.rb
index 294abd0f6..e7d4db011 100644
--- a/BrainPortal/app/controllers/tasks_controller.rb
+++ b/BrainPortal/app/controllers/tasks_controller.rb
@@ -25,7 +25,7 @@ class TasksController < ApplicationController
 
   Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
 
-  api_available
+  api_available :except => [:update, :destroy]
 
   before_filter :login_required
 
diff --git a/BrainPortal/app/views/tasks/show.html.erb b/BrainPortal/app/views/tasks/show.html.erb
index 00fb7acc2..cd307a851 100644
--- a/BrainPortal/app/views/tasks/show.html.erb
+++ b/BrainPortal/app/views/tasks/show.html.erb
@@ -40,7 +40,16 @@
 
     <!-- FAILURE RECOVERY -->
     <% if @task.status =~ /^Failed*/ %>
-      <%= link_to 'Recover From Failure', { :action => 'operation', :operation => 'recover', 'tasklist[]' => @task.id }, :class  => "button menu_button", :method => :post %>
+      <%
+        label = (
+          case @task.status
+          when /Setup/       then "Retry Setting Up"
+          when /Cluster/     then "Retry Processing"
+          when /PostProcess/ then "Retry Post Processing"
+          end
+        )
+      %>
+      <%= link_to label, { :action => 'operation', :operation => 'recover', 'tasklist[]' => @task.id }, :class  => "button menu_button", :method => :post %>
     <% end %>
 
     <!-- RESTART -->

From 5163ad8a130096ef77fdb99cba950198788b608d Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Tue, 1 Sep 2015 11:15:05 -0400
Subject: [PATCH 29/85] Issue #182 - Report remote resource cache usage

The new column is hidden by default for both admins and normal users
(normal users see the cache size of their files only).
---
 .../app/views/bourreaux/_bourreaux_display.html.erb  | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/BrainPortal/app/views/bourreaux/_bourreaux_display.html.erb b/BrainPortal/app/views/bourreaux/_bourreaux_display.html.erb
index c2665acb2..a15ac3e15 100644
--- a/BrainPortal/app/views/bourreaux/_bourreaux_display.html.erb
+++ b/BrainPortal/app/views/bourreaux/_bourreaux_display.html.erb
@@ -180,6 +180,18 @@
       contents
     end))
 
+    t.column("Cache Space (#{check_role(:admin_user) ? 'all' : 'own'})", :cache_space,
+      :hidden => true
+    ) do |r|
+      size = r.sync_status
+        .joins(:userfile)
+        .where(check_role(:admin_user) ?  {} : { 'userfiles.user_id' => current_user.id })
+        .sum('userfiles.size')
+        .to_i
+
+      colored_pretty_size(size)
+    end
+
     t.column("Description", :description,
       :hidden   => true,
       :sortable => true

From a8025f033bdc2f3e68a4d2f2c75d5eaf05c13895 Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Tue, 1 Sep 2015 17:27:03 -0400
Subject: [PATCH 30/85] Link scope helpers, minor fixes

scope_*_params helpers now have matching scope_*_link helpers to
directly create links without going through url_for and
ajax_link/link_to.

This changeset also includes other minor fixes:
- Reworked pagination application to correctly cover more cases and fix
  incorrect handling of Ruby collections.
- The keys of hashes given to scope_custom_params are now stringified to
  avoid serializing Symbols (which will cause issues when deserializing
  back).
- Decompression now throws an exception on failure instead of just
  leaving the value as-is.
---
 BrainPortal/app/helpers/scope_helper.rb | 54 ++++++++++++++++++++++++-
 BrainPortal/lib/view_scopes.rb          | 29 ++++++++++---
 2 files changed, 76 insertions(+), 7 deletions(-)

diff --git a/BrainPortal/app/helpers/scope_helper.rb b/BrainPortal/app/helpers/scope_helper.rb
index c88c5bdc5..ed7682310 100644
--- a/BrainPortal/app/helpers/scope_helper.rb
+++ b/BrainPortal/app/helpers/scope_helper.rb
@@ -127,10 +127,49 @@ def scope_custom_params(scope, custom)
     name ||= scope || default_scope_name
 
     { '_scopes' => { name => ViewScopes.compress_scope({
-      'c' => custom
+      'c' => custom.stringify_keys
     }) } }
   end
 
+  # Link version of +scope_params+; acts identically to +scope_params+ but
+  # generates a link instead of URL parameters. All arguments but +label+ and
+  # +options+ are passed directly to +scope_params+ in order to create the
+  # link's URL and thus behave identically to +scope_params+'s corresponding
+  # parameters.
+  #
+  # +label+ is expected to be the link's text label and +options+ is expected
+  # to be a hash of options to pass to link_to or ajax_link. Only the special
+  # option :ajax (whether or not to use ajax_link instead of link_to,
+  # defaulting to link_to) is not passed.
+  def scope_link(label, name, scope, compress: true, options: {})
+    url = url_for(scope_params(name, scope, compress: compress))
+    generic_scope_link(label, url, options)
+  end
+
+  # Link version of +scope_filter_params+. Identical to +scope_link+ but uses
+  # +scope_filter_params+ in order to generate the URL. See +scope_link+ for more
+  # information.
+  def scope_filter_link(label, scope, operation, filters, options: {})
+    url = url_for(scope_filter_params(scope, operation, filters))
+    generic_scope_link(label, url, options)
+  end
+
+  # Link version of +scope_order_params+. Identical to +scope_link+ but uses
+  # +scope_order_params+ in order to generate the URL. See +scope_link+ for more
+  # information.
+  def scope_order_link(label, scope, operation, orders, options: {})
+    url = url_for(scope_order_params(scope, operation, orders))
+    generic_scope_link(label, url, options)
+  end
+
+  # Link version of +scope_custom_params+. Identical to +scope_link+ but uses
+  # +scope_custom_params+ in order to generate the URL. See +scope_link+ for more
+  # information.
+  def scope_custom_link(label, scope, custom, options: {})
+    url = url_for(scope_custom_params(scope, custom))
+    generic_scope_link(label, url, options)
+  end
+
   # Generate a pretty string representation of +filter+, optionally using
   # +model+ (as the model +filter+ is applied to) to resolve associations
   # to names (instead of IDs). For example, a filter for +:user_id == 1+
@@ -363,4 +402,17 @@ def scope_items_url_params(scope, operation, attr, changes) #:nodoc:
     }
   end
 
+  # Generate a link to +url+ with label +label+. Paper-thin wrapper around
+  # link_to and ajax_link intended for scope_*_link methods, this method just
+  # passes +label+, +url+ and +options+ to one of the two based on +options+'s
+  # :ajax key (only key which is not passed down).
+  def generic_scope_link(label, url, options)
+    return link_to(label, url, options) unless options.delete(:ajax)
+
+    ajax_link(label, url, options.reverse_merge({
+      :class    => 'action_link',
+      :datatype => :script
+    }))
+  end
+
 end
diff --git a/BrainPortal/lib/view_scopes.rb b/BrainPortal/lib/view_scopes.rb
index d76537b52..cfe60e747 100644
--- a/BrainPortal/lib/view_scopes.rb
+++ b/BrainPortal/lib/view_scopes.rb
@@ -361,6 +361,9 @@ def self.compact_hash(hash)
     # - +self.from_hash+
     # - +to_hash+
     # - +self.compact_hash+
+    # Note that subclasses need to make sure their generated hash
+    # representations have the correct +type+ (+t+) key, or +from_hash+ wont
+    # be able to recreate the right object.
     class Filter
       # Name of the collection/model attribute to filter on, as a string or
       # symbol. Must be present as an attribute in collection/model elements or
@@ -742,6 +745,9 @@ def apply_on_collection(collection) #:nodoc:
     # - +self.from_hash+
     # - +to_hash+
     # - +self.compact_hash+
+    # Note that subclasses need to make sure their generated hash
+    # representations have the correct +type+ (+t+) key, or +from_hash+ wont
+    # be able to recreate the right object.
     class Order
       # Name of the collection/model attribute to order/sort the
       # collection/model with, as a string or symbol. Must be present as an
@@ -971,11 +977,22 @@ def apply(collection)
         page     = [1,  [@page.to_i,     99_999].min].max
         per_page = [25, [@per_page.to_i, 1000  ].min].max
 
-        collection.paginate(
-          :page          => page,
-          :per_page      => per_page,
-          :total_entries => @total
-        )
+        # Is there a native paginate method available?
+        if collection.respond_to?(:paginate)
+          collection.paginate(
+            :page          => page,
+            :per_page      => per_page,
+            :total_entries => @total
+          )
+
+        # Otherwise, just manually create a WillPaginate::Collection
+        else
+          total = @total || collection.length
+
+          WillPaginate::Collection.create(page, per_page, total) do |pager|
+            pager.replace(collection[pager.offset, pager.per_page].to_a)
+          end
+        end
       end
 
       # Create a new Pagination object described by the contents of +hash+. Just
@@ -1183,7 +1200,7 @@ def update_session_scopes
       params['_default_scope']
     scopes = scopes.map do |n, s|
       return [n, s] if s.is_a?(Hash)
-      [ n, (ViewScopes.decompress_scope(s) rescue s) ]
+      [ n, ViewScopes.decompress_scope(s) ]
     end.to_h
 
     current_session.apply_changes([mode, { 'scopes' => scopes }]) unless scopes.blank?

From af9a51fb5220569bc90cbaf02240409d33e16965 Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Tue, 1 Sep 2015 17:32:33 -0400
Subject: [PATCH 31/85] Improved dynamic table pagination handling

Dynamic tables now handle pagination the same way Scopes do; by trying a
native paginate method first then falling back on
WillPaginate::Collection's create method. This is mainly required as
Ruby collections (Enumerables) unexpectedly  do not have a paginate
method.
---
 .../app/helpers/dynamic_table_helper.rb        | 18 +++++++++++++-----
 1 file changed, 13 insertions(+), 5 deletions(-)

diff --git a/BrainPortal/app/helpers/dynamic_table_helper.rb b/BrainPortal/app/helpers/dynamic_table_helper.rb
index 1171c3f1d..026e3651c 100644
--- a/BrainPortal/app/helpers/dynamic_table_helper.rb
+++ b/BrainPortal/app/helpers/dynamic_table_helper.rb
@@ -694,11 +694,19 @@ def initialize(location, collection, options = {})
           collection.respond_to?(:current_page) &&
           collection.current_page
         )
-          collection = collection.to_a.paginate(
-            :page          => page,
-            :per_page      => per_page,
-            :total_entries => total_entries
-          )
+          # Is there a paginate method available?
+          if collection.respond_to?(:paginate)
+            collection.paginate(
+              :page          => page,
+              :per_page      => per_page,
+              :total_entries => total_entries
+            )
+          # Otherwise, just manually create a WillPaginate::Collection
+          else
+            WillPaginate::Collection.create(page, per_page, total_entries) do |pager|
+              pager.replace(collection[pager.offset, pager.per_page].to_a)
+            end
+          end
         end
 
         @collection = collection

From 93bbb95025757f05e6f138b54953facd75dea706 Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Tue, 1 Sep 2015 18:01:56 -0400
Subject: [PATCH 32/85] Port of userfiles controller to the new Scope API

This changeset completely replaces the old @filter_params based logic in
the userfiles controller and related views by the new Scope filtering
mechanism, and reworks the main index code path in the process.

While summarily checked, further testing is required as the old
filtering API was quite deeply rooted in the controller and the new one
isn't a drop-in replacement at all.
---
 .../app/controllers/userfiles_controller.rb   | 504 ++++++++++++------
 BrainPortal/app/helpers/userfiles_helper.rb   |   2 +-
 .../custom_filters/_custom_filter_li.html.erb |  15 +-
 .../app/views/shared/_active_filters.html.erb |  93 ++--
 BrainPortal/app/views/tags/_tag_li.html.erb   |  16 +-
 .../app/views/userfiles/_file_menu.html.erb   |  18 +-
 .../userfiles/_userfiles_display.html.erb     |  96 ++--
 .../userfiles/_view_option_button.html.erb    |  25 +-
 8 files changed, 483 insertions(+), 286 deletions(-)

diff --git a/BrainPortal/app/controllers/userfiles_controller.rb b/BrainPortal/app/controllers/userfiles_controller.rb
index 5a80214b3..be8067737 100644
--- a/BrainPortal/app/controllers/userfiles_controller.rb
+++ b/BrainPortal/app/controllers/userfiles_controller.rb
@@ -41,110 +41,85 @@ class UserfilesController < ApplicationController
   # GET /userfiles
   # GET /userfiles.xml
   def index #:nodoc:
-
-    #------------------------------
-    # Header scope
-    #------------------------------
-
-    @header_scope = header_scope(@filter_params)
-
-    #------------------------------
-    # Filtered scope
-    #------------------------------
-
-    @filtered_scope = filter_scope(@filter_params,@header_scope)
-
-    #------------------------------
-    # Sorted scope
-    #------------------------------
-
-    sorted_scope, joins = sorted_scope(@filter_params,@header_scope,@filtered_scope)
-
-    #------------------------------
-    # Tags
-    #------------------------------
-
-    tags_and_total_counts = @header_scope.select("tags.name as tag_name, tags.id as tag_id, COUNT(tags.name) as tag_count").joins(:tags).group("tags.name")
-    filt_tag_counts       = @filtered_scope.joins(:tags).group("tags.name").count
-    @tag_filters          = tags_and_total_counts.map { |tc| ["#{tc.tag_name} (#{filt_tag_counts[tc.tag_name].to_i}/#{tc.tag_count})", { :parameter  => :filter_tags_array, :value => tc.tag_id, :class => "#{"filter_zero" if filt_tag_counts[tc.tag_name].blank?}" }]  }
-
-    #------------------------------
-    # Pagination preparation
-    #------------------------------
-
-    # For Pagination
-    unless [:html, :js].include?(request.format.to_sym)
-      @per_page = 999_999_999
-    end
-    @current_offset = offset = (@current_page - 1) * @per_page
-
-
-    #------------------------------
-    # Final paginated array of objects
-    #------------------------------
-
-    includes = [ :user, :data_provider, :sync_status, :tags, :group ] # used only when fetching objects for rendering the page
-
-    # ---- NO tree sort ----
-    @filter_params["tree_sort"] = "on" if @filter_params["tree_sort"].blank?
-    if @filter_params["tree_sort"] == "off" || ![:html, :js].include?(request.format.to_sym)
-      @filtered_scope  = @filtered_scope.scoped( :joins => :user ) if current_user.has_role?(:site_manager)
-      # use 'distinct userfiles.id' on count in order to remove duplicate entry
-      # due to the presence of file with multiple status
-      @userfiles_total      = @filtered_scope.count("distinct userfiles.id")
-      ordered_real          = sorted_scope.includes(includes - joins).offset(offset).limit(@per_page).all
-    # ---- WITH tree sort ----
-    else
-      # We first get a list of 'simple' objects [ id, parent_id ]
-      simple_pairs      = sorted_scope.raw_rows( [ "userfiles.id", "userfiles.parent_id" ] )
-      simple_pairs      = tree_sort_by_pairs(simple_pairs) # private method in this controller
-      # At this point, each simple_pair is [ userfile_id, parent_id, [ child1_id, child2_id... ], orig_idx, level ]
-      @userfiles_total  = simple_pairs.size
-
-      # Paginate the list of simple objects
-      page_of_userfiles = simple_pairs[offset, @per_page] || []
-
-      # Fetch the real objects and collect them in the same order
-      userfile_ids      = page_of_userfiles.collect { |u| u[0] }
-      real_subset       = @filtered_scope.includes( includes ).where( :id => userfile_ids )
-      real_subset_index = real_subset.index_by { |u| u.id }
-      ordered_real      = []
-
-      page_of_userfiles.each do |simple|
-        full = real_subset_index[simple[0].to_i]
-        next unless full # this can happen when the userfile list change between fetching the simple and real lists
-        full.level = simple[4]
-        ordered_real << full
+    @scope = scope_from_session('userfiles')
+    @scope.name ||= 'userfiles'
+
+    # Base userfiles scope, without any filtering or ordering
+    @base_scope = base_scope
+    # Ordered, filtered view scope
+    @view_scope = view_scope(@base_scope)
+
+    # Generate tag filters
+    tag_counts   = @view_scope.joins(:tags).group('tags.name').count
+    @tag_filters = @base_scope
+      .joins(:tags)
+      .group('tags.name')
+      .raw_rows(['tags.name', 'tags.id', 'COUNT(tags.name)'])
+      .map do |name, id, count|
+        {
+          :value     => id,
+          :label     => name,
+          :indicator => tag_counts[name].to_i,
+          :empty     => tag_counts[name].blank?
+        }
       end
 
-    end
-
-    @userfiles_total_size = @filtered_scope.sum(:size)
-
-
+    # Join in other models to display additional view information
+    @view_scope = @view_scope.includes([
+      :user, :data_provider, :sync_status, :tags, :group
+    ])
+
+    # Generate display totals
+    @userfiles_total = @view_scope.count('distinct userfiles.id')
+    @archived_total  = @view_scope.where(:archived => true).count
+    @immutable_total = @view_scope.where(:immutable => true).count
+    @hidden_total    = @view_scope.undo_where(:hidden).where(:hidden => true).count unless
+      @scope.custom[:view_hidden]
+
+    # Prepare the Pagination object
+    @scope.pagination ||= Scope::Pagination.from_hash({ :per_page => 25 })
+    @scope.pagination.per_page = 999_999_999 unless
+      [:html, :js].include?(request.format.to_sym)
+    @current_offset = (@scope.pagination.page - 1) * @scope.pagination.per_page
+
+    # Tree sort
+    if @scope.custom[:tree_sort]
+      # Sort using just IDs and parent IDs then paginate, giving the final
+      # userfiles list in tuple (see +tree_sort_by_pairs+) form.
+      tuples = tree_sort_by_pairs(@view_scope.raw_rows([:id, :parent_id]))
+      tuples = @scope.pagination.apply(tuples)
+
+      # Keep just ID and depth/level; there is no need for the parent ID,
+      # children list, original index, etc.
+      tuples.map! { |t| [t[0].to_i, t[4]] }
+
+      # Map the corresponding Userfile objects in @view_scope by ID.
+      mapping = @view_scope
+        .where(:id => tuples.map { |t| t.first })
+        .index_by { |u| u.id }
+
+      # Convert the tuple list to Userfile objects using the mapping, conserving
+      # the tuple list's ordering and pagination information.
+      @userfiles = tuples.map! do |id, level|
+        userfile = mapping[id]
+        next unless userfile
+
+        userfile.level = level
+        userfile
+      end
 
-    #------------------------------
-    # Real page of userfile objects
-    #------------------------------
+      # Remove invalid entries (occur when the list changes between the sort
+      # and conversion).
+      @userfiles.compact!
 
-    # Turn the array ordered_real into the final paginated collection
-    @userfiles = WillPaginate::Collection.create(@current_page, @per_page) do |pager|
-      pager.replace(ordered_real || [])
-      pager.total_entries = @userfiles_total
-      pager
-    end
-
-    # Count the number of hidden files, only if the current view option is not showing them.
-    # This code depends on AREL's 'where_values' method, which is not official ?
-    @hidden_total = nil
-    if @filter_params["view_hidden"] != 'on'
-      @hidden_total  = @filtered_scope.undo_where(:hidden).where(:hidden => true).count
+    else
+      @userfiles = @scope.pagination.apply(@view_scope)
     end
 
-    @archived_total  = @filtered_scope.where(:archived => true).count
-    @immutable_total = @filtered_scope.where(:immutable => true).count
-
+    # Save the modified scope object
+    scope_to_session(@scope, 'userfiles')
     current_session.save_preferences
+
     respond_to do |format|
       format.html
       format.js
@@ -302,10 +277,9 @@ def show #:nodoc:
       @sort_index     = [ 0, params[:sort_index].to_i, 999_999_999 ].sort[1]
 
       # Rebuild the sorted Userfile scope
-      @filter_params  = current_session.params_for(params[:proxy_destination_controller] || params[:controller])
-      header_scope    = header_scope(@filter_params)
-      filtered_scope  = filter_scope(@filter_params, header_scope)
-      sorted_scope, _ = sorted_scope(@filter_params, header_scope, filtered_scope)
+      @scope        = scope_from_session('userfiles')
+      @scope.name ||= 'userfiles'
+      sorted_scope  = view_scope
 
       # Fetch the neighbors of the shown userfile in the ordered scope's order
       neighbors = sorted_scope.where("userfiles.id != ?", @userfile.id).offset([0, @sort_index - 1].max).limit(2).all
@@ -941,11 +915,14 @@ def change_provider #:nodoc:
   # Adds the selected userfile IDs to the session's persistent list
   def manage_persistent
 
+    @scope = scope_from_session('userfiles')
+    @scope.name ||= 'userfiles'
+
     operation  = (params[:operation] || 'clear').downcase
-    persistent = (current_session[:persistent_userfiles] || Set.new)
+    persistent = Set.new(current_session[:persistent_userfiles])
 
     if operation =~ /select/
-      files = filter_scope(@filter_params, header_scope(@filter_params))
+      files = view_scope
         .select(&:available?)
         .map(&:id)
         .map(&:to_s)
@@ -973,7 +950,7 @@ def manage_persistent
       flash[:notice] = "Peristent selection list now empty."
     end
 
-    current_session[:persistent_userfiles] = persistent
+    current_session[:persistent_userfiles] = persistent.to_a
     redirect_to :action => :index, :page => params[:page]
   end
 
@@ -1611,93 +1588,274 @@ def all_tree_children_by_pairs(top,level = nil) #:nodoc:
     result
   end
 
-  # Reduce Userfile scoped according with the header scope
-  # selected by user
-  def header_scope(filters)
-    header_scope = Userfile.scoped
+  # Base userfiles scope; all userfiles currently visible to the user, without any
+  # filtering yet. Requires a valid @scope object.
+  def base_scope
+    base = Userfile.scoped
 
     # Restrict by 'view all' or not
-    filters["view_all"] ||= current_user.has_role?(:admin_user) ? 'off' : 'on'
-    if filters["view_all"] == 'on'
-      header_scope = Userfile.restrict_access_on_query(current_user, header_scope, :access_requested => :read)
+    @scope.custom[:view_all] = !current_user.has_role?(:admin_user) if
+      @scope.custom[:view_all].nil?
+
+    if @scope.custom[:view_all]
+      base = Userfile.restrict_access_on_query(current_user, base, :access_requested => :read)
     else
-      header_scope = header_scope.where( :user_id => current_user.id )
+      base = base.where(:user_id => current_user.id)
     end
 
-    # Filter by current project
-    if current_project
-      header_scope = header_scope.where( :group_id  => current_project.id )
-    end
+    base = base.where(:group_id => current_project.id) if current_project
+    base = base.where(:hidden => false) unless @scope.custom[:view_hidden]
+    base
+  end
 
-    # Filter by 'view hidden' or not
-    unless filters["view_hidden"] == 'on'
-      header_scope = header_scope.where( :hidden => false ) # show only the non-hidden files
+  # View userfiles scope; filtered and sorted list of userfiles to display.
+  # +base+ is expected to be the base scope to filter and sort (defaults to
+  # +base_scope+). Requires a valid @scope object.
+  def view_scope(base = nil)
+    base ||= base_scope
+
+    custom_filters  = (@scope.custom[:custom_filters] || []).dup
+    custom_filters &= current_user.custom_filter_ids.map(&:to_s)
+    custom_filters.map! { |id| UserfileCustomFilter.find(id) }
+
+    @scope.order << Scope::Order.from_hash({
+      :attribute => 'name',
+      :direction => 'asc'
+    }) if @scope.order.blank?
+
+    view = @scope.apply(base)
+    view = custom_filters.inject(view) do |scope, filter|
+      filter.filter_scope(scope)
     end
 
-    header_scope
+    view
   end
 
-  # Reduce Userfile scoped according with the filters
-  # selected by user
-  def filter_scope(filters,header_scope)
-    # Prepare filters
-    filters["filter_hash"]                 ||= {}
-    filters["filter_custom_filters_array"] ||= []
-    filters["filter_custom_filters_array"]  &= current_user.custom_filter_ids.map(&:to_s)
-    filters["filter_tags_array"]           ||= []
-    filters["filter_tags_array"]            &= current_user.available_tags.map{ |t| t.id.to_s }
+  # Userfiles-specific tag Scope filter; filter by a set of tags which must
+  # all be on a given userfile for it to pass the filter. Note that this is
+  # an all-or-nothing filter; to pass, an userfile needs *all* tags.
+  #
+  # Note that this filter uses Scope::Filter's *value* attribute to hold the
+  # tags to check against, and that the *attribute* attribute is statically
+  # set to 'tags' (as this filter will only ever filter tags).
+  class TagFilter < Scope::Filter
+    # Create a new blank TagFilter. Only present to pre-set *attribute*.
+    def initialize #:nodoc:
+      @attribute = 'tags'
+    end
+
+    # Nice string representation of this filter for +pretty_scope_filter+.
+    def to_s
+      "Tags: " + Tag.find(@value).map(&:name).uniq.join(', ') rescue ''
+    end
+
+    # The methods below are TagFilter specific versions of the Scope::Filter
+    # interface. See Scope::Filter for more details on how these methods
+    # operate and for detailed parameter information.
+
+    # Type name to recognize this filter when in hash representation
+    # (+type+ (+t+) key).
+    def self.type_name
+      'uf.tags'
+    end
+
+    # Apply this filter on +collection+, which is expected to be a userfiles
+    # model or scope or a collection of Userfile objects.
+    #
+    # Note that this filter is specific to Userfiles and will not operate
+    # correctly with any other kind of object.
+    def apply(collection)
+      raise "no tags to filter with" unless @value.present?
+      tags = Set.new(@value)
+
+      # With an Userfile model (or scope)
+      if (collection <= ActiveRecord::Base rescue nil)
+        placeholders = tags.map { '?' }.join(',')
+        collection.where(<<-"SQL".strip_heredoc, *tags)
+          ((
+            SELECT COUNT(DISTINCT tags_userfiles.tag_id)
+            FROM tags_userfiles
+            WHERE
+              tags_userfiles.userfile_id = userfiles.id AND
+              tags_userfiles.tag_id IN (#{placeholders})
+          ) = #{tags.size})
+        SQL
+
+      # With a Ruby Enumerable
+      else
+        collection.select { |u| (tags - u.tags.map(&:id)).empty? }
+      end
+    end
+
+    # Check if this filter is valid (+apply+ can be used). A TagFilter only
+    # requires a valid *value* to be useable.
+    def valid?
+      @value.present?
+    end
 
-    # Prepare custom filters
-    custom_filter_tags = filters["filter_custom_filters_array"].map { |filter| UserfileCustomFilter.find(filter).tag_ids }.flatten.uniq
+    # Create a new TagFilter from a hash representation. The following keys
+    # are recognized in +hash+:
+    #
+    # [+value+ or +v+]
+    #  *value* attribute: an Enumerable of tags (tag IDs as integers) for the
+    #  userfiles to have.
+    #
+    # Note that no other key from Scope::Filter's +from_hash+ is recognized.
+    def self.from_hash(hash)
+        return nil unless hash.is_a?(Hash)
 
-    # Prepare tag filters
-    tag_filters        = filters["filter_tags_array"] + custom_filter_tags
-    #Apply filters
-    filtered_scope     = base_filtered_scope(header_scope)
+        hash = hash.with_indifferent_access unless
+          hash.is_a?(HashWithIndifferentAccess)
 
-    filters["filter_custom_filters_array"].each do |custom_filter_id|
-      custom_filter    = UserfileCustomFilter.find(custom_filter_id)
-      filtered_scope   = custom_filter.filter_scope(filtered_scope)
+        filter = self.new
+        filter.value = Array(hash['value'] || hash['v'])
+          .map { |v| Integer(v) rescue nil }
+          .compact
+
+        filter
     end
 
-    unless tag_filters.blank?
-      filtered_scope   = filtered_scope.where( "((SELECT COUNT(DISTINCT tags_userfiles.tag_id) FROM tags_userfiles WHERE tags_userfiles.userfile_id = userfiles.id AND tags_userfiles.tag_id IN (#{tag_filters.join(",")})) = #{tag_filters.size})" )
+    # Convert this TagFilter into a hash representation, doing the exact
+    # opposite of +from_hash+.
+    def to_hash(compact: false)
+      hash = {
+        'type'  => self.class.type_name,
+        'value' => @value
+      }
+
+      compact ? self.class.compact_hash(hash) : hash
+    end
+
+    # Compact +hash+, a hash representation of TagFilter (matching +from_hash+'s
+    # structure).
+    def self.compact_hash(hash)
+      ViewScopes::Scope.generic_compact_hash(
+        hash,
+        {
+          'type'  => 't',
+          'value' => 'v',
+        },
+        defaults: { 'value' => [] }
+      )
     end
-    return filtered_scope
   end
 
-  # Sort a scoped Userfile according with the parameters
-  # selected by user
-  # Returns the sorted scoped Userfile and the set of joins
-  # placed on it.
-  # FIXME the sorting joins are required by some callers of
-  # sorted_scope and both solutions (returning the joins and
-  # recomputing them) are awkward
-  def sorted_scope(filters,header_scope,filtered_scope)
-    # Prepare sorting options
-    filters["sort_hash"]["order"] ||= 'userfiles.name'
-
-    # Apply the sorting parameters
-    sorted_scope          = base_sorted_scope filtered_scope
-
-    # Identify and add necessary table joins
-    joins                 = []
-    sort_table            = filters["sort_hash"]["order"].split(".")[0]
-    if sort_table == "users" || current_user.has_role?(:site_manager)
-      joins << :user
-    end
-    case sort_table
-    when "groups"
-      joins << :group
-    when "data_providers"
-      joins << :data_provider
-    end
-    sorted_scope = sorted_scope.joins(joins) unless joins.empty?
-
-    # Add a secondary sorting column (name)
-    sorted_scope = sorted_scope.order('userfiles.name') unless filters["sort_hash"]["order"] == 'userfiles.name'
-
-    return sorted_scope, joins
+  # Crude Userfiles-specific child/parent relationship Scope filter; filter by
+  # whether or not a given userfile has children or a parent.
+  #
+  # Note that this filter uses Scope::Filter's *operator* attribute to hold
+  # which condition to filter on. The following conditions (values for
+  # *operator*) are available:
+  # [+no_child+]  Userfiles without any children (shortened to 'c').
+  # [+no_parent+] Userfiles without a parent (shortened to 'p').
+  class HierarchyFilter < Scope::Filter
+    # Nice string representation of this filter for +pretty_scope_filter+.
+    def to_s
+      case @operator.to_s
+      when 'no_child'  then 'Has no children'
+      when 'no_parent' then 'Has no parent'
+      else @operator.to_s.humanize
+      end
+    end
+
+    # The methods below are HierarchyFilter specific versions of the
+    # Scope::Filter interface. See Scope::Filter for more details on how these
+    # methods operate and for detailed parameter information.
+
+    # Type name to recognize this filter when in hash representation
+    # (+type+ (+t+) key).
+    def self.type_name
+      'uf.hier'
+    end
+
+    # Apply this filter on +collection+, which is expected to be a userfiles
+    # model or scope or a collection of Userfile objects.
+    #
+    # Note that this filter is specific to Userfiles and will not operate
+    # correctly with any other kind of object.
+    def apply(collection)
+      raise "nothing to filter with" unless valid?
+
+      # With an Userfile model (or scope)
+      if (collection <= ActiveRecord::Base rescue nil)
+        case @operator.to_s.downcase
+        when 'no_child'
+          collection.where(<<-"SQL".strip_heredoc)
+            (NOT EXISTS(
+              SELECT 1
+              FROM userfiles AS children
+              WHERE children.parent_id = userfiles.id
+            ))
+          SQL
+        when 'no_parent'
+          collection.where(:parent_id => nil)
+        end
+
+      # With a Ruby Enumerable
+      else
+        case @operator.to_s.downcase
+        when 'no_child'
+          collection.select { |u| u.children.exists? }
+        when 'no_parent'
+          collection.reject(&:parent_id)
+        end
+      end
+    end
+
+    # Check if this filter is valid (+apply+ can be used). A HierarchyFilter
+    # only requires a valid *operator*.
+    def valid?
+      ['no_child', 'no_parent'].include?(@operator.to_s)
+    end
+
+    # Create a new HierarchyFilter from a hash representation. The following
+    # keys are recognized in +hash+:
+    #
+    # [+operator+ or +o+]
+    #  *operator* attribute: either no_child/c or no_parent/p
+    #
+    # Note that no other key from Scope::Filter's +from_hash+ is recognized.
+    def self.from_hash(hash)
+      return nil unless hash.is_a?(Hash)
+
+      hash = hash.with_indifferent_access unless
+        hash.is_a?(HashWithIndifferentAccess)
+
+      filter = self.new
+
+      operator = (hash['operator'] || hash['o'] || 'no_child').to_s.downcase
+      filter.operator = operator if ['no_child', 'no_parent'].include?(operator)
+
+      filter
+    end
+
+    # Convert this HierarchyFilter into a hash representation, doing the exact
+    # opposite of +from_hash+.
+    def to_hash(compact: false)
+      hash = {
+        'type'     => self.class.type_name,
+        'operator' => @operator.to_s
+      }
+
+      compact ? self.class.compact_hash(hash) : hash
+    end
+
+    # Compact +hash+, a hash representation of HierarchyFilter (matching
+    # +from_hash+'s structure).
+    def self.compact_hash(hash)
+      ViewScopes::Scope.generic_compact_hash(
+        hash,
+        {
+          'type'     => 't',
+          'operator' => 'o',
+        },
+        defaults: { 'operator' => 'no_child' },
+        values: [
+          [ 'operator', 'no_child'  => 'c' ],
+          [ 'operator', 'no_parent' => 'p' ]
+        ]
+      )
+    end
   end
 
 end
diff --git a/BrainPortal/app/helpers/userfiles_helper.rb b/BrainPortal/app/helpers/userfiles_helper.rb
index 79186826c..48f630556 100644
--- a/BrainPortal/app/helpers/userfiles_helper.rb
+++ b/BrainPortal/app/helpers/userfiles_helper.rb
@@ -30,7 +30,7 @@ module UserfilesHelper
   # link to show page, sync status and formats.
   def filename_listing(userfile, link_options={})
     html = []
-    html << tree_view_icon(userfile.level) if @filter_params["tree_sort"] == "on" && userfile.level.to_i > 0
+    html << tree_view_icon(userfile.level) if @scope.custom[:tree_sort] && userfile.level.to_i > 0
     html << link_to_userfile_if_accessible(userfile, nil, link_options)
     if userfile.hidden?
       html << " "
diff --git a/BrainPortal/app/views/custom_filters/_custom_filter_li.html.erb b/BrainPortal/app/views/custom_filters/_custom_filter_li.html.erb
index 48413f703..14de8ec61 100644
--- a/BrainPortal/app/views/custom_filters/_custom_filter_li.html.erb
+++ b/BrainPortal/app/views/custom_filters/_custom_filter_li.html.erb
@@ -23,7 +23,20 @@
 -%>
 
 <b>
-<%= filter_add_link crop_text_to(15, filter.name), :controller => @custom_filter.filtered_class_controller, :parameter  => :filter_custom_filters_array, :value => filter.id  %>
+<%=
+  ajax_link(
+    crop_text_to(15, filter.name),
+    url_for(scope_custom_params(@scope, {
+        'custom_filters' => [filter.id]
+      }).merge({
+        :controller  => @custom_filter.filtered_class_controller,
+        :_scope_mode => :append
+      })
+    ),
+    :class    => 'action_link',
+    :datatype => :script
+  )
+%>
 </b>
 <small><small>
    <%= overlay_ajax_link "Edit", edit_custom_filter_path(filter) %>
diff --git a/BrainPortal/app/views/shared/_active_filters.html.erb b/BrainPortal/app/views/shared/_active_filters.html.erb
index c66d3238a..33188009b 100644
--- a/BrainPortal/app/views/shared/_active_filters.html.erb
+++ b/BrainPortal/app/views/shared/_active_filters.html.erb
@@ -1,4 +1,3 @@
-
 <%-
 #
 # CBRAIN Project
@@ -23,61 +22,49 @@
 -%>
 
 <%
-  filter_links = []
-  controller = params[:controller].to_sym || :unknown
-  (@filter_params["filter_hash"].presence || []).each do |att, val|
-    filter =
-    if att == "time_interval"
-      s = val[0].to_i
-      e = val[1].to_i
-      s,e = e,s if e > s
-      s_text = pretty_elapsed(s, :num_components  => 1) + " ago"
-      s_text = "now"          if s == 0
-      s_text = "the big bang" if s > 10.years
-      e_text = pretty_elapsed(e, :num_components  => 1) + " ago"
-      e_text = "now"          if e == 0
-      e_text = "the big bang" if e > 10.years
-      text = "Time interval: between #{s_text} and #{e_text}"
-      "<span class=\"current_filters_item\">#{h(text).capitalize}</span>"
-    elsif att == "critical"
-      text = val == '1' ? "Critical" : "Not critical"
-      "<span class=\"current_filters_item\">#{text}</span>"
-    elsif att == "read"
-      text = val == '1' ? "Read" : "Unread"
-      "<span class=\"current_filters_item\">#{text}</span>"
-    elsif att == "type"
-      "<span class=\"current_filters_item\">#{crop_text_to(30, Array(val).map(&:constantize).map(&:pretty_type).join(", "))}</span>"
-    elsif att == "account_locked"
-      text = val == '1' ? "Locked" : "Unlocked"
-      "<span class=\"current_filters_item\">#{text}</span>"
-    else
-      "<span class=\"current_filters_item\">#{crop_text_to(30, display_filter(model, att, val, {:user  => :login}))}</span>"
-    end
-    filter += filter_remove_link(delete_icon, att)
-    filter_links << filter
-  end
-
-  if @filter_params["filter_tags_array"].present?
-    current_user.available_tags.find(@filter_params["filter_tags_array"]).each do |tag|
-      filter_links << "<span class=\"current_filters_item\">#{crop_text_to(30, "Tag: #{tag.name}")}</span>" + filter_remove_link(delete_icon, tag.id, :parameter  => :filter_tags_array)
-    end
-  end
-
-  if @filter_params["filter_custom_filters_array"].present?
-    current_user.custom_filters.find(@filter_params["filter_custom_filters_array"]).each do |filter|
-      filter_links << "<span class=\"current_filters_item\">#{crop_text_to(30, "Custom: #{filter.name}")}</span>" + filter_remove_link(delete_icon, filter.id, :parameter  => :filter_custom_filters_array)
-    end
-  end
+  return if scope.blank? || (
+    scope.filters.blank? &&
+    scope.custom[:custom_filters].blank?
+  )
 %>
 
-<% if filter_links.size > 0 %>
-
 <div class="active_status">
   <span class="active_status_left_side">
-    <span class="active_label">Active Filters</span> (<%= filter_clear_link 'clear', :class  => "action_link" %>):
-    <span id="current_filters"><%= filter_links.join(", ").html_safe %></span>
+    <span class="active_label">Active Filters</span>
+    (<%=
+      scope_filter_link('clear',
+        scope, :clear, nil,
+        options: { :ajax => true }
+      )
+    %>)
+    <span id="current_filters">
+      <% scope.filters.each do |filter| %>
+        <span class="current_filters_item">
+          <%= crop_text_to(30, pretty_scope_filter(filter, model: model)) %>
+        </span>
+        <%=
+          scope_filter_link(delete_icon,
+            scope, :remove, filter,
+            options: { :ajax => true }
+          )
+        %>
+      <% end %>
+      <% Array(scope.custom[:custom_filters]).each do |id| %>
+        <span class="current_filters_item">
+          <%= crop_text_to(30, UserfileCustomFilter.find(id).name) %>
+        </span>
+        <%=
+          ajax_link(
+            delete_icon,
+            url_for(
+              scope_custom_params(scope, { 'custom_filters' => [id] })
+                .merge({ '_scope_mode' => 'delete' })
+            ),
+            :class    => 'action_link',
+            :datatype => :script
+          )
+        %>
+      <% end %>
+    </span>
   </span>
 </div>
-
-<% end %>
-
diff --git a/BrainPortal/app/views/tags/_tag_li.html.erb b/BrainPortal/app/views/tags/_tag_li.html.erb
index 4133029d3..7f59c64c9 100644
--- a/BrainPortal/app/views/tags/_tag_li.html.erb
+++ b/BrainPortal/app/views/tags/_tag_li.html.erb
@@ -23,7 +23,21 @@
 -%>
 
 <b>
-  <%= filter_add_link crop_text_to(15, tag.name), :controller => :userfiles, :parameter  => :filter_tags_array, :value => tag.id  %>
+  <%=
+    ajax_link(
+      crop_text_to(15, tag.name),
+      url_for(
+        scope_filter_params(@scope, :set, {
+          'type'  => 'uf.tags',
+          'value' => [tag.id]
+        }).reverse_merge({
+          :controller => :userfiles
+        })
+      ),
+      :class    => 'action_link',
+      :datatype => :script
+    )
+  %>
 </b>
 
 <small><small>
diff --git a/BrainPortal/app/views/userfiles/_file_menu.html.erb b/BrainPortal/app/views/userfiles/_file_menu.html.erb
index d3dab34ba..bbf1952e7 100644
--- a/BrainPortal/app/views/userfiles/_file_menu.html.erb
+++ b/BrainPortal/app/views/userfiles/_file_menu.html.erb
@@ -174,8 +174,22 @@
 
       <h4>Other Filters</h4>
       <ul class="filter_menu">
-        <li><%= filter_add_link "Has No Parent", :filters => {:has_no_parent  => true} %></li>
-        <li><%= filter_add_link "Has No Children", :filters => {:has_no_child  => true} %></li>
+        <li>
+          <%=
+            scope_filter_link('Has no parent',
+              @scope, :add, { 'type' => 'uf.hier', 'operator' => 'no_parent' },
+              options: { :ajax => true }
+            )
+          %>
+        </li>
+        <li>
+          <%=
+            scope_filter_link('Has no children',
+              @scope, :add, { 'type' => 'uf.hier', 'operator' => 'no_child' },
+              options: { :ajax => true }
+            )
+          %>
+        </li>
       </ul>
     <% end %>
     <span id="view_option_button">
diff --git a/BrainPortal/app/views/userfiles/_userfiles_display.html.erb b/BrainPortal/app/views/userfiles/_userfiles_display.html.erb
index 1a6c9dc6d..532cbd5d9 100644
--- a/BrainPortal/app/views/userfiles/_userfiles_display.html.erb
+++ b/BrainPortal/app/views/userfiles/_userfiles_display.html.erb
@@ -22,12 +22,23 @@
 #
 -%>
 
-<%= render :partial => 'shared/active_filters', :locals => { :model => :userfile } %>
+<%=
+  render(:partial => 'shared/active_filters', :locals  => {
+    :scope => @scope,
+    :model => Userfile
+  })
+%>
 
 <div class="pagination">
   <% if current_session[:persistent_userfiles].present? %>
     <div class="pagination_left_side">
-      <blink><%= html_colorize("(#{pluralize(current_session[:persistent_userfiles].size," file")} persistently selected)") %></blink>
+      <blink>
+        <%=
+          html_colorize(
+            "(#{pluralize(current_session[:persistent_userfiles].size," file")} persistently selected)"
+          )
+        %>
+      </blink>
     </div>
   <% end %>
   <div class="page_links">
@@ -51,37 +62,24 @@
 </div>
 
 <%=
-  dynamic_index_table(@userfiles,
+  dynamic_scoped_table(@userfiles,
     :id           => 'userfiles_table',
     :request_type => :server_javascript,
-    :sort_map     => {
-      :name           => 'userfiles.name',
-      :type           => 'userfiles.type',
-      :login          => 'users.login',
-      :creation_date  => 'userfiles.created_at',
-      :size           => 'userfiles.size',
-      :group          => 'groups.name',
-      :group_writable => 'userfiles.group_writable',
-      :data_provider  => 'data_providers.name'
+    :order_map    => {
+      :creation_date => { :a => 'created_at' },
+      :login         => { :a => 'users.login',         :j => User         },
+      :group         => { :a => 'groups.name',         :j => Group        },
+      :data_provider => { :a => 'data_providers.name', :j => DataProvider },
     },
     :filter_map   => {
-      :login          => 'user_id',
-      :group          => 'group_id',
-      :data_provider  => 'data_provider_id'
+      :login         => { :a => 'user_id'          },
+      :group         => { :a => 'group_id'         },
+      :data_provider => { :a => 'data_provider_id' },
     }
   ) do |t|
 %>
   <%
-    filters_for = lambda do |target,options = {}|
-      return unless @filtered_scope && @header_scope
-      if target.is_a?(Symbol)
-        basic_filters_for(@filtered_scope, @header_scope, Userfile, target)
-      else
-        association_filters_for(@filtered_scope, @header_scope, Userfile, target, options)
-      end
-    end
-
-    t.paginate(@per_page > 50 ? :both : :top)
+    t.paginate(@scope.pagination.per_page > 50 ? :both : :top)
 
     t.row do |u|
       {
@@ -117,12 +115,16 @@
     t.column("File Type", :type,
       :field_name => :pretty_type,
       :sortable   => true,
-      :filters    => filters_for.(:type)
+      :filters    => filter_values_for(@view_scope, :type)
     )
 
     t.column("Owner", :login,
       :sortable => true,
-      :filters  => filters_for.(User, :name_method => "login")
+      :filters  => filter_values_for(
+        @view_scope, :user_id,
+        label: 'users.login',
+        association: User
+      )
     ) { |u| link_to_user_if_accessible(u.user) }
 
     t.column("Creation Date", :creation_date,
@@ -158,20 +160,24 @@
   <% end %>
 
   <%
+    filtering_tags = ((
+      @scope.filters.find do |f|
+        f.attribute == 'tags' && f.is_a?(UserfilesController::TagFilter)
+      end
+    ).try(:value) || []).dup
+
     t.column("Tags", :tags,
-      :filters => @tag_filters.map do |label, filter|
-        {
-          :label => label,
-          :value => filter[:value],
-          :empty => filter[:class].to_s =~ /filter_zero/
-        }
-      end,
+      :filters       => @tag_filters,
       :filter_target => lambda do |column, filter|
-        filter_add_link('', {
-          :parameter => :filter_tags_array,
-          :value     => filter.value,
-          :class     => ""
-        }).match(/href="(.+?)"/)[1]
+        ({
+          :controller      => params[:controller],
+          :action          => params[:action],
+          :page            => 1,
+          :_pag_scope_name => @scope.name
+        }).merge(scope_filter_params(@scope, :set, {
+          'type'  => 'uf.tags',
+          'value' => (filtering_tags + [filter.value]).uniq
+        }))
       end
     ) do |u|
       u.get_tags_for_user(current_user)
@@ -183,7 +189,11 @@
     unless current_project
       t.column("Project", :group,
         :sortable => true,
-        :filters  => filters_for.(Group)
+        :filters  => filter_values_for(
+          @view_scope, :group_id,
+          label: 'groups.name',
+          association: Group
+        )
       ) do |u|
         link_to_group_if_accessible(u.group) if u.group
       end
@@ -197,7 +207,11 @@
 
     t.column("Provider", :data_provider,
       :sortable => true,
-      :filters  => filters_for.(DataProvider)
+      :filters  => filter_values_for(
+        @view_scope, :data_provider_id,
+        label: 'data_providers.name',
+        association: DataProvider
+      )
     ) do |u|
       link_to_data_provider_if_accessible(u.data_provider)
     end
diff --git a/BrainPortal/app/views/userfiles/_view_option_button.html.erb b/BrainPortal/app/views/userfiles/_view_option_button.html.erb
index d686e6d5a..d63f30296 100644
--- a/BrainPortal/app/views/userfiles/_view_option_button.html.erb
+++ b/BrainPortal/app/views/userfiles/_view_option_button.html.erb
@@ -24,21 +24,18 @@
 
 <%= button_with_dropdown_menu("View Options") do %>
   <div class="view_options">
-    <%=
-        filter_add_link (@filter_params["tree_sort"] == "off" ? "Enable Tree View" : "Disable Tree View"),
-                        :parameter => :tree_sort,
-                        :value     => set_toggle(@filter_params["tree_sort"])
-    %>
-    <br>
-    <%= filter_add_link @filter_params["view_all"] == 'on' ? "Show only your own files": "Show all available files",
-                        :parameter => :view_all,
-                        :value     => set_toggle(@filter_params["view_all"])
-    %>
-    <br>
-    <%= filter_add_link @filter_params["view_hidden"] == 'on' ? "Do not show hidden files": "Show hidden files",
-                        :parameter => :view_hidden,
-                        :value     => set_toggle(@filter_params["view_hidden"])
+    <%
+      toggle_link = lambda do |on, off, key|
+        scope_custom_link((@scope.custom[key] ? off : on),
+          @scope, { key => !@scope.custom[key] },
+          options: { :ajax_link => true }
+        )
+      end
     %>
+
+    <%= toggle_link.("Enable Tree View",         "Disable Tree View",        :tree_sort)   %><br />
+    <%= toggle_link.("Show all available files", "Show only your own files", :view_all)    %><br />
+    <%= toggle_link.("Show hidden files",        "Do not show hidden files", :view_hidden) %>
     (<%= hidden_icon %>)
   </div>
 <% end %>

From 1e58da67001c934af5b1a5fed031515e749db925 Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Wed, 2 Sep 2015 15:57:04 -0400
Subject: [PATCH 33/85] Restored userfiles name search

The name search functionality is now correctly ported to the new Scopes
API (although handled manually to avoid an hefty JS partial).

This changeset also fixes two other minor bugs; handling of empty
collections in filter_values_for and incorrect types for custom filter
ids.
---
 .../app/controllers/userfiles_controller.rb   | 23 ++++++++++++-------
 BrainPortal/app/helpers/scope_helper.rb       |  1 +
 .../userfiles/_userfiles_display.html.erb     |  2 +-
 3 files changed, 17 insertions(+), 9 deletions(-)

diff --git a/BrainPortal/app/controllers/userfiles_controller.rb b/BrainPortal/app/controllers/userfiles_controller.rb
index be8067737..13aa486af 100644
--- a/BrainPortal/app/controllers/userfiles_controller.rb
+++ b/BrainPortal/app/controllers/userfiles_controller.rb
@@ -42,7 +42,17 @@ class UserfilesController < ApplicationController
   # GET /userfiles.xml
   def index #:nodoc:
     @scope = scope_from_session('userfiles')
-    @scope.name ||= 'userfiles'
+
+    # Manually handle the 'name_like' input, as it cant be pre-computed
+    # server-side (and going the JS route would be overkill).
+    if (name_like = params[:name_like])
+      @scope.filters.reject! { |f| f.attribute.to_s == 'name' }
+      @scope.filters << Scope::Filter.from_hash({
+        :attribute => 'name',
+        :operator  => 'match',
+        :value     => name_like
+      })
+    end
 
     # Base userfiles scope, without any filtering or ordering
     @base_scope = base_scope
@@ -277,9 +287,8 @@ def show #:nodoc:
       @sort_index     = [ 0, params[:sort_index].to_i, 999_999_999 ].sort[1]
 
       # Rebuild the sorted Userfile scope
-      @scope        = scope_from_session('userfiles')
-      @scope.name ||= 'userfiles'
-      sorted_scope  = view_scope
+      @scope       = scope_from_session('userfiles')
+      sorted_scope = view_scope
 
       # Fetch the neighbors of the shown userfile in the ordered scope's order
       neighbors = sorted_scope.where("userfiles.id != ?", @userfile.id).offset([0, @sort_index - 1].max).limit(2).all
@@ -915,9 +924,7 @@ def change_provider #:nodoc:
   # Adds the selected userfile IDs to the session's persistent list
   def manage_persistent
 
-    @scope = scope_from_session('userfiles')
-    @scope.name ||= 'userfiles'
-
+    @scope     = scope_from_session('userfiles')
     operation  = (params[:operation] || 'clear').downcase
     persistent = Set.new(current_session[:persistent_userfiles])
 
@@ -1615,7 +1622,7 @@ def view_scope(base = nil)
     base ||= base_scope
 
     custom_filters  = (@scope.custom[:custom_filters] || []).dup
-    custom_filters &= current_user.custom_filter_ids.map(&:to_s)
+    custom_filters &= current_user.custom_filter_ids
     custom_filters.map! { |id| UserfileCustomFilter.find(id) }
 
     @scope.order << Scope::Order.from_hash({
diff --git a/BrainPortal/app/helpers/scope_helper.rb b/BrainPortal/app/helpers/scope_helper.rb
index ed7682310..e69b1f61e 100644
--- a/BrainPortal/app/helpers/scope_helper.rb
+++ b/BrainPortal/app/helpers/scope_helper.rb
@@ -302,6 +302,7 @@ def pretty_scope_filter(filter, model: nil)
   # model (only applicable if +collection+ is an ActiveRecord model).
   def filter_values_for(collection, attribute, label: nil, association: nil)
     # TODO Unscoped/base scope/total item count.
+    return [] if collection.blank?
 
     if (collection <= ActiveRecord::Base rescue nil)
       # Resolve and validate the main +attribute+ to fetch the values of
diff --git a/BrainPortal/app/views/userfiles/_userfiles_display.html.erb b/BrainPortal/app/views/userfiles/_userfiles_display.html.erb
index 532cbd5d9..ae8083109 100644
--- a/BrainPortal/app/views/userfiles/_userfiles_display.html.erb
+++ b/BrainPortal/app/views/userfiles/_userfiles_display.html.erb
@@ -57,7 +57,7 @@
     )
   </div>
   <div class="pagination_right_side">
-    Search by name: <%= ajax_search_box "name_like", userfiles_path(:update_filter => :filter_hash) %>
+    Search by name: <%= ajax_search_box("name_like", userfiles_path) %>
   </div>
 </div>
 

From 0a099229a911c318fb98a9f569a7fc3f95bb3f9d Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Wed, 2 Sep 2015 17:24:35 -0400
Subject: [PATCH 34/85] Port of tasks controller to the new Scope API

As with the userfiles controller port, this changeset completely
replaces the old @filter_params based logic by the new Scopes filtering
mechanism. The port also brought a modification to the controller (and
views) behavior; batch view is now completely independent from sorting
rules, and it is now possible to sort batches without automatically
falling back to list view.

Further testing is necessary to ensure nothing broke during this port.
---
 .../app/controllers/tasks_controller.rb       | 185 +++++++++---------
 .../app/views/tasks/_tasks_display.html.erb   | 150 +++++++-------
 2 files changed, 159 insertions(+), 176 deletions(-)

diff --git a/BrainPortal/app/controllers/tasks_controller.rb b/BrainPortal/app/controllers/tasks_controller.rb
index 280d31b9b..04026596b 100644
--- a/BrainPortal/app/controllers/tasks_controller.rb
+++ b/BrainPortal/app/controllers/tasks_controller.rb
@@ -30,105 +30,104 @@ class TasksController < ApplicationController
   before_filter :login_required
 
   def index #:nodoc:
-    bourreaux    = Bourreau.find_all_accessible_by_user(current_user).all
-    bourreau_ids = bourreaux.map(&:id)
-
-    scope = filter_variable_setup current_user.available_tasks.real_tasks.where( :bourreau_id => bourreau_ids )
-
-    if request.format.to_sym == :xml || request.format.to_sym == :json
-      @filter_params["sort_hash"]["order"] ||= "cbrain_tasks.updated_at"
-      @filter_params["sort_hash"]["dir"]   ||= "DESC"
+    @scope      = scope_from_session('tasks')
+    api_request = [:xml, :json].include?(request.format.to_sym)
+
+    # Default sorting order and batch mode
+    if api_request
+      @scope.order << Scope::Order.from_hash({
+        :attribute => 'updated_at',
+        :direction => :desc
+      }) if @scope.order.blank?
     else
-      @filter_params["sort_hash"]["order"] ||= "cbrain_tasks.batch"
-    end
-
-    # Set sort order and make it persistent.
-    @sort_order = @filter_params["sort_hash"]["order"]
-    @sort_dir   = @filter_params["sort_hash"]["dir"]
-
-    @showing_batch = false #i.e. don't show levels for individual entries.
-
-    # In batch view...
-    if @sort_order == "cbrain_tasks.batch"
-      if @filter_params["filter_hash"]["batch_id"]  # we show a specific batch
-        @sort_order      = "cbrain_tasks.rank, cbrain_tasks.level, cbrain_tasks.id"
-        @sort_dir        = ""
-        @showing_batch   = true
-      else # batch view with several batches visible
-        @sort_order = "cbrain_tasks.batch_id"
-        @sort_dir   = 'DESC'
-      end
-    end
-
-    scope = scope.includes( [:bourreau, :user, :group] ).readonly
-
-    @total_tasks       = scope.count    # number of TASKS
-    @total_space_known = scope.sum(:cluster_workdir_size)
-    @total_space_unkn  = scope.where(:cluster_workdir_size => nil).where("cluster_workdir IS NOT NULL").count
-
-    # For Pagination
-    offset = (@current_page - 1) * @per_page
-
-    if @filter_params["sort_hash"]["order"] == "cbrain_tasks.batch" && !@filter_params["filter_hash"]["batch_id"] && request.format.to_sym != :xml  && request.format.to_sym != :json
-      batch_ids                 = scope.order( "#{@sort_order} #{@sort_dir}" ).offset( offset ).limit( @per_page ).raw_first_column("distinct(cbrain_tasks.batch_id)")
-      task_counts_in_batch      = scope.where(:batch_id => batch_ids).group(:batch_id).count
-      full_batch_ids            = scope.raw_first_column("distinct(cbrain_tasks.batch_id)")
-      full_task_counts_in_batch = scope.where(:batch_id => full_batch_ids).group(:batch_id).count
-      @total_entries            = full_task_counts_in_batch.count
-
-      @tasks = {} # hash batch_id => task_info
-      batch_ids.each do |batch_id|
-         num_tasks  = task_counts_in_batch[batch_id] || 0
-         first_task = num_tasks == 1 ?
-            scope.where(:batch_id => batch_id).first :
-            scope.where(:batch_id => batch_id).order( [ :rank, :level, :id ] ).first
-         next unless first_task.present? # in rare case a delete operation happens in background
-         @tasks[batch_id] = { :first_task => first_task, :num_tasks => num_tasks }
+      @scope.order << Scope::Order.from_hash({
+        :attribute => 'rank',
+        :direction => :asc
+      }) if @scope.order.blank?
+
+      @scope.custom[:batch] = true if @scope.custom[:batch].nil?
+    end
+
+    @scope.pagination ||= Scope::Pagination.from_hash({ :per_page => 25 })
+    @view_scope = view_scope(current_user.available_tasks)
+      .includes([:bourreau, :user, :group])
+
+    # Display totals
+    @total_tasks       = @view_scope.count
+    @total_space_known = @view_scope.sum(:cluster_workdir_size)
+    @total_space_unkn  = @view_scope
+      .where(:cluster_workdir_size => nil)
+      .where('cluster_workdir IS NOT NULL')
+      .count
+
+    # Batch mode & pagination
+    single_batch    = @scope.filters.any? { |f| f.attribute == 'batch_id' }
+    @showing_batch  = @scope.custom[:batch] && single_batch
+
+    if ! api_request && @scope.custom[:batch] && ! single_batch
+      @tasks = @scope.pagination.apply(@view_scope.group(:batch_id).count.to_a)
+      @tasks.map! do |id, count|
+        first = @view_scope
+            .where(:batch_id => id)
+            .order([:rank, :level, :id])
+            .first
+
+        { :batch => id, :first => first, :count => count } if first
       end
-      pagination_list = batch_ids
+      @tasks.compact!
     else
-      @total_entries = @total_tasks
-      task_list = scope.order( "#{@sort_order} #{@sort_dir}" ).offset( offset ).limit( @per_page ).all
-
-      @tasks = {} # hash task_id -> task_info for a single task
-      task_list.each do |t|
-        @tasks[t.id] = { :first_task => t, :statuses => [t.status], :num_tasks => 1 }
+      @tasks = @scope.pagination.apply(@view_scope).to_a
+      @tasks.map! do |task|
+        { :batch => task.batch_id, :first => task, :count => 1 }
       end
-      pagination_list = task_list.map(&:id)
     end
 
-    @paginated_list = WillPaginate::Collection.create(@current_page, @per_page) do |pager|
-      pager.replace(pagination_list)
-      pager.total_entries = @total_entries
-      pager
-    end
+    # Bourreaux status
+    @bourreau_status = Bourreau.find_all_accessible_by_user(current_user)
+      .map { |b| [b.id, b.online?] }
+      .to_h
 
+    # Save the modified scope object
+    scope_to_session(@scope, 'tasks')
     current_session.save_preferences
 
-    @bourreau_status = bourreaux.map { |b| [b.id, b.online?] }.to_h
     respond_to do |format|
       format.html
-      format.xml   { render :xml  => @tasks }
-      format.json  { render :json => task_list }
       format.js
+
+      # For backwards compatibility with old XML/JSON API clients.
+      format.xml do
+        render :xml => (@tasks.map do |task|
+          task = task[:first]
+          [task.id, {
+            :first_task => task,
+            :statuses   => [task.status],
+            :num_tasks  => 1
+          }]
+        end).to_h
+      end
+
+      format.json do
+        render :json => @tasks.map { |task| task[:first] }
+      end
     end
   end
 
   # Renders a set of tasks associated with a batch.
   def batch_list
-    @tasks = filter_variable_setup(
+    @scope = scope_from_session('tasks')
+    @tasks = view_scope(
       current_user
         .available_tasks
         .real_tasks
         .where(:batch_id => params[:batch_id])
     )
-      .includes([ :bourreau, :user, :group ])
-      .order("cbrain_tasks.rank, cbrain_tasks.level, cbrain_tasks.id")
-      .readonly(false)
+      .includes([:bourreau, :user, :group])
+      .order([:rank, :level, :id])
+      .map { |task| { :batch => task.batch_id, :first => task, :count => 1 } }
 
     @bourreau_status = Bourreau
       .find_all_accessible_by_user(current_user)
-      .all
       .map { |b| [b.id, b.online?] }
       .to_h
 
@@ -582,9 +581,9 @@ def update_multiple
     batch_ids   = Array(params[:batch_ids] || [])
 
     if batch_ids.delete "nil"
-      task_ids += filter_variable_setup(CbrainTask.real_tasks.where( :batch_id => nil )).select("id").raw_first_column
+      task_ids += view_scope(CbrainTask.real_tasks.where( :batch_id => nil )).select("id").raw_first_column
     end
-    task_ids   += filter_variable_setup(CbrainTask.real_tasks.where( :batch_id => batch_ids )).select("id").raw_first_column
+    task_ids   += view_scope(CbrainTask.real_tasks.where( :batch_id => batch_ids )).select("id").raw_first_column
     task_ids    = task_ids.map(&:to_i).uniq
 
     commit_name = extract_params_key([ :update_user_id, :update_group_id, :update_results_data_provider_id, :update_tool_config_id ])
@@ -745,10 +744,10 @@ def operation
     batch_ids   = [ batch_ids ] unless batch_ids.is_a?(Array)
 
     if batch_ids.delete "nil"
-      tasklist += filter_variable_setup(CbrainTask.where( :batch_id => nil )).select("id").raw_first_column
+      tasklist += view_scope(CbrainTask.where( :batch_id => nil )).select("id").raw_first_column
     end
 
-    tasklist   += filter_variable_setup(CbrainTask.where( :batch_id => batch_ids )).select("id").raw_first_column
+    tasklist   += view_scope(CbrainTask.where( :batch_id => batch_ids )).select("id").raw_first_column
     tasklist    = tasklist.map(&:to_i).uniq
 
     flash[:error]  ||= ""
@@ -989,25 +988,25 @@ def resource_class #:nodoc:
     CbrainTask
   end
 
-  def filter_variable_setup(starting_scope) #:nodoc:
-    @header_scope = starting_scope
-    @header_scope = @header_scope.where( :group_id => current_project.id ) if current_project
-
-    @filtered_scope = base_filtered_scope(@header_scope)
+  def view_scope(base) #:nodoc:
+    base = base.where(:group_id => current_project.id) if current_project
+    base = base.where(
+      :bourreau_id => Bourreau
+        .find_all_accessible_by_user(current_user)
+        .raw_rows(:id)
+        .flatten
+    )
 
-    if @filter_params["filter_hash"]["bourreau_id"].blank?
-      @filtered_scope = @filtered_scope.where( :bourreau_id => Bourreau.find_all_accessible_by_user(current_user).all.map(&:id) )
-    end
+    custom_filters  = (@scope.custom[:custom_filters] || []).dup
+    custom_filters &= current_user.custom_filter_ids
+    custom_filters.map! { |id| TaskCustomFilter.find(id) }
 
-    # Handle custom filters
-    @filter_params["filter_custom_filters_array"] ||= []
-    @filter_params["filter_custom_filters_array"] &= current_user.custom_filter_ids.map(&:to_s)
-    @filter_params["filter_custom_filters_array"].each do |custom_filter_id|
-      custom_filter = TaskCustomFilter.find(custom_filter_id)
-      @filtered_scope = custom_filter.filter_scope(@filtered_scope)
+    view = @scope.apply(base)
+    view = custom_filters.inject(view) do |scope, filter|
+      filter.filter_scope(scope)
     end
 
-    @filtered_scope
+    view
   end
 
   # Warning: private context in effect here.
diff --git a/BrainPortal/app/views/tasks/_tasks_display.html.erb b/BrainPortal/app/views/tasks/_tasks_display.html.erb
index 6b5bc2170..5b5422b5c 100644
--- a/BrainPortal/app/views/tasks/_tasks_display.html.erb
+++ b/BrainPortal/app/views/tasks/_tasks_display.html.erb
@@ -23,69 +23,41 @@
 -%>
 
 <%
-  batch_view = @filter_params["sort_hash"]["order"] == 'cbrain_tasks.batch' rescue nil
+  batch_view = @scope.custom[:batch] rescue nil
+  list = @tasks.map { |t| [(t[:count] == 1 ? :task : :batch), t[:batch], t[:count], t[:first]] }
 
-  if @row_fetch
-    # In row fetch mode, @tasks will contain a list of tasks for a single batch.
-    # The loaded batch header is created from this list and the first task of the batch.
-    list = @tasks.map { |task| [ :task, task.batch_id, nil, task ] }
-  else
-    # In table display mode, @paginated_list will contain an already paginated list
-    # of batch ids which maps into @tasks, a hash of task_info structures. In this
-    # context, a task is a batch with just one task.
-    list = @paginated_list.map do |id|
-      batch = @tasks[id]
-      [ (batch[:num_tasks] == 1 ? :task : :batch), id, batch, batch[:first_task] ] if
-        batch.present? && batch[:first_task].present?
-    end.compact
-  end
-
-  # This table's columns accept 4 arguments (type, id, batch and task) are specially made
+  # This table's columns accept 4 arguments (type, id, count and task) and are specially made
   # to render 3 row types;
   #
-  # - Task rows (+type+ is :task). +id+ is the task's batch id, +batch+ is not used (can be nil)
+  # - Task rows (+type+ is :task). +id+ is the task's batch id, +count+ is not used (can be nil)
   #   and +task+ is the task object to render.
   #
-  # - Batch rows (+type+ is :batch). +id+ is the batch's id, +batch+ is a hash containing various
-  #   attributes of the batch (task_info) and +task+ is the first task of the batch.
+  # - Batch rows (+type+ is :batch). +id+ is the batch's id, +count+ is the batch's task count
+  #   and +task+ is the first task of the batch.
   #
-  # - Loaded batch rows (+type+ is :loaded_batch). +id+ is the batch's id, +batch+ is not used and
+  # - Loaded batch rows (+type+ is :loaded_batch). +id+ is the batch's id, +count+ is not used and
   #   +task+ is the first task of the batch. This row type is used for AJAX-loaded batch headers.
-  table = dynamic_index_table(list,
+  table = dynamic_scoped_table(list,
     :id         => "tasks_table",
     :class      => [ :resource_list ],
     :render     => false,
-    :sort_map   => {
-      :type         => 'cbrain_tasks.type',
-      :description  => 'cbrain_tasks.description',
-      :owner        => 'users.login',
-      :project      => 'groups.name',
-      :server       => 'remote_resources.name',
-      :status       => 'cbrain_tasks.status',
-      :workdir_size => 'cbrain_tasks.cluster_workdir_size',
-      :created_at   => 'cbrain_tasks.created_at',
-      :updated_at   => 'cbrain_tasks.updated_at'
+    :order_map  => {
+      :owner        => { :a => 'users.login',           :j => User     },
+      :project      => { :a => 'groups.name',           :j => Group    },
+      :server       => { :a => 'remote_resources.name', :j => Bourreau },
+      :workdir_size => { :a => 'cluster_workdir_size' }
     },
     :filter_map => {
-      :owner   => 'user_id',
-      :project => 'group_id',
-      :server  => 'bourreau_id'
+      :owner   => { :a => 'user_id'     },
+      :project => { :a => 'group_id'    },
+      :server  => { :a => 'bourreau_id' }
     }
   ) do |t|
 %>
   <%
-    filters_for = lambda do |target, opts = {}|
-      return if @row_fetch
-      if target.is_a?(Symbol)
-        basic_filters_for(@filtered_scope, @header_scope, CbrainTask, target)
-      else
-        association_filters_for(@filtered_scope, @header_scope, CbrainTask, target, opts)
-      end
-    end
+    t.paginate(:collection => @tasks) unless @row_fetch
 
-    t.paginate(:collection => @paginated_list) unless @row_fetch
-
-    t.row do |type,id,batch,task|
+    t.row do |type,id,count,task|
       case type
       when :task
         available = @bourreau_status[task.bourreau.id]
@@ -117,7 +89,7 @@
     <%
       t.column('', :expand,
         :pretty_name => "Batch"
-      ) do |type,id,batch,task|
+      ) do |type,id,count,task|
     %>
       <% next if type == :task %>
       <%
@@ -126,7 +98,7 @@
             :class => [ 'batch-btn', 'ui-icon', 'ui-icon-minus' ],
             :title => "Expand batch"
           }
-        elsif batch[:num_tasks] <= @per_page
+        elsif count <= @scope.pagination.per_page.to_i
           attributes = {
             :class => [ 'batch-btn', 'ui-icon', 'ui-icon-plus' ],
             :title => "Expand batch",
@@ -139,11 +111,10 @@
             :title => "Open batch",
             :'data-batch-type' => 'html_link',
             :'data-batch-url'  =>
-              filter_add_link('',
-                :controller => :tasks,
-                :filters    => { :batch_id => task.batch_id },
-                :ajax       => false
-              ).match(/href="(.+?)"/)[1]
+              url_for(scope_filter_params(@scope, :set, {
+                :attribute => 'batch_id',
+                :value     => task.batch_id
+              }))
           }
         end
       %>
@@ -154,8 +125,8 @@
   <%
     t.column("Task Type", :type,
       :sortable => true,
-      :filters  => filters_for.(:type)
-    ) do |type,id,batch,task|
+      :filters  => filter_values_for(@view_scope, :type)
+    ) do |type,id,count,task|
   %>
     <% case type %>
     <% when :task %>
@@ -169,28 +140,40 @@
   <%
     t.column("Description", :description,
       :sortable => true
-    ) do |type,id,batch,task|
+    ) do |type,id,count,task|
       overlay_description(task.description, :header_width => 35) unless type == :loaded_batch
     end
 
     t.column("Owner", :owner,
       :sortable => true,
-      :filters  => filters_for.(User, :name_method => :login)
-    ) do |type,id,batch,task|
+      :filters  => filter_values_for(
+        @view_scope, :user_id,
+        label: 'users.login',
+        association: User
+      )
+    ) do |type,id,count,task|
       link_to_user_if_accessible(task.user) unless type == :loaded_batch
     end
 
     t.column("Project", :project,
       :sortable => true,
-      :filters  => filters_for.(Group)
-    ) do |type,id,batch,task|
+      :filters  => filter_values_for(
+        @view_scope, :group_id,
+        label: 'groups.name',
+        association: Group
+      )
+    ) do |type,id,count,task|
       link_to_group_if_accessible(task.group) unless type == :loaded_batch
     end unless current_project
 
     t.column("Execution Server", :server,
       :sortable => true,
-      :filters  => filters_for.(Bourreau, :association_table => :remote_resources)
-    ) do |type,id,batch,task|
+      :filters  => filter_values_for(
+        @view_scope, :bourreau_id,
+        label: 'remote_resources.name',
+        association: [Bourreau, 'id', 'bourreau_id']
+      )
+    ) do |type,id,count,task|
       link_to_bourreau_if_accessible(task.bourreau) unless type == :loaded_batch
     end
   %>
@@ -198,15 +181,15 @@
   <%
     t.column("Current Status", :status,
       :sortable => true,
-      :filters  => filters_for.(:status)
-    ) do |type,id,batch,task|
+      :filters  => filter_values_for(@view_scope, :status)
+    ) do |type,id,count,task|
   %>
     <%
       case type
       when :task
         next colored_status(task.status)
       when :batch
-        ntasks   = batch[:num_tasks]
+        ntasks   = count
         statuses = {}
         CbrainTask
           .real_tasks
@@ -222,7 +205,7 @@
         ntasks   = @tasks.size
         statuses = {}
         @tasks
-          .to_a
+          .map { |t| t[:first] }
           .hashed_partitions { |t| t.status =~ /Fail/i ? 'Failed' : t.status }
           .each { |s,t| statuses[s] = t.size }
       end
@@ -238,12 +221,12 @@
     %>
   <% end %>
 
-  <% t.column("Run Number", :run) { |type,id,batch,task| task.run_number.to_s if type == :task } %>
+  <% t.column("Run Number", :run) { |type,id,count,task| task.run_number.to_s if type == :task } %>
 
   <%
     t.column("Workdir Size", :workdir_size,
       :sortable => true
-    ) do |type,id,batch,task|
+    ) do |type,id,count,task|
   %>
     <% case type %>
     <% when :task %>
@@ -266,7 +249,7 @@
   <%
     t.column("Time Submitted", :created_at,
       :sortable => true
-    ) do |type,id,batch,task|
+    ) do |type,id,count,task|
       case type
       when :task
         to_localtime(task.created_at, :datetime)
@@ -277,7 +260,7 @@
 
     t.column("Last Updated", :updated_at,
       :sortable => true
-    ) do |type,id,batch,task|
+    ) do |type,id,count,task|
       case type
       when :task
         to_localtime(task.updated_at, :datetime)
@@ -312,25 +295,26 @@
       </td>
     </tr>
   <% else %>
-    <%= table.render :row, [[ :loaded_batch, @tasks.first.batch_id, nil, @tasks.first ]] %>
+    <%= table.render :row, [[ :loaded_batch, @tasks.first[:batch], nil, @tasks.first[:first] ]] %>
     <%= table.render :row, list %>
   <% end %>
 <% else %>
-  <%= render :partial => 'shared/active_filters', :locals => {:model => :cbrain_task} %>
+  <%=
+    render(:partial => 'shared/active_filters', :locals  => {
+      :scope => @scope,
+      :model => CbrainTask
+    })
+  %>
 
   <div class="pagination">
     <div class="pagination_left_side">
-      <% if batch_view %>
-        <strong>Currently in Batch View</strong>
-      <% else %>
-        <%=
-          ajax_link(
-            "Switch to Batch View",
-            { params[:controller] => { :sort_hash => { :order => 'cbrain_tasks.batch', :dir => 'ASC' } } },
-            { :datatype => 'script' }
-          )
-        %>
-      <% end %>
+      <%=
+        scope_custom_link(
+          "Switch to #{batch_view ? 'List' : 'Batch'} View",
+          @scope, { 'batch' => !batch_view },
+          options: { :ajax => true }
+        )
+      %>
     </div>
     <div class="page_links">
       (<%= pluralize @total_tasks, "task" %>)

From b334f4bdbaa3673d4b1f67a91259672907f979e5 Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Thu, 3 Sep 2015 11:35:28 -0400
Subject: [PATCH 35/85] Issue #202 - Pink task rows when the corresponding
 bourreau is offline

Self-explanatory. Also includes a minor style fix for dynamic tables.
---
 BrainPortal/app/views/tasks/_tasks_display.html.erb | 2 +-
 BrainPortal/public/stylesheets/cbrain.css           | 8 ++++++++
 BrainPortal/public/stylesheets/dynamic-table.css    | 1 +
 3 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/BrainPortal/app/views/tasks/_tasks_display.html.erb b/BrainPortal/app/views/tasks/_tasks_display.html.erb
index 6b5bc2170..393d129e4 100644
--- a/BrainPortal/app/views/tasks/_tasks_display.html.erb
+++ b/BrainPortal/app/views/tasks/_tasks_display.html.erb
@@ -91,7 +91,7 @@
         available = @bourreau_status[task.bourreau.id]
         {
           :id    => "task_#{task.id}",
-          :class => [ :task ],
+          :class => [:task, (available ? :available : :unavailable)],
           :select_param => ('tasklist[]' if available),
           :select_value => (task.id      if available),
           :html => {
diff --git a/BrainPortal/public/stylesheets/cbrain.css b/BrainPortal/public/stylesheets/cbrain.css
index 9b98ece17..4a1ee7022 100644
--- a/BrainPortal/public/stylesheets/cbrain.css
+++ b/BrainPortal/public/stylesheets/cbrain.css
@@ -1663,6 +1663,14 @@ img {
   background-color: #e3f2fb;
 }
 
+#tasks_table tr.task.unavailable:nth-child(odd) {
+  background-color: #fcd1de;
+}
+
+#tasks_table tr.task.unavailable:nth-child(even) {
+  background-color: #fee5ec;
+}
+
 /* % ######################################################### */
 /* % Styles for Data Provider Browse page */
 /* % ######################################################### */
diff --git a/BrainPortal/public/stylesheets/dynamic-table.css b/BrainPortal/public/stylesheets/dynamic-table.css
index aa253974d..d3b62439e 100644
--- a/BrainPortal/public/stylesheets/dynamic-table.css
+++ b/BrainPortal/public/stylesheets/dynamic-table.css
@@ -52,6 +52,7 @@
   border: 0;
   color: inherit;
   font-family: inherit;
+  height: 22px;
   padding: 0.2em 0.5em 0.2em 0.9em;
   text-align: left;
 }

From 0c3a032f4414535a331b15da9d0f26464f400bbe Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Wed, 9 Sep 2015 13:44:31 -0400
Subject: [PATCH 36/85] Extra view & controller utility/helper methods

The new methods assoc_filter_values_for, scope_filter_from_params and
scope_default_order are designed around common use cases for the
scope-based filtering system and help cut down some boilerplate.

This changeset also includes a bunch of various fixes to the scoping
mechanism:
- Link helpers (scope_*_link methods) now accept both url options
  (url_for) and link options (link_to and ajax_link).
- pretty_scope_filter now correctly recognizes booleans in string
  format.
- New format parameter for +filter_values_for+ to manually format the
  generated filter values (hashes).
- Fix for unexpected HashWithIndifferentAccess behavior
- Compressed Scopes can now contain Date, Time and DateTime objects.
---
 BrainPortal/app/helpers/scope_helper.rb  | 111 +++++++++++++++++------
 BrainPortal/app/models/cbrain_session.rb |   6 ++
 BrainPortal/lib/view_scopes.rb           |  43 ++++++++-
 3 files changed, 130 insertions(+), 30 deletions(-)

diff --git a/BrainPortal/app/helpers/scope_helper.rb b/BrainPortal/app/helpers/scope_helper.rb
index e69b1f61e..f87b66951 100644
--- a/BrainPortal/app/helpers/scope_helper.rb
+++ b/BrainPortal/app/helpers/scope_helper.rb
@@ -137,37 +137,38 @@ def scope_custom_params(scope, custom)
   # link's URL and thus behave identically to +scope_params+'s corresponding
   # parameters.
   #
-  # +label+ is expected to be the link's text label and +options+ is expected
-  # to be a hash of options to pass to link_to or ajax_link. Only the special
-  # option :ajax (whether or not to use ajax_link instead of link_to,
-  # defaulting to link_to) is not passed.
-  def scope_link(label, name, scope, compress: true, options: {})
-    url = url_for(scope_params(name, scope, compress: compress))
-    generic_scope_link(label, url, options)
+  # +label+ is expected to be the link's text label and +url_options+ and
+  # +link_options+ are expected to be hashes of options to pass to url_for and
+  # link_to (or ajax_link), respectively. Only the special link option :ajax
+  # (whether or not to use ajax_link instead of link_to, defaulting to link_to)
+  # is not passed.
+  def scope_link(label, name, scope, compress: true, url_options: {}, link_options: {})
+    url = url_for(scope_params(name, scope, compress: compress).merge(url_options))
+    generic_scope_link(label, url, link_options)
   end
 
   # Link version of +scope_filter_params+. Identical to +scope_link+ but uses
   # +scope_filter_params+ in order to generate the URL. See +scope_link+ for more
   # information.
-  def scope_filter_link(label, scope, operation, filters, options: {})
-    url = url_for(scope_filter_params(scope, operation, filters))
-    generic_scope_link(label, url, options)
+  def scope_filter_link(label, scope, operation, filters, url_options: {}, link_options: {})
+    url = url_for(scope_filter_params(scope, operation, filters).merge(url_options))
+    generic_scope_link(label, url, link_options)
   end
 
   # Link version of +scope_order_params+. Identical to +scope_link+ but uses
   # +scope_order_params+ in order to generate the URL. See +scope_link+ for more
   # information.
-  def scope_order_link(label, scope, operation, orders, options: {})
-    url = url_for(scope_order_params(scope, operation, orders))
-    generic_scope_link(label, url, options)
+  def scope_order_link(label, scope, operation, orders, url_options: {}, link_options: {})
+    url = url_for(scope_order_params(scope, operation, orders).merge(url_options))
+    generic_scope_link(label, url, link_options)
   end
 
   # Link version of +scope_custom_params+. Identical to +scope_link+ but uses
   # +scope_custom_params+ in order to generate the URL. See +scope_link+ for more
   # information.
-  def scope_custom_link(label, scope, custom, options: {})
-    url = url_for(scope_custom_params(scope, custom))
-    generic_scope_link(label, url, options)
+  def scope_custom_link(label, scope, custom, url_options: {}, link_options: {})
+    url = url_for(scope_custom_params(scope, custom).merge(url_options))
+    generic_scope_link(label, url, link_options)
   end
 
   # Generate a pretty string representation of +filter+, optionally using
@@ -187,11 +188,11 @@ def pretty_scope_filter(filter, model: nil)
     }
 
     # Explanatory flag (boolean attributes) value names to use instead of
-    # '<attribute>: true' or '<attribute>: false'.
+    # '<attribute>: true/1' or '<attribute>: false/0'.
     flag_names = {
-      'critical' => ['Critical', 'Not critical'],
-      'read'     => ['Read',     'Unread'],
-      'locked'   => ['Locked',   'Unlocked']
+      'critical'       => ['Critical', 'Not critical'],
+      'read'           => ['Read',     'Unread'],
+      'account_locked' => ['Locked',   'Unlocked']
     }
 
     # Model methods/attributes to use as representation of a model record
@@ -212,7 +213,7 @@ def pretty_scope_filter(filter, model: nil)
     # attribute is in flag_names, the corresponding flag value name is
     # the filter's representation.
     if flag = flag_names[attribute]
-      return values.first ? flag.first : flag.last
+      return values.first.to_s =~ /^(true|t|yes|y|on|1)$/i ? flag.first : flag.last
     end
 
     # Is +filter+'s attribute an association attribute? If so, resolve it
@@ -283,11 +284,13 @@ def pretty_scope_filter(filter, model: nil)
   # +collection+, which is either a Ruby Enumerable or ActiveRecord model.
   # As this method is intended as a view helper to create the list of values to
   # filter a collection/model with, the possible values are returned as a list
-  # of hashes matching +DynamicTable+'s filter format, containing:
+  # of hashes matching +DynamicTable+'s filter format (unless +format+ is
+  # specified. See below), containing:
   # [:value]
   #  Possible value for +attribute+.
   # [:label]
-  #  String representation of +:value+ (or just +:value+ if unavailable).
+  #  Label (string representation) for +:value+ (or just +:value+ if
+  #  unavailable).
   # [:indicator]
   #  Count of how many times this specific +:value: was found for +attribute+ in
   #  +collection+.
@@ -300,10 +303,24 @@ def pretty_scope_filter(filter, model: nil)
   # +Scope+::+Filter+'s *association* attribute, and fulfills roughly the same
   # purpose; allow +attribute+ and +label+ to refer to attributes on the joined
   # model (only applicable if +collection+ is an ActiveRecord model).
-  def filter_values_for(collection, attribute, label: nil, association: nil)
-    # TODO Unscoped/base scope/total item count.
+  #
+  # If +format+ is specified, it is expected to be a lambda (or proc) accepting
+  # three arguments; a possible value for +attribute+, a label for the value,
+  # and a count of how many times this value was present and will be used to
+  # format the list of filter values, overriding the default +DynamicTable+
+  # format specified above. Specifying +format+ is roughly equivalent to using
+  # map on the  the generated filter values but without having to unpack the
+  # +DynamicTable+'s filter format hash.
+  #
+  # TODO Unscoped/base scope/total item count.
+  def filter_values_for(collection, attribute, label: nil, association: nil, format: nil)
     return [] if collection.blank?
 
+    # DynamicTable's filter hashes are the default output format
+    format ||= lambda do |value, label, count|
+      { :value => value, :label => label, :indicator => count }
+    end
+
     if (collection <= ActiveRecord::Base rescue nil)
       # Resolve and validate the main +attribute+ to fetch the values of
       attribute, model = ViewScopes.resolve_model_attribute(attribute, collection, association)
@@ -326,7 +343,7 @@ def filter_values_for(collection, attribute, label: nil, association: nil)
         .group(attribute, label)
         .raw_rows(attribute, "#{label} AS #{label_alias}", "COUNT(#{attribute})")
         .reject { |r| r.first.blank? }
-        .map    { |v, l, c| { :value => v, :label => l, :indicator => c } }
+        .map(&format)
 
     else
       # Make sure +attribute+ and +label+ can be accessed in
@@ -346,11 +363,49 @@ def filter_values_for(collection, attribute, label: nil, association: nil)
         .reject  { |v, l| v.blank? }
         .sort_by { |v, l| v }
         .inject(Hash.new(0)) { |h, i| h[i] += 1; h }
-        .map { |(v, l), c| { :value => v, :label => l, :indicator => c } }
+        .map { |(v, l), c| format.(v, l, c) }
     end
   end
 
-  # Utility/internal methods
+  # Fetch the possible values (and their count) for +model+'s (an ActiveRecord
+  # model) association +assoc+ (again an ActiveRecord model), using the
+  # attribute +label+ as labels. This method is a small wrapper around
+  # +filter_values_for+ to make generating association filters easier. For
+  # example, to get group filters for a given @view_scope, one can do:
+  #   assoc_filter_values_for(@view_scope, Group)
+  # which is equivalent to
+  #   filter_values_for(
+  #     @view_scope, :group_id,
+  #     label: 'groups.name',
+  #     association: Group
+  #   )
+  #
+  # Note that +assoc_filter_values_for+ will take the first association on
+  # +model+ matching +assoc+. For a more flexible version of this method (to
+  # use the full association format (which supports arbitrary joins), for
+  # example), use +filter_values_for+ instead.
+  def assoc_filter_values_for(model, assoc, label: 'name')
+    return [] unless (model <= ActiveRecord::Base rescue nil)
+
+    assoc = assoc.klass if assoc.respond_to?(:klass)
+    reflection = model
+      .reflect_on_all_associations
+      .find { |r| r.klass == assoc }
+    raise "no associations on '#{model.table_name}' matching '#{assoc.table_name}'" unless
+      reflection
+
+    filter_values_for(
+      model, reflection.foreign_key,
+      label: ("#{reflection.table_name}.#{label}" if label),
+      association: [
+        assoc,
+        reflection.association_primary_key,
+        reflection.association_foreign_key
+      ]
+    )
+  end
+
+  # Internal methods
 
   # Generate URL parameters suitable for +url_for+ to update the session +scope+
   # items (ordering or filtering rules). This method is the internal
diff --git a/BrainPortal/app/models/cbrain_session.rb b/BrainPortal/app/models/cbrain_session.rb
index 609627240..fb7ccbba6 100644
--- a/BrainPortal/app/models/cbrain_session.rb
+++ b/BrainPortal/app/models/cbrain_session.rb
@@ -190,6 +190,12 @@ def apply_changes(changes)
       # Avoid adding new keys when merging in delete mode
       new.select! { |k,v| base.has_key?(k) } if mode == :delete
 
+      # FIXME: Unlike regular Ruby hashes, Rails' HashWithIndifferentAccess
+      # hash subclass does not support a collision-handling block/proc. To work
+      # around this, HashWithIndifferentAccess objects are converted back into
+      # regular hashes.
+      base = base.to_hash if base.is_a?(HashWithIndifferentAccess)
+
       base.merge!(new) do |key, old, new|
         # Recursively merge hashes with the same key
         next apply.(old, new, mode) if old.is_a?(Hash) && new.is_a?(Hash)
diff --git a/BrainPortal/lib/view_scopes.rb b/BrainPortal/lib/view_scopes.rb
index cfe60e747..d38b0e168 100644
--- a/BrainPortal/lib/view_scopes.rb
+++ b/BrainPortal/lib/view_scopes.rb
@@ -1217,7 +1217,46 @@ def update_session_scopes
       pagination.empty?
   end
 
-  # Utility/internal methods
+  # Utility/helper methods
+
+  # Add a +filter+ (a Filter instance or a hash representation) to a given
+  # +scope+ (a Scope instance) with a value taken from the request parameter
+  # +param+. Unless +unique+ is specified to be false, other filters in +scope+
+  # acting on the same attribute will be removed before adding the new filter.
+  #
+  # Intended to be a simpler/quicker way to do:
+  #   if (value = params[param])
+  #     scope.filters << Scope::Filter.from_hash({
+  #       :attribute => 'field',
+  #       :value     => value
+  #     })
+  #   end
+  def scope_filter_from_params(scope, param, filter, unique: true)
+    return unless params[param]
+
+    filter = Scope::Filter.from_hash(filter) unless filter.is_a?(Scope::Filter)
+    filter.value = params[param]
+
+    scope.filters.reject! { |f| f.attribute.to_s == filter.attribute } if
+      unique && filter.attribute
+
+    scope.filters << filter
+  end
+
+  # Add a default Order instance to a +scope+ (a Scope instance) with the
+  # specified +attribute+ and +direction+ if it doesn't have any yet. This
+  # method is intended as a simpler/quicker way to set a default sorting order
+  # on a scope.
+  def scope_default_order(scope, attribute, direction = :asc)
+    return unless scope.order.blank?
+
+    scope.order << Scope::Order.from_hash({
+      :attribute => attribute,
+      :direction => direction
+    })
+  end
+
+  # Internal methods
 
   # Compress +scope+, which is expected to be a hash representation of a Scope,
   # into a string intended to be embedded in a URL. The +decompress_scope+
@@ -1249,7 +1288,7 @@ def self.decompress_scope(scope)
     scope.tr!('-_', '+/')
     scope = Base64.decode64(scope)
     scope = ActiveSupport::Gzip.decompress(scope)
-    scope = YAML.safe_load(scope)
+    scope = YAML.safe_load(scope, [Date, Time, DateTime])
     scope
   end
 

From 1178d6ddaa6a99e73632143efc57c9a0debfaf8f Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Wed, 9 Sep 2015 15:01:20 -0400
Subject: [PATCH 37/85] Missing JSON descriptor loader

Similar to cbrain_task_class_loader.rb, this loader loads JSON
descriptors as CbrainTask classes. Missed from the last commits due to
the various .gitignores in the plugin directories.
---
 .../cbrain_task_descriptors/.gitignore        |  3 ++
 .../cbrain_task_descriptor_loader.rb          | 41 +++++++++++++++++++
 2 files changed, 44 insertions(+)
 create mode 100644 BrainPortal/cbrain_plugins/installed-plugins/cbrain_task_descriptors/.gitignore
 create mode 100644 BrainPortal/cbrain_plugins/installed-plugins/cbrain_task_descriptors/cbrain_task_descriptor_loader.rb

diff --git a/BrainPortal/cbrain_plugins/installed-plugins/cbrain_task_descriptors/.gitignore b/BrainPortal/cbrain_plugins/installed-plugins/cbrain_task_descriptors/.gitignore
new file mode 100644
index 000000000..8947531f0
--- /dev/null
+++ b/BrainPortal/cbrain_plugins/installed-plugins/cbrain_task_descriptors/.gitignore
@@ -0,0 +1,3 @@
+*
+!.gitignore
+!cbrain_task_descriptor_loader.rb
diff --git a/BrainPortal/cbrain_plugins/installed-plugins/cbrain_task_descriptors/cbrain_task_descriptor_loader.rb b/BrainPortal/cbrain_plugins/installed-plugins/cbrain_task_descriptors/cbrain_task_descriptor_loader.rb
new file mode 100644
index 000000000..9a7711fc5
--- /dev/null
+++ b/BrainPortal/cbrain_plugins/installed-plugins/cbrain_task_descriptors/cbrain_task_descriptor_loader.rb
@@ -0,0 +1,41 @@
+
+#
+# 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 <http://www.gnu.org/licenses/>.  
+#
+
+#
+# CbrainTask descriptor loader
+#
+
+1.times do # just starts a block so local variables don't pollute anything
+
+  basename = File.basename(__FILE__)
+  if basename == 'cbrain_task_descriptor_loader.rb' # usually, the symlink destination
+    puts "Weird. Trying to load the loader?!?"
+    break
+  end
+
+  schema     = SchemaTaskGenerator.default_schema
+  descriptor = __FILE__.sub(/.rb$/,'.json')
+
+  SchemaTaskGenerator.generate(schema, descriptor).integrate if
+    File.exists?(descriptor)
+
+end

From a71ead4779d7b3db2847b001804735f206a3a63a Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Wed, 9 Sep 2015 15:44:20 -0400
Subject: [PATCH 38/85] Port of most controllers and views to the Scopes API

This changeset ports most controllers and views to use the new Scopes
mechanism instead of the basic filters one. The recently ported
controllers and views have a few differences stemming from the API
change:
- Total filter counts are no longer available (TODO), and available
  filter values correspond to the currently shown object list only.
- There is no more @header_scope, @filtered_scope and @filter_params;
  they have been replaced by @view_scope, which corresponds to
  @filtered_scope and @scope, which somewhat corresponds to
  @filter_params.
- The messages index has been reworked, as the old version was somewhat
  clunky and, most importantly, hard to port correctly.

This changeset also refactors some previously ported controllers and
views to use the new helpers introduced in the previous commit (extra
helpers).

Note that this changeset most likely horribly breaks a bunch of things,
as it is very wide reaching and completely refactors a key component in
many places.
---
 .../app/controllers/bourreaux_controller.rb   |  17 ++-
 .../controllers/data_providers_controller.rb  |  17 ++-
 .../controllers/exception_logs_controller.rb  |  21 ++--
 .../app/controllers/feedbacks_controller.rb   |  17 ++-
 .../app/controllers/groups_controller.rb      |  72 ++++-------
 .../app/controllers/messages_controller.rb    |  27 ++--
 .../app/controllers/sites_controller.rb       |  29 ++---
 .../app/controllers/tasks_controller.rb       |  15 +--
 .../app/controllers/tools_controller.rb       |   7 +-
 .../app/controllers/userfiles_controller.rb   |  12 +-
 .../app/controllers/users_controller.rb       |  32 +++--
 .../bourreaux/_bourreaux_display.html.erb     |  40 +++---
 .../custom_filters/_custom_filter_li.html.erb |  20 ++-
 .../_data_providers_table.html.erb            |   9 +-
 .../_one_data_provider_table.html.erb         |  28 ++---
 .../_exception_logs_table.html.erb            |  33 +++--
 .../views/feedbacks/_feedbacks_table.html.erb |  17 +--
 .../app/views/groups/_groups_table.html.erb   |  81 +++++++-----
 .../app/views/messages/_filters.html.erb      |  91 --------------
 .../messages/_message_index_display.html.erb  | 118 +++++++++++++++---
 .../app/views/shared/_active_filters.html.erb |  20 ++-
 .../app/views/sites/_sites_table.html.erb     |  37 +++---
 BrainPortal/app/views/tags/_tag_li.html.erb   |  16 +--
 .../app/views/tasks/_tasks_display.html.erb   |  21 ++--
 .../app/views/tools/_tools_table.html.erb     |  30 ++---
 .../app/views/userfiles/_file_menu.html.erb   |   4 +-
 .../userfiles/_userfiles_display.html.erb     |  25 ++--
 .../userfiles/_view_option_button.html.erb    |   2 +-
 .../app/views/users/_users_table.html.erb     |  70 +++++++----
 BrainPortal/public/stylesheets/cbrain.css     |  11 ++
 30 files changed, 456 insertions(+), 483 deletions(-)
 delete mode 100644 BrainPortal/app/views/messages/_filters.html.erb

diff --git a/BrainPortal/app/controllers/bourreaux_controller.rb b/BrainPortal/app/controllers/bourreaux_controller.rb
index 1e4bd7c7a..84de2a1e2 100644
--- a/BrainPortal/app/controllers/bourreaux_controller.rb
+++ b/BrainPortal/app/controllers/bourreaux_controller.rb
@@ -38,15 +38,14 @@ 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
-
-    if current_user.has_role? :admin_user
-      @filter_params['details'] = 'on' unless @filter_params.has_key?('details')
-    end
+    @scope = scope_from_session('bourreaux')
+    scope_default_order(@scope, 'type')
+
+    @bourreaux = @scope.apply(
+      RemoteResource
+        .find_all_accessible_by_user(current_user)
+        .includes(:user, :group)
+    )
 
     respond_to do |format|
       format.html
diff --git a/BrainPortal/app/controllers/data_providers_controller.rb b/BrainPortal/app/controllers/data_providers_controller.rb
index 0dceb9913..083cbc109 100644
--- a/BrainPortal/app/controllers/data_providers_controller.rb
+++ b/BrainPortal/app/controllers/data_providers_controller.rb
@@ -36,15 +36,14 @@ 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"
-
-    @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
+    @scope = scope_from_session('data_providers')
+    scope_default_order(@scope, 'name')
+
+    @data_providers = @scope.apply(
+      DataProvider
+        .find_all_accessible_by_user(current_user)
+        .includes(:user, :group)
+    )
 
     respond_to do |format|
       format.html
diff --git a/BrainPortal/app/controllers/exception_logs_controller.rb b/BrainPortal/app/controllers/exception_logs_controller.rb
index 6efdbd9de..1129b140a 100644
--- a/BrainPortal/app/controllers/exception_logs_controller.rb
+++ b/BrainPortal/app/controllers/exception_logs_controller.rb
@@ -17,24 +17,27 @@
 # 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)
+
+    @view_scope = @scope.apply(ExceptionLog)
 
+    @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|
@@ -56,7 +59,7 @@ 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|
diff --git a/BrainPortal/app/controllers/feedbacks_controller.rb b/BrainPortal/app/controllers/feedbacks_controller.rb
index d227691ee..d3af05021 100644
--- a/BrainPortal/app/controllers/feedbacks_controller.rb
+++ b/BrainPortal/app/controllers/feedbacks_controller.rb
@@ -17,23 +17,22 @@
 # 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)
+
+    @feedbacks = @scope.apply(Feedback.includes(:user))
 
     respond_to do |format|
       format.js
@@ -106,7 +105,7 @@ 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 }
diff --git a/BrainPortal/app/controllers/groups_controller.rb b/BrainPortal/app/controllers/groups_controller.rb
index 7e30695a8..323953f9c 100644
--- a/BrainPortal/app/controllers/groups_controller.rb
+++ b/BrainPortal/app/controllers/groups_controller.rb
@@ -30,54 +30,27 @@ class GroupsController < ApplicationController
   # GET /groups
   # GET /groups.xml
   def index  #:nodoc:
-    @filter_params["sort_hash"]["order"] ||= "groups.name"
-    if current_user.has_role?(:normal_user)
-      @filter_params["button_view"] ||= "on"
-    end
+    @scope = scope_from_session('groups')
+    scope_default_order(@scope, 'groups.name')
 
-    @header_scope   = current_user.available_groups
-    @filtered_scope = base_filtered_scope @header_scope.includes(:site)
-    @sorted_scope   = base_sorted_scope @filtered_scope
-    @total_entries  = @sorted_scope.count
+    scope_filter_from_params(@scope, :name_like, {
+      :attribute => 'name',
+      :operator  => 'match'
+    })
 
-    # For Pagination
-    @per_page = 50 unless @filter_params["per_page"]
-    offset = (@current_page - 1) * @per_page
+    @scope.custom[:button] = true if
+      current_user.has_role?(:normal_user) && @scope.custom[:button].nil?
 
-    unless [:html, :js].include?(request.format.to_sym)
-      @per_page = 999_999_999
-      offset = 0
-    end
+    @view_scope = @scope.apply(current_user.available_groups.includes(:site))
 
-    if @filter_params["button_view"] == "on"
-      pagination_list = @sorted_scope.limit(@per_page).offset(offset).where("groups.type = 'WorkGroup'").all.sort_by(&:short_pretty_type)
-      num_workgroups  = pagination_list.size
-      num_missing     = @per_page - num_workgroups
+    @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 num_missing > 0
-        total_workgroups = @sorted_scope.where("groups.type = 'WorkGroup'").count
-        sys_offset = [offset - total_workgroups, 0].max
-        pagination_list += @sorted_scope.limit(num_missing).offset(sys_offset).where("groups.type <> 'WorkGroup'").all
-      end
-      num_missing = @per_page - pagination_list.size
-      if num_missing > 0
-        pagination_list << "ALL"
-      end
-      @total_entries += 1
-    else
-      pagination_list  = @sorted_scope.limit(@per_page).offset(offset)
-    end
-
-    @groups = WillPaginate::Collection.create(@current_page, @per_page) do |pager|
-      pager.replace(pagination_list)
-      pager.total_entries = @total_entries
-      pager
-    end
-
-    @group_id_2_userfile_counts      = Userfile.group("group_id").count
-    @group_id_2_task_counts          = CbrainTask.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
-    if @filter_params["button_view"] == "on"
+    @group_id_2_userfile_counts = Userfile.group("group_id").count
+    @group_id_2_task_counts     = CbrainTask.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
+    if @scope.custom[:button]
       @group_id_2_userfile_counts[nil] = Userfile.find_all_accessible_by_user(current_user, :access_requested => :read).count
       @group_id_2_task_counts[nil]     = current_user.available_tasks.count
     else
@@ -87,12 +60,13 @@ def index  #:nodoc:
       @group_id_2_brain_portal_counts  = BrainPortal.group("group_id").count
     end
 
+    scope_to_session(@scope)
     current_session.save_preferences
 
     respond_to do |format|
       format.js
-      format.html  # index.html.erb
-      format.xml   { render :xml => @groups }
+      format.html # index.html.erb
+      format.xml  { render :xml  => @groups }
       format.json { render :json => @groups.to_json(methods: :type) }
     end
   end
@@ -235,8 +209,12 @@ def switch #:nodoc:
     redirect_action     = params[:redirect_action]     || :index
     redirect_id         = params[:redirect_id]
 
-    current_session.params_for(:userfiles)['filter_hash'].delete('group_id')
-    current_session.params_for(:tasks)['filter_hash'].delete('group_id')
+    ['userfiles', 'tasks'].each do |name|
+      scope = scope_from_session(name)
+      scope.filters.reject! { |f| f.attribute.to_s == 'group_id' }
+      scope_to_session(scope)
+    end
+
     current_session[:persistent_userfiles].clear rescue nil
 
     redirect_path = { :controller => redirect_controller, :action => redirect_action }
diff --git a/BrainPortal/app/controllers/messages_controller.rb b/BrainPortal/app/controllers/messages_controller.rb
index 5b4c4419a..416f351c5 100644
--- a/BrainPortal/app/controllers/messages_controller.rb
+++ b/BrainPortal/app/controllers/messages_controller.rb
@@ -31,23 +31,22 @@ class MessagesController < ApplicationController
   # GET /messages
   # GET /messages.xml
   def index #:nodoc:
-    @filter_params["sort_hash"]["order"] ||= "messages.last_sent"
-    @filter_params["sort_hash"]["dir"]   ||= "DESC"
+    @scope = scope_from_session('messages')
+    scope_default_order(@scope, 'last_sent', :desc)
 
-    scope = base_filtered_scope
-    if @filter_params["sort_hash"]["order"] == "messages.sender"
-      scope = scope.joins("LEFT JOIN users as senders ON senders.id = messages.sender_id").
-                      order("senders.login #{@filter_params["sort_hash"]["dir"]}")
-    else
-      scope = base_sorted_scope(scope)
-    end
-    scope = scope.includes(:user)
-    unless current_user.has_role?(:admin_user)
-      scope = scope.where(:user_id => current_user.available_users.map(&:id))
-    end
+    @view_scope = @messages = @scope.apply(
+      Message.where(current_user.has_role?(:admin_user) ?
+        {} : { :user_id => current_user.available_users.map(&:id) }
+      )
+    )
+
+    @read_count   = @view_scope.where(:read => true).count
+    @unread_count = @view_scope.count - @read_count
 
-    @messages = scope.paginate(:page => @current_page, :per_page => @per_page)
+    @scope.pagination ||= Scope::Pagination.from_hash({ :per_page => 25 })
+    @messages = @scope.pagination.apply(@view_scope)
 
+    scope_to_session(@scope)
     current_session.save_preferences
 
     respond_to do |format|
diff --git a/BrainPortal/app/controllers/sites_controller.rb b/BrainPortal/app/controllers/sites_controller.rb
index e27fc7c5c..5b58741fe 100644
--- a/BrainPortal/app/controllers/sites_controller.rb
+++ b/BrainPortal/app/controllers/sites_controller.rb
@@ -17,24 +17,25 @@
 # 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 Site resource.
 class SitesController < ApplicationController
-  
+
   Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
-  
-  before_filter :login_required 
+
+  before_filter :login_required
   before_filter :admin_role_required, :except  => :show
   before_filter :site_membership_required, :only => :show
-  
+
   # GET /sites
   # GET /sites.xml
   def index #:nodoc:
-    @filter_params["sort_hash"]["order"] ||= 'sites.name'
-    
-    @sites = base_sorted_scope(base_filtered_scope Site.includes( [:users, :groups] ))
+    @scope = scope_from_session('sites')
+    scope_default_order(@scope, 'name')
+
+    @sites = @scope.apply(Site.includes(:users, :groups))
 
     respond_to do |format|
       format.js
@@ -47,13 +48,13 @@ def index #:nodoc:
   # GET /sites/1.xml
   def show #:nodoc:
     @site = current_user.has_role?(:admin_user) ? Site.find(params[:id]) : current_user.site
-    
+
     respond_to do |format|
       format.html # show.html.erb
       format.xml  { render :xml => @site }
     end
   end
- 
+
   def new #:nodoc:
     @site = Site.new
     render :partial => "new"
@@ -63,7 +64,7 @@ def new #:nodoc:
   # POST /sites.xml
   def create #:nodoc:
     @site = Site.new(params[:site])
-    
+
     respond_to do |format|
       if @site.save
         @site.addlog_context(self,"Created by '#{current_user.login}'")
@@ -81,7 +82,7 @@ def create #:nodoc:
   # PUT /sites/1.xml
   def update #:nodoc:
     @site = Site.find(params[:id])
-    
+
     params[:site] ||= {}
 
     original_user_ids    = @site.user_ids
@@ -89,12 +90,12 @@ def update #:nodoc:
     original_group_ids   = @site.group_ids
 
     commit_name = extract_params_key([ :update_users, :update_groups ])
-    
+
     unless commit_name == :update_users
       params[:site][:user_ids]    = original_user_ids    # we need to make sure they stay the same
       params[:site][:manager_ids] = original_manager_ids # we need to make sure they stay the same
     end
-    
+
     unless commit_name == :update_groups
       params[:site][:group_ids] = original_group_ids    # we need to make sure they stay the same
     end
diff --git a/BrainPortal/app/controllers/tasks_controller.rb b/BrainPortal/app/controllers/tasks_controller.rb
index 04026596b..d03426f7a 100644
--- a/BrainPortal/app/controllers/tasks_controller.rb
+++ b/BrainPortal/app/controllers/tasks_controller.rb
@@ -35,16 +35,9 @@ def index #:nodoc:
 
     # Default sorting order and batch mode
     if api_request
-      @scope.order << Scope::Order.from_hash({
-        :attribute => 'updated_at',
-        :direction => :desc
-      }) if @scope.order.blank?
+      scope_default_order(@scope, 'updated_at', :desc)
     else
-      @scope.order << Scope::Order.from_hash({
-        :attribute => 'rank',
-        :direction => :asc
-      }) if @scope.order.blank?
-
+      scope_default_order(@scope, 'rank')
       @scope.custom[:batch] = true if @scope.custom[:batch].nil?
     end
 
@@ -69,7 +62,7 @@ def index #:nodoc:
       @tasks.map! do |id, count|
         first = @view_scope
             .where(:batch_id => id)
-            .order([:rank, :level, :id])
+            .order(['cbrain_tasks.rank', 'cbrain_tasks.level', 'cbrain_tasks.id'])
             .first
 
         { :batch => id, :first => first, :count => count } if first
@@ -993,7 +986,7 @@ def view_scope(base) #:nodoc:
     base = base.where(
       :bourreau_id => Bourreau
         .find_all_accessible_by_user(current_user)
-        .raw_rows(:id)
+        .raw_rows("#{Bourreau.quoted_table_name}.id")
         .flatten
     )
 
diff --git a/BrainPortal/app/controllers/tools_controller.rb b/BrainPortal/app/controllers/tools_controller.rb
index 20151a13c..d7370a76e 100644
--- a/BrainPortal/app/controllers/tools_controller.rb
+++ b/BrainPortal/app/controllers/tools_controller.rb
@@ -31,11 +31,10 @@ class ToolsController < ApplicationController
   # GET /tools
   # GET /tools.xml
   def index #:nodoc:
-    @filter_params["sort_hash"]["order"] ||= 'tools.name'
+    @scope = scope_from_session('tools')
+    scope_default_order(@scope, 'name')
 
-    @header_scope   = current_user.available_tools
-    @filtered_scope = base_filtered_scope(@header_scope.includes(:user, :group))
-    @tools          = base_sorted_scope @filtered_scope
+    @tools = @scope.apply(current_user.available_tools.includes(:user, :group))
 
     respond_to do |format|
       format.js
diff --git a/BrainPortal/app/controllers/userfiles_controller.rb b/BrainPortal/app/controllers/userfiles_controller.rb
index 13aa486af..fa178d8c5 100644
--- a/BrainPortal/app/controllers/userfiles_controller.rb
+++ b/BrainPortal/app/controllers/userfiles_controller.rb
@@ -45,14 +45,10 @@ def index #:nodoc:
 
     # Manually handle the 'name_like' input, as it cant be pre-computed
     # server-side (and going the JS route would be overkill).
-    if (name_like = params[:name_like])
-      @scope.filters.reject! { |f| f.attribute.to_s == 'name' }
-      @scope.filters << Scope::Filter.from_hash({
-        :attribute => 'name',
-        :operator  => 'match',
-        :value     => name_like
-      })
-    end
+    scope_filter_from_params(@scope, :name_like, {
+      :attribute => 'name',
+      :operator  => 'match'
+    })
 
     # Base userfiles scope, without any filtering or ordering
     @base_scope = base_scope
diff --git a/BrainPortal/app/controllers/users_controller.rb b/BrainPortal/app/controllers/users_controller.rb
index 504a82940..efad8351c 100644
--- a/BrainPortal/app/controllers/users_controller.rb
+++ b/BrainPortal/app/controllers/users_controller.rb
@@ -35,29 +35,27 @@ class UsersController < ApplicationController
   API_HIDDEN_ATTRIBUTES = [ :salt, :crypted_password ]
 
   def index #:nodoc:
-    @filter_params["sort_hash"]["order"] ||= 'users.full_name'
+    @scope = scope_from_session('users')
+    scope_default_order(@scope, 'full_name')
 
-    sort_order = "#{@filter_params["sort_hash"]["order"]} #{@filter_params["sort_hash"]["dir"]}"
+    scope_filter_from_params(@scope, :name_like, {
+      :attribute => 'full_name',
+      :operator  => 'match'
+    })
 
-    @header_scope = current_user.available_users
+    @view_scope = @scope.apply(current_user.available_users.includes(:groups, :site))
 
-    @filtered_scope = base_filtered_scope @header_scope.includes( [:groups, :site] ).order( sort_order )
-    @users          = base_sorted_scope @filtered_scope
+    @scope.pagination ||= Scope::Pagination.from_hash({ :per_page => 50 })
+    @users = @scope.pagination.apply(@view_scope) if
+      [:html, :js].include?(request.format.to_sym)
 
     # Precompute file, task and locked/unlocked counts.
-    @users_file_counts  = Userfile.where(:user_id => @users.map(&:id)).group(:user_id).count
-    @users_task_counts  = CbrainTask.real_tasks.where(:user_id => @users.map(&:id)).group(:user_id).count
-    @locked_users_count   = @users.where(:account_locked => true).count
-    @unlocked_users_count = @users.count - @locked_users_count
-
-    # For Pagination
-    unless [:html, :js].include?(request.format.to_sym)
-      @per_page = 999_999_999
-    end
-
-    # Turn the array ordered_real into the final paginated collection
-    @users = @users.paginate(:page => @current_page, :per_page => @per_page)
+    @users_file_counts  = Userfile.where(:user_id => @view_scope).group(:user_id).count
+    @users_task_counts  = CbrainTask.real_tasks.where(:user_id => @view_scope).group(:user_id).count
+    @locked_users_count   = @view_scope.where(:account_locked => true).count
+    @unlocked_users_count = @view_scope.count - @locked_users_count
 
+    scope_to_session(@scope)
     current_session.save_preferences
 
     respond_to do |format|
diff --git a/BrainPortal/app/views/bourreaux/_bourreaux_display.html.erb b/BrainPortal/app/views/bourreaux/_bourreaux_display.html.erb
index a15ac3e15..7ba98227e 100644
--- a/BrainPortal/app/views/bourreaux/_bourreaux_display.html.erb
+++ b/BrainPortal/app/views/bourreaux/_bourreaux_display.html.erb
@@ -23,22 +23,18 @@
 -%>
 
 <%
-  table = dynamic_index_table(@bourreaux,
+  table = dynamic_scoped_table(@bourreaux,
     :id         => "bourreaux_table",
     :class      => [ :resource_list ],
+    :scope      => @scope,
     :render     => false,
     :sort_map   => {
-      :type        => 'remote_resources.type',
-      :name        => 'remote_resources.name',
-      :owner       => 'users.login',
-      :group       => 'groups.name',
-      :time_zone   => 'remote_resources.time_zone',
-      :online      => 'remote_resources.online',
-      :description => 'remote_resources.description'
+      :owner => { :a => 'users.login', :j => User  },
+      :group => { :a => 'groups.name', :j => Group }
     },
     :filter_map => {
-      :owner => 'user_id',
-      :group => 'group_id'
+      :owner => { :a => 'user_id'  },
+      :group => { :a => 'group_id' }
     }
   ) do |t|
 %>
@@ -50,20 +46,11 @@
       (@row_fetch && resource.info(:ping))
     end
 
-    filters_for = lambda do |target, opts = {}|
-      return if @row_fetch
-      if target.is_a?(Symbol)
-        basic_filters_for(@filtered_scope, @header_scope, RemoteResource, target)
-      else
-        association_filters_for(@filtered_scope, @header_scope, RemoteResource, target, opts)
-      end
-    end
-
     t.row { |r| { :html => { 'data-info-url' => row_data_bourreau_path(r) } } unless loaded.(r) }
 
     t.column("Server Type", :type,
       :sortable => true,
-      :filters  => filters_for.(:type)
+      :filters  => filter_values_for(@bourreaux, :type)
     ) { |r| r.is_a?(Bourreau) ? "Execution" : "Portal" }
 
     t.column("Server Name", :name,
@@ -88,12 +75,12 @@
     t.column("Owner", :owner,
       :hidden   => true,
       :sortable => true,
-      :filters  => filters_for.(User, :name_method => :login)
+      :filters  => assoc_filter_values_for(@bourreaux, User, label: 'login')
     ) { |r| link_to_user_with_tooltip(r.user) }
 
     t.column("Project", :group,
       :sortable => true,
-      :filters  => filters_for.(Group)
+      :filters  => assoc_filter_values_for(@bourreaux, Group)
     ) { |r| link_to_group_if_accessible(r.group) }
 
     t.column("Site", :site,
@@ -103,7 +90,7 @@
     t.column("Time Zone", :time_zone,
       :hidden   => true,
       :sortable => true,
-      :filters  => filters_for.(:time_zone)
+      :filters  => filter_values_for(@bourreaux, :time_zone)
     ) { |r| r.time_zone || "(Unset)" }
 
     t.column("Online?", :online,
@@ -261,7 +248,12 @@
     <%= overlay_ajax_link "Help", "/doc/server/view_server.html", :class  => "button" %>
   </div>
 
-  <%= render :partial => 'shared/active_filters', :locals => {:model => :bourreau} %>
+  <%=
+    render(:partial => 'shared/active_filters', :locals  => {
+      :scope => @scope,
+      :model => RemoteResource
+    })
+  %>
 
   <% content_for :scripts do %>
     <% javascript_tag (render :partial => "fetch_row.js.erb", :formats => [:js]).to_s %>
diff --git a/BrainPortal/app/views/custom_filters/_custom_filter_li.html.erb b/BrainPortal/app/views/custom_filters/_custom_filter_li.html.erb
index 14de8ec61..8d54ecbee 100644
--- a/BrainPortal/app/views/custom_filters/_custom_filter_li.html.erb
+++ b/BrainPortal/app/views/custom_filters/_custom_filter_li.html.erb
@@ -24,17 +24,15 @@
 
 <b>
 <%=
-  ajax_link(
-    crop_text_to(15, filter.name),
-    url_for(scope_custom_params(@scope, {
-        'custom_filters' => [filter.id]
-      }).merge({
-        :controller  => @custom_filter.filtered_class_controller,
-        :_scope_mode => :append
-      })
-    ),
-    :class    => 'action_link',
-    :datatype => :script
+  scope_custom_link(crop_text_to(15, filter.name),
+    @scope, { 'custom_filters' => [filter.id] },
+    url_options:  {
+      'controller'  => @custom_filter.filtered_class_controller,
+      '_scope_mode' => 'append'
+    },
+    link_options: {
+      :ajax => true
+    }
   )
 %>
 </b>
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 6f48f60b1..85816741e 100644
--- a/BrainPortal/app/views/data_providers/_data_providers_table.html.erb
+++ b/BrainPortal/app/views/data_providers/_data_providers_table.html.erb
@@ -54,9 +54,12 @@
   <%= help_button("data_providers/info") %>
 </div>
 
-
-<%= render :partial => 'shared/active_filters', :locals => {:model => :data_provider} %>
-
+<%=
+  render(:partial => 'shared/active_filters', :locals  => {
+    :scope => @scope,
+    :model => DataProvider
+  })
+%>
 
 <fieldset>
 <legend>Official Data Storage</legend>
diff --git a/BrainPortal/app/views/data_providers/_one_data_provider_table.html.erb b/BrainPortal/app/views/data_providers/_one_data_provider_table.html.erb
index e79960dd0..8cff9bf10 100644
--- a/BrainPortal/app/views/data_providers/_one_data_provider_table.html.erb
+++ b/BrainPortal/app/views/data_providers/_one_data_provider_table.html.erb
@@ -23,23 +23,19 @@
 -%>
 
 <%=
-  dynamic_index_table(data_providers,
+  dynamic_scoped_table(data_providers,
     :class      => [ :resource_list, :whole_width ],
     :id         => "data_provider_table_#{id}",
-    :sort_map   => {
-      :name        => 'data_providers.name',
-      :type        => 'data_providers.type',
-      :owner       => 'users.login',
-      :group       => 'groups.name',
-      :time_zone   => 'data_providers.time_zone',
-      :online      => 'data_providers.online',
-      :mode        => 'data_providers.read_only',
-      :sync        => 'data_providers.not_syncable',
-      :description => 'data_providers.description'
+    :scope      => @scope,
+    :order_map  => {
+      :owner => { :a => 'users.login', :j => User  },
+      :group => { :a => 'groups.name', :j => Group },
+      :mode  => { :a => 'data_providers.read_only'    },
+      :sync  => { :a => 'data_providers.not_syncable' }
     },
     :filter_map => {
-      :owner => 'user_id',
-      :group => 'group_id'
+      :owner => { :a => 'user_id'  },
+      :group => { :a => 'group_id' }
     }
   ) do |t|
 %>
@@ -51,18 +47,18 @@
     t.column("Type", :type,
       :sortable => true,
       :hidden   => true,
-      :filters  => basic_filters_for(@filtered_scope, @header_scope, :data_provider, :type) { |v| v.to_s }
+      :filters  => filter_values_for(@data_providers, :type)
     ) { |dp| dp.class.to_s } if current_user.has_role? :admin_user
 
     t.column("Owner", :owner,
       :hidden   => true,
       :sortable => true,
-      :filters  => association_filters_for(@filtered_scope, @header_scope, :data_provider, :user, :name_method => :login)
+      :filters  => assoc_filter_values_for(@data_providers, User, label: 'login')
     ) { |dp| link_to_user_with_tooltip(dp.user) }
 
     t.column("Project", :group,
       :sortable => true,
-      :filters  => association_filters_for(@filtered_scope, @header_scope, :data_provider, :group)
+      :filters  => assoc_filter_values_for(@data_providers, Group)
     ) { |dp| link_to_group_if_accessible(dp.group) }
 
     t.column("Site", :site,
diff --git a/BrainPortal/app/views/exception_logs/_exception_logs_table.html.erb b/BrainPortal/app/views/exception_logs/_exception_logs_table.html.erb
index dc9657b42..f2277291b 100644
--- a/BrainPortal/app/views/exception_logs/_exception_logs_table.html.erb
+++ b/BrainPortal/app/views/exception_logs/_exception_logs_table.html.erb
@@ -26,7 +26,12 @@
   <%= external_submit_button "Delete Checked Exceptions", "exception_form", :class  => "button", :confirm  => "Are you sure you want to delete the selected logs?"  %>
 </div>
 
-<%= render :partial => 'shared/active_filters', :locals => {:model => :exception_log} %>
+<%=
+  render(:partial => 'shared/active_filters', :locals  => {
+    :scope => @scope,
+    :model => ExceptionLog
+  })
+%>
 
 <div class="pagination">
   <span class="page_links">
@@ -36,33 +41,23 @@
 
 <%= ajax_form_tag(url_for(:action => :destroy), :method => :delete, :datatype => :script, :id => "exception_form") do %>
   <%=
-    dynamic_index_table(@exception_logs,
+    dynamic_scoped_table(@exception_logs,
       :id         => 'exception_logs_table',
       :class      => [ :resource_list ],
-      :sort_map   => {
-        :exception_class    => 'exception_logs.exception_class',
-        :request_method     => 'exception_logs.request_method',
-        :request_controller => 'exception_logs.request_controller',
-        :request_action     => 'exception_logs.request_action',
-        :request_format     => 'exception_logs.request_format',
-        :user               => 'users.login',
-        :revision_no        => 'exception_logs.revision_no',
-        :created_at         => 'exception_logs.created_at'
+      :scope      => @scope,
+      :order_map  => {
+        :user => { :a => 'users.login', :j => User }
       },
       :filter_map => {
-        :user => 'user_id'
+        :user => { :a => 'user_id' }
       }
     ) do |t|
   %>
     <%
-      filters_for = lambda do |field|
-        basic_filters_for(@filtered_scope, ExceptionLog.scoped, ExceptionLog, field)
-      end
-
       generic_column = lambda do |label,field|
         t.column(label, field,
           :sortable => true,
-          :filters  => filters_for.(field)
+          :filters  => filter_values_for(@view_scope, field)
         )
       end
 
@@ -71,7 +66,7 @@
 
       t.column("Exception", :exception_class,
         :sortable => true,
-        :filters  => filters_for.(:exception_class)
+        :filters  => filter_values_for(@view_scope, :exception_class)
       ) { |e| link_to e.exception_class, e }
 
       t.column("Message", :message) { |e| crop_text_to(75, e.message) }
@@ -83,7 +78,7 @@
 
       t.column("User", :user,
         :sortable => true,
-        :filters  => association_filters_for(@filtered_scope, ExceptionLog.scoped, "exception_log", "user", :name_method => "login")
+        :filters  => assoc_filter_values_for(@view_scope, User, label: 'login')
       ) { |e| link_to_user_with_tooltip(e.user) }
 
       generic_column.("Revision",   :revision_no)
diff --git a/BrainPortal/app/views/feedbacks/_feedbacks_table.html.erb b/BrainPortal/app/views/feedbacks/_feedbacks_table.html.erb
index a65801714..f34c73cdf 100644
--- a/BrainPortal/app/views/feedbacks/_feedbacks_table.html.erb
+++ b/BrainPortal/app/views/feedbacks/_feedbacks_table.html.erb
@@ -27,19 +27,22 @@
   <%= overlay_ajax_link "Help", "/doc/feedback/feedback.html", :class  => "button" %>
 </div>
 
-<%= render :partial => 'shared/active_filters', :locals => {:model => :feedback} %>
+<%=
+  render(:partial => 'shared/active_filters', :locals => {
+    :scope => @scope,
+    :model => Feedback
+  })%>
 
 <%=
-  dynamic_index_table(@feedbacks,
+  dynamic_scoped_table(@feedbacks,
     :id         => 'feedbacks_table',
     :class      => [ :resource_list ],
+    :scope      => @scope,
     :sort_map   => {
-      :summary    => 'feedbacks.summary',
-      :author     => 'users.login',
-      :created_at => 'feedbacks.created_at'
+      :author => { :a => 'users.login', :j => User }
     },
     :filter_map => {
-      :author => 'user_id'
+      :author => { :a => 'user_id' }
     }
   ) do |t|
 %>
@@ -50,7 +53,7 @@
 
     t.column("Author", :author,
       :sortable => true,
-      :filters  => association_filters_for(@filtered_scope, Feedback.scoped, "feedback", "user", :name_method => "login")
+      :filters  => assoc_filter_values_for(@feedbacks, User, label: 'login')
     ) { |f| link_to_user_with_tooltip(f.user) }
 
     t.column("Posted at", :created_at,
diff --git a/BrainPortal/app/views/groups/_groups_table.html.erb b/BrainPortal/app/views/groups/_groups_table.html.erb
index 43db35d0d..7ce07a12f 100644
--- a/BrainPortal/app/views/groups/_groups_table.html.erb
+++ b/BrainPortal/app/views/groups/_groups_table.html.erb
@@ -27,50 +27,71 @@
    <%= overlay_ajax_link "Help", "/doc/groups/groups_info.html", :class  => "button" %>
 </div>
 
-<%= render :partial => 'shared/active_filters', :locals => {:model => :group} %>
+<%=
+  render(:partial => 'shared/active_filters', :locals  => {
+    :scope => @scope,
+    :model => Group
+  })
+%>
 
-<% button_view = (@filter_params["button_view"] == "on") %>
+<% button_view = @scope.custom[:button] %>
 
 <div class="pagination">
   <div class="pagination_left_side">
     <%=
-      filter_add_link (button_view ? "Switch to List View" : "Switch to Button View"),
-        :parameter => :button_view,
-        :value     => set_toggle(@filter_params["button_view"])
+      scope_custom_link(
+        "Switch to #{button_view ? 'List' : 'Button'} View",
+        @scope, { 'button' => !button_view }
+      )
+    %>
+    &nbsp;
+    <%=
+      scope_custom_link(
+        "#{@scope.custom[:small_buttons] ? 'Large' : 'Small'} buttons",
+        @scope, { 'small_buttons' => !@scope.custom[:small_buttons] }
+      ) if button_view
     %>
-    <% if button_view %>
-      &nbsp;
-      <%=
-        filter_add_link (@filter_params["small_buttons"] == 'on' ? "Large buttons" : "Small buttons"),
-          :parameter => :small_buttons,
-          :value     => set_toggle(@filter_params["small_buttons"])
-      %>
-    <% end %>
   </div>
   <div class="page_links">
     <% if current_user.has_role?(:normal_user) && button_view %>
       <%= will_paginate @groups, :inner_window => 5, :outer_window => 4, :container => false, :params => { :file_ids => nil } %>
     <% end %>
-    (<%= pluralize @total_entries, "projects" %>)
+    (<%= pluralize @view_scope.count, "projects" %>)
   </div>
   <div class="pagination_right_side">
-    Search by name: <%= ajax_search_box "name_like", groups_path(:update_filter => :filter_hash) %>
+    Search by name: <%= ajax_search_box "name_like", groups_path %>
   </div>
 </div>
 
 <% if button_view %>
   <% unless current_user.has_role?(:normal_user) %>
     <%=
-      dynamic_index_table([],
+      dynamic_scoped_table([],
         :id         => "project_button_table",
         :class      => "project_button_header",
-        :sort_map   => { :name => 'groups.name', :site => 'sites.name' },
-        :filter_map => { :site => 'site_id' }
+        :scope      => @scope,
+        :order_map  => {
+          :site => { :a => 'sites.name', :j => Site }
+        },
+        :filter_map => {
+          :site => { :a => 'site_id' }
+        }
       ) do |t|
         t.paginate(:collection => @groups)
-        t.column("Name",         :name, :sortable => true)
-        t.column("Project Type", :type, :filters  => basic_filters_for(@filtered_scope, @header_scope, Group, :type))
-        t.column("Site",         :site, :filters  => association_filters_for(@filtered_scope, @header_scope, Group, :site))
+
+        t.column("Name", :name,
+          :sortable => true
+        )
+
+        t.column("Project Type", :type,
+          :sortable => true,
+          :filters  => filter_values_for(@view_scope, :type)
+        )
+
+        t.column("Site", :site,
+          :sortable => true,
+          :filters  => assoc_filter_values_for(@view_scope, Site)
+        )
       end
     %>
   <% end %>
@@ -78,7 +99,7 @@
     <%= group_legend(@groups) %>
   </div>
   <div>
-    <% css_small = "small" if @filter_params["small_buttons"] == 'on' %>
+    <% css_small = "small" if @scope.custom[:small_buttons] %>
     <% @groups.each do |g| %>
       <% if g == "ALL" %>
         <div style="color:black" data-href="<%= url_for(:action => :switch, :id => "all") %>" data-method="post" class="project_button <%= css_small %>">
@@ -130,17 +151,15 @@
   </div>
 <% else %>
   <%=
-    dynamic_index_table(@groups,
+    dynamic_scoped_table(@groups,
       :id         => 'groups_table',
       :class      => [ :resource_list ],
-      :sort_map   => {
-        :name        => 'groups.name',
-        :description => 'groups.description',
-        :type        => 'groups.type',
-        :site        => 'sites.name'
+      :scope      => @scope,
+      :order_map  => {
+        :site => { :a => 'sites.name', :j => Site }
       },
       :filter_map => {
-        :site => 'site_id'
+        :site => { :a => 'site_id' }
       }
     ) do |t|
       t.paginate
@@ -155,12 +174,12 @@
 
       t.column("Project Type", :type,
         :sortable => true,
-        :filters  => basic_filters_for(@filtered_scope, @header_scope, Group, :type)
+        :filters  => filter_values_for(@view_scope, :type)
       ) { |g| g.pretty_category_name(current_user) }
 
       t.column("Site", :site,
         :sortable => true,
-        :filters  => association_filters_for(@filtered_scope, @header_scope, Group, :site)
+        :filters  => assoc_filter_values_for(@view_scope, Site)
       ) { |g| link_to_site_if_accessible(g.site) }
 
       t.column("Users", :users) do |g|
diff --git a/BrainPortal/app/views/messages/_filters.html.erb b/BrainPortal/app/views/messages/_filters.html.erb
deleted file mode 100644
index 618f69187..000000000
--- a/BrainPortal/app/views/messages/_filters.html.erb
+++ /dev/null
@@ -1,91 +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 <http://www.gnu.org/licenses/>.  
-#
--%>
-
-<div class="filter_menu">
-  <%= form_tag({:controller => :messages, :action => :index}, :method => :get) do %>
-
-    <%
-      offset_times = [
-        [ 'now',            "0" ],
-        [ 'ten minutes ago', 10.minutes.to_i.to_s ],
-        [ 'one hour ago',    1.hour.to_i.to_s ],
-        [ 'one day ago',     1.day.to_i.to_s ],
-        [ 'two days ago',    2.days.to_i.to_s ],
-        [ 'one week ago',    1.week.to_i.to_s ],
-        [ 'one month ago',   1.month.to_i.to_s ],
-        [ 'two months ago',  2.months.to_i.to_s ],
-        [ 'one year ago',    1.year.to_i.to_s ],
-        [ 'the big bang',   50.years.to_i.to_s ]
-      ]
-    %>
-    
-    <% if current_user.has_role?(:admin_user) %>
-      Message belongs to user:
-      <%= user_select :user_id, { :selector => @filter_params["filter_hash"]["user_id"] }, { :include_blank => '(Any)' } %>
-      <p/>
-    <% end %>
-    
-    Message is of type:
-    <%= select_tag :message_type,
-      options_for_select(
-        [
-          [ '(Any)',  "" ],
-          [ 'Notice', 'notice' ],
-          [ 'Error',  'error' ],
-          [ 'System', 'system' ],
-        ],
-        @filter_params["filter_hash"]["message_type"]
-      )
-    %>
-    <p/>
-    
-    <% between_dates_set = @filter_params["filter_hash"] && @filter_params["filter_hash"]["between_dates"] %>
-    
-    Message content was updated between:
-      <%= select_tag("time_interval[]", options_for_select( offset_times, between_dates_set ? @filter_params["filter_hash"]["between_dates"][0] : 50.years.to_i.to_s )) %> and
-      <%= select_tag("time_interval[]", options_for_select( offset_times, between_dates_set ? @filter_params["filter_hash"]["between_dates"][1] : "0"  )) %>
-    <p/>
-    
-    Messages are marked as
-    <%= select_tag(:critical, options_for_select( [ 
-        [ '(Critical or not)', '' ],
-        [ 'Critical',   '1' ],
-        [ 'Not critical', '0' ]
-      ], @filter_params["filter_hash"]["critical"] ) )
-    %>
-    and
-    <%= select_tag(:read, options_for_select( [ 
-        [ '(Read or not)', '' ],
-        [ 'Read',   '1' ],
-        [ 'Not read', '0' ]
-      ], @filter_params["filter_hash"]["read"] ) )
-    %>
-    <p/>
-    
-    <%= hidden_field_tag :update_filter, "filter_hash" %>
-    
-    <%= submit_tag 'Apply' %>
-  <% end %>
-</div>
-
diff --git a/BrainPortal/app/views/messages/_message_index_display.html.erb b/BrainPortal/app/views/messages/_message_index_display.html.erb
index 41c536cf5..9694b404e 100644
--- a/BrainPortal/app/views/messages/_message_index_display.html.erb
+++ b/BrainPortal/app/views/messages/_message_index_display.html.erb
@@ -26,32 +26,59 @@
   <% if current_user.has_role?(:site_manager) || current_user.has_role?(:admin_user) %>
     <%= new_model_button "Leave Message", new_message_path %>
   <% end %>
-  <%= button_with_dropdown_menu("Filters") do %>
-    <%= render :partial => 'messages/filters' %>
-  <% end %>
   <%= overlay_ajax_link "Help", "/doc/messages/message_info.html", :class  => "button" %>
 
   <%= external_submit_button "Delete Checked Messages", "message_form", :class  => "button", :confirm  => "Are you sure you want to delete the selected messages?"  %>
 </div>
 
-<%= render :partial => 'shared/active_filters', :locals => {:model => :message} %>
+<%=
+  render(:partial => 'shared/active_filters', :locals  => {
+    :scope => @scope,
+    :model => Message
+  })
+%>
 
+<%# TODO this interface is not as good as it should be... %>
 <div class="pagination">
-  <span class="page_links">
-    (<%= pluralize @messages.total_entries, "message" %>)
+  <span class="pagination_center">
+    (
+      <%= pluralize @messages.total_entries, "message" %>
+      <% if @unread_count > 0 %>,
+        <%=
+          scope_filter_link(
+            html_colorize("#{@unread_count} unread"),
+            @scope, :set, { :a => 'read', :v => 0 },
+            link_options: { :ajax => true }
+          )
+        %>
+      <% end %>
+      <% if @read_count > 0 %>,
+        <%=
+          scope_filter_link(
+            "#{@read_count} read",
+            @scope, :set, { :a => 'read', :v => 1 },
+            link_options: { :ajax => true }
+          )
+        %>
+      <% end %>
+    )
   </span>
 </div>
 
 <%= form_tag({ :controller => :messages, :action => :delete_messages }, :method => :delete, :id => "message_form") do %>
   <%=
-    dynamic_index_table(@messages,
-      :id       => "message_table",
-      :class    => [ :resource_list ],
-      :sort_map => {
-        :header    => 'messages.header',
-        :sender    => 'messages.sender',
-        :recipient => 'users.login',
-        :last_sent => 'messages.last_sent'
+    dynamic_scoped_table(@messages,
+      :id         => "message_table",
+      :class      => [ :resource_list ],
+      :scope      => @scope,
+      :order_map  => {
+        :sender    => { :a => 'users.login', :j => [User, 'id', 'sender_id'] },
+        :recipient => { :a => 'users.login', :j => [User, 'id', 'user_id']   }
+      },
+      :filter_map => {
+        :sender    => { :a => 'sender_id' },
+        :recipient => { :a => 'user_id'   },
+        :last_sent => { :a => 'last_sent', :o => '<=' }
       }
     ) do |t|
   %>
@@ -68,6 +95,32 @@
       } end
     %>
 
+    <%
+      # Unicode character 'WARNING SIGN' (U+26A0)
+      t.column("&#9888;".html_safe, :critical,
+        :pretty_name => 'Critical',
+        :hidden      => true,
+        :filters     => filter_values_for(
+          @view_scope, :critical,
+          format: lambda do |value, label, count|
+            label = (! value || value == 0) ? 'Not critical' : 'Critical'
+            { :value => value, :label => label, :indicator => count }
+          end
+        )
+      ) { |m| html_colorize("!!!") if m.critical }
+
+      t.column("Type", :message_type,
+        :hidden   => true,
+        :sortable => true,
+        :filters  => filter_values_for(
+          @view_scope, :message_type,
+          format: lambda do |value, label, count|
+            { :value => value, :label => label.humanize, :indicator => count }
+          end
+        )
+      ) { |m| m.message_type.humanize }
+    %>
+
     <% t.column("Message", :header, :sortable => true) do |m| %>
       <%= show_hide_toggle(Message.parse_markup(m.header), "#message_table_details_#{m.id}") %>
       <div id="message_table_details_<%= m.id %>" style="display: none">
@@ -77,15 +130,44 @@
 
     <%
       t.column("Sender", :sender,
-        :sortable => true
+        :sortable => true,
+        :filters  => filter_values_for(
+          @view_scope, :sender_id,
+          label: 'users.login',
+          association: [User, 'id', 'sender_id'],
+        ) + [{
+          :value     => nil,
+          :label     => 'System',
+          :indicator => @view_scope
+            .where('sender_id' => nil)
+            .count
+        }]
       ) { |m| m.sender.try(:login) || "System" }
 
       t.column("Recipient", :recipient,
-        :sortable => true
-      ) { |m| m.user.login } unless current_user.has_role?(:normal_user)
+        :sortable => true,
+        :filters  => filter_values_for(
+          @view_scope, :user_id,
+          label: 'users.login',
+          association: [User, 'id', 'user_id']
+        )
+      ) { |m| m.user.login } unless
+        current_user.has_role?(:normal_user)
 
       t.column("Last Updated", :last_sent,
-        :sortable => true
+        :sortable => true,
+        :filters  => ([
+          [10.minutes, 'Ten minutes'],
+          [1.hour,     'One hour'   ],
+          [1.day,      'One day'    ],
+          [2.days,     'Two days'   ],
+          [1.week,     'One week'   ],
+          [1.month,    'One month'  ],
+          [2.months,   'Two months' ],
+          [1.year,     'One year'   ]
+        ]).map do |value, label|
+          [value.ago.to_datetime, label + ' old']
+        end
       ) { |m| to_localtime(m.last_sent, :datetime) }
     %>
 
diff --git a/BrainPortal/app/views/shared/_active_filters.html.erb b/BrainPortal/app/views/shared/_active_filters.html.erb
index 33188009b..bfdfd72a8 100644
--- a/BrainPortal/app/views/shared/_active_filters.html.erb
+++ b/BrainPortal/app/views/shared/_active_filters.html.erb
@@ -34,34 +34,30 @@
     (<%=
       scope_filter_link('clear',
         scope, :clear, nil,
-        options: { :ajax => true }
+        link_options: { :ajax => true }
       )
     %>)
     <span id="current_filters">
       <% scope.filters.each do |filter| %>
         <span class="current_filters_item">
-          <%= crop_text_to(30, pretty_scope_filter(filter, model: model)) %>
+          <%= pretty_scope_filter(filter, model: model) %>
         </span>
         <%=
           scope_filter_link(delete_icon,
             scope, :remove, filter,
-            options: { :ajax => true }
+            link_options: { :ajax => true }
           )
         %>
       <% end %>
-      <% Array(scope.custom[:custom_filters]).each do |id| %>
+      <% Array(scope.custom[:custom_filters]).uniq.each do |id| %>
         <span class="current_filters_item">
           <%= crop_text_to(30, UserfileCustomFilter.find(id).name) %>
         </span>
         <%=
-          ajax_link(
-            delete_icon,
-            url_for(
-              scope_custom_params(scope, { 'custom_filters' => [id] })
-                .merge({ '_scope_mode' => 'delete' })
-            ),
-            :class    => 'action_link',
-            :datatype => :script
+          scope_custom_link(delete_icon,
+            scope, { 'custom_filters' => [id] },
+            url_options:  { '_scope_mode' => 'delete' },
+            link_options: { :ajax         => true     }
           )
         %>
       <% end %>
diff --git a/BrainPortal/app/views/sites/_sites_table.html.erb b/BrainPortal/app/views/sites/_sites_table.html.erb
index ac222572d..70dbef511 100644
--- a/BrainPortal/app/views/sites/_sites_table.html.erb
+++ b/BrainPortal/app/views/sites/_sites_table.html.erb
@@ -27,18 +27,20 @@
   <%= overlay_ajax_link "Help", "/doc/sites/site_info.html", :class  => "button" %>
 </div>
 
-<%= render :partial => 'shared/active_filters', :locals => {:model => :site} %>
+<%=
+  render(:partial => 'shared/active_filters', :locals  => {
+    :scope => @scope,
+    :model => Site
+  })
+%>
 
 <div class="centered"> (<%= pluralize @sites.count, "site" %>) </div>
 
 <%=
-  dynamic_index_table(@sites,
-    :id       => 'sites_table',
-    :class    => [ :resource_list ],
-    :sort_map => {
-      :name        => 'sites.name',
-      :description => 'sites.description'
-    }
+  dynamic_scoped_table(@sites,
+    :id    => 'sites_table',
+    :class => [ :resource_list ],
+    :scope => @scope
   ) do |t|
 %>
   <%
@@ -57,18 +59,21 @@
       ) { |m,r,c| link_to_user_with_tooltip(m) }
     end
 
+    users_scope  = scope_from_session('users')
+    groups_scope = scope_from_session('groups')
+
     t.column("Number of Users", :nusers) do |s|
-      filter_add_link s.users.count.to_s,
-        :controller => :users,
-        :filters    => { :site_id => s.id },
-        :ajax       => false
+      scope_filter_link(s.users.count.to_s,
+        users_scope, :set, { :a => 'site_id', :v => s.id },
+        url_options: { :controller => :users }
+      )
     end
 
     t.column("Number of Projects", :nprojects) do |s|
-      filter_add_link s.groups.count.to_s,
-        :controller => :groups,
-        :filters    => { :site_id => s.id },
-        :ajax       => false
+      scope_filter_link(s.groups.count.to_s,
+        groups_scope, :set, { :a => 'site_id', :v => s.id },
+        url_options: { :controller => :groups }
+      )
     end
   %>
 <% end %>
diff --git a/BrainPortal/app/views/tags/_tag_li.html.erb b/BrainPortal/app/views/tags/_tag_li.html.erb
index 7f59c64c9..6f10223a3 100644
--- a/BrainPortal/app/views/tags/_tag_li.html.erb
+++ b/BrainPortal/app/views/tags/_tag_li.html.erb
@@ -24,18 +24,10 @@
 
 <b>
   <%=
-    ajax_link(
-      crop_text_to(15, tag.name),
-      url_for(
-        scope_filter_params(@scope, :set, {
-          'type'  => 'uf.tags',
-          'value' => [tag.id]
-        }).reverse_merge({
-          :controller => :userfiles
-        })
-      ),
-      :class    => 'action_link',
-      :datatype => :script
+    scope_filter_link(crop_text_to(15, tag.name),
+      @scope, :set, { 'type' => 'uf.tags', 'value' => [tag.id] },
+      url_options:  { :controller => :userfiles },
+      link_options: { :ajax       => true       }
     )
   %>
 </b>
diff --git a/BrainPortal/app/views/tasks/_tasks_display.html.erb b/BrainPortal/app/views/tasks/_tasks_display.html.erb
index 5b5422b5c..772722246 100644
--- a/BrainPortal/app/views/tasks/_tasks_display.html.erb
+++ b/BrainPortal/app/views/tasks/_tasks_display.html.erb
@@ -125,7 +125,12 @@
   <%
     t.column("Task Type", :type,
       :sortable => true,
-      :filters  => filter_values_for(@view_scope, :type)
+      :filters  => filter_values_for(@view_scope, :type,
+        format: lambda do |value, label, count|
+          label = label.constantize.pretty_type rescue label
+          { :value => value, :label => label, :indicator => count }
+        end
+      )
     ) do |type,id,count,task|
   %>
     <% case type %>
@@ -146,22 +151,14 @@
 
     t.column("Owner", :owner,
       :sortable => true,
-      :filters  => filter_values_for(
-        @view_scope, :user_id,
-        label: 'users.login',
-        association: User
-      )
+      :filters  => assoc_filter_values_for(@view_scope, User, label: 'login')
     ) do |type,id,count,task|
       link_to_user_if_accessible(task.user) unless type == :loaded_batch
     end
 
     t.column("Project", :project,
       :sortable => true,
-      :filters  => filter_values_for(
-        @view_scope, :group_id,
-        label: 'groups.name',
-        association: Group
-      )
+      :filters  => assoc_filter_values_for(@view_scope, Group)
     ) do |type,id,count,task|
       link_to_group_if_accessible(task.group) unless type == :loaded_batch
     end unless current_project
@@ -312,7 +309,7 @@
         scope_custom_link(
           "Switch to #{batch_view ? 'List' : 'Batch'} View",
           @scope, { 'batch' => !batch_view },
-          options: { :ajax => true }
+          link_options: { :ajax => true }
         )
       %>
     </div>
diff --git a/BrainPortal/app/views/tools/_tools_table.html.erb b/BrainPortal/app/views/tools/_tools_table.html.erb
index 8c8ddf6eb..2f350e8a5 100644
--- a/BrainPortal/app/views/tools/_tools_table.html.erb
+++ b/BrainPortal/app/views/tools/_tools_table.html.erb
@@ -32,23 +32,25 @@
   <%= overlay_ajax_link "Help", "/doc/tool/tool_info.html", :class  => "button menu_button" %>
 </div>
 
-
-<%= render :partial => 'shared/active_filters', :locals => {:model => :tool} %>
+<%=
+  render(:partial => 'shared/active_filters', :locals  => {
+    :scope => @scope,
+    :model => Tool
+  })
+%>
 
 <%=
-  dynamic_index_table(@tools,
+  dynamic_scoped_table(@tools,
     :id         => 'tools_table',
     :class      => [ :resource_list ],
-    :sort_map   => {
-      :name        => 'tools.name',
-      :description => 'tools.description',
-      :category    => 'tools.category',
-      :owner       => 'users.login',
-      :group       => 'groups.name'
+    :scope      => @scope,
+    :order_map  => {
+      :owner => { :a => 'users.login', :j => User  },
+      :group => { :a => 'groups.name', :j => Group }
     },
     :filter_map => {
-      :owner    => 'user_id',
-      :group    => 'group_id'
+      :owner => { :a => 'user_id'  },
+      :group => { :a => 'group_id' }
     }
   ) do |t|
 %>
@@ -69,17 +71,17 @@
 
     t.column("Category", :category,
       :sortable => true,
-      :filters  => basic_filters_for(@filtered_scope, @header_scope, Tool, :category)
+      :filters  => filter_values_for(@tools, :category)
     )
 
     t.column("Owner", :owner,
       :sortable => true,
-      :filters  => association_filters_for(@filtered_scope, @header_scope, Tool, :user, :name_method => :login)
+      :filters  => assoc_filter_values_for(@tools, User, label: 'login')
     ) { |tool| link_to_user_with_tooltip(tool.user) }
 
     t.column("Project", :group,
       :sortable => true,
-      :filters  => association_filters_for(@filtered_scope, @header_scope, Tool, :group)
+      :filters  => assoc_filter_values_for(@tools, Group)
     ) { |tool| link_to_group_if_accessible(tool.group) }
 
     t.column("Execution & Versions", :exec) do |tool|
diff --git a/BrainPortal/app/views/userfiles/_file_menu.html.erb b/BrainPortal/app/views/userfiles/_file_menu.html.erb
index bbf1952e7..51a219113 100644
--- a/BrainPortal/app/views/userfiles/_file_menu.html.erb
+++ b/BrainPortal/app/views/userfiles/_file_menu.html.erb
@@ -178,7 +178,7 @@
           <%=
             scope_filter_link('Has no parent',
               @scope, :add, { 'type' => 'uf.hier', 'operator' => 'no_parent' },
-              options: { :ajax => true }
+              link_options: { :ajax => true }
             )
           %>
         </li>
@@ -186,7 +186,7 @@
           <%=
             scope_filter_link('Has no children',
               @scope, :add, { 'type' => 'uf.hier', 'operator' => 'no_child' },
-              options: { :ajax => true }
+              link_options: { :ajax => true }
             )
           %>
         </li>
diff --git a/BrainPortal/app/views/userfiles/_userfiles_display.html.erb b/BrainPortal/app/views/userfiles/_userfiles_display.html.erb
index ae8083109..6b68a1572 100644
--- a/BrainPortal/app/views/userfiles/_userfiles_display.html.erb
+++ b/BrainPortal/app/views/userfiles/_userfiles_display.html.erb
@@ -115,16 +115,17 @@
     t.column("File Type", :type,
       :field_name => :pretty_type,
       :sortable   => true,
-      :filters    => filter_values_for(@view_scope, :type)
+      :filters    => filter_values_for(@view_scope, :type,
+        format: lambda do |value, label, count|
+          label = label.constantize.pretty_type rescue label
+          { :value => value, :label => label, :indicator => count }
+        end
+      )
     )
 
     t.column("Owner", :login,
       :sortable => true,
-      :filters  => filter_values_for(
-        @view_scope, :user_id,
-        label: 'users.login',
-        association: User
-      )
+      :filters  => assoc_filter_values_for(@view_scope, User, label: 'login')
     ) { |u| link_to_user_if_accessible(u.user) }
 
     t.column("Creation Date", :creation_date,
@@ -189,11 +190,7 @@
     unless current_project
       t.column("Project", :group,
         :sortable => true,
-        :filters  => filter_values_for(
-          @view_scope, :group_id,
-          label: 'groups.name',
-          association: Group
-        )
+        :filters  => assoc_filter_values_for(@view_scope, Group)
       ) do |u|
         link_to_group_if_accessible(u.group) if u.group
       end
@@ -207,11 +204,7 @@
 
     t.column("Provider", :data_provider,
       :sortable => true,
-      :filters  => filter_values_for(
-        @view_scope, :data_provider_id,
-        label: 'data_providers.name',
-        association: DataProvider
-      )
+      :filters  => assoc_filter_values_for(@view_scope, DataProvider)
     ) do |u|
       link_to_data_provider_if_accessible(u.data_provider)
     end
diff --git a/BrainPortal/app/views/userfiles/_view_option_button.html.erb b/BrainPortal/app/views/userfiles/_view_option_button.html.erb
index d63f30296..8389d4b57 100644
--- a/BrainPortal/app/views/userfiles/_view_option_button.html.erb
+++ b/BrainPortal/app/views/userfiles/_view_option_button.html.erb
@@ -28,7 +28,7 @@
       toggle_link = lambda do |on, off, key|
         scope_custom_link((@scope.custom[key] ? off : on),
           @scope, { key => !@scope.custom[key] },
-          options: { :ajax_link => true }
+          link_options: { :ajax => true }
         )
       end
     %>
diff --git a/BrainPortal/app/views/users/_users_table.html.erb b/BrainPortal/app/views/users/_users_table.html.erb
index 2cd40d359..d7879f95f 100644
--- a/BrainPortal/app/views/users/_users_table.html.erb
+++ b/BrainPortal/app/views/users/_users_table.html.erb
@@ -26,50 +26,52 @@
   <%= new_model_button 'Create User', new_user_path %>
 </div>
 
-<%= render :partial => 'shared/active_filters', :locals => { :model => :user } %>
+<%=
+  render(:partial => 'shared/active_filters', :locals  => {
+    :scope => @scope,
+    :model => User
+  })
+%>
 
 <div class="pagination">
-  <div class="page_links">
+  <div class="pagination_center">
     (
       <%= pluralize @users.total_entries, "user" %>
       <% if @unlocked_users_count > 0 %>,
         <%=
-          filter_add_link "#{@unlocked_users_count} active",
-            :filters => { :account_locked => 0 }
+          scope_filter_link("#{@unlocked_users_count} active",
+            @scope, :set, { :a => 'account_locked', :v => 0 },
+            link_options: { :ajax => true }
+          )
         %>
       <% end %>
       <% if @locked_users_count > 0 %>,
         <%=
-          filter_add_link "#{@locked_users_count} locked",
-            :filters => { :account_locked => 1 }
+          scope_filter_link("#{@locked_users_count} locked",
+            @scope, :set, { :a => 'account_locked', :v => 1 },
+            link_options: { :ajax => true }
+          )
         %>
       <% end %>
     )
   </div>
   <div class="pagination_right_side">
-    Search by name:
-    <%= ajax_search_box "name_like", users_path(:update_filter => :filter_hash) %>
+    Search by name: <%= ajax_search_box "name_like", users_path %>
   </div>
 </div>
 
 <%=
-  dynamic_index_table(@users,
+  dynamic_scoped_table(@users,
     :id         => 'users_table',
     :class      => [ :resource_list ],
-    :sort_map   => {
-      :login           => 'users.login',
-      :full_name       => 'users.full_name',
-      :email           => 'users.email',
-      :last_connection => 'users.last_connected_at',
-      :type            => 'users.type',
-      :site            => 'sites.name',
-      :city            => 'users.city',
-      :country         => 'users.country',
-      :time_zone       => 'users.time_zone'
+    :scope      => @scope,
+    :order_map  => {
+      :last_connection => { :a => 'last_connected_at' },
+      :site            => { :a => 'sites.name', :j => Site }
     },
     :filter_map => {
-      :login => 'account_locked',
-      :site  => 'site_id'
+      :login => { :a => 'account_locked' },
+      :site  => { :a => 'site_id' }
     }
   ) do |t|
 %>
@@ -78,8 +80,17 @@
 
     t.column("Login", :login,
       :sortable => true,
-      :filters  => basic_filters_for(@filtered_scope, @header_scope, 'users', 'account_locked') { |l| l ? "Locked" : "Unlocked"  }
-    ) { |u| link_to_user_if_accessible(u, current_user, :html_options => { :class => u.account_locked ? 'error_link' : nil }) }
+      :filters  => filter_values_for(@view_scope, :account_locked,
+        format: lambda do |value, label, count|
+          label = (!value || value == 0 ? 'Unlocked' : 'Locked')
+          { :value => value, :label => label, :indicator => count }
+        end
+      )
+    ) do |u|
+      link_to_user_if_accessible(u, current_user,
+        :html_options => { :class => u.account_locked ? 'error_link' : nil }
+      )
+    end
 
     t.column("Full name", :full_name,
       :sortable => true
@@ -110,22 +121,27 @@
 
     t.column("Role", :type,
       :sortable => true,
-      :filters  => basic_filters_for(@filtered_scope, @header_scope, 'users', 'type')
+      :filters  => filter_values_for(@view_scope, :type,
+        format: lambda do |value, label, count|
+          label = label.constantize.pretty_type rescue label
+          { :value => value, :label => label, :indicator => count }
+        end
+      )
     ) { |u| u.type.underscore.titleize }
 
     t.column("Site", :site,
       :sortable => true,
-      :filters  => association_filters_for(@filtered_scope, User.scoped, "user", "site")
+      :filters  => assoc_filter_values_for(@view_scope, Site)
     ) { |u| link_to_site_if_accessible(u.site) }
 
     t.column("City", :city,
       :sortable => true,
-      :filters  => basic_filters_for(@filtered_scope, @header_scope, 'users', 'city')
+      :filters  => filter_values_for(@view_scope, :city)
     )
 
     t.column("Country", :country,
       :sortable => true,
-      :filters  => basic_filters_for(@filtered_scope, @header_scope, 'users', 'country')
+      :filters  => filter_values_for(@view_scope, :country)
     )
 
     t.column("Time Zone", :time_zone,
diff --git a/BrainPortal/public/stylesheets/cbrain.css b/BrainPortal/public/stylesheets/cbrain.css
index 9b98ece17..c3c306f05 100644
--- a/BrainPortal/public/stylesheets/cbrain.css
+++ b/BrainPortal/public/stylesheets/cbrain.css
@@ -1424,6 +1424,7 @@ pre {
   padding-left: 2em;
 }
 
+.pagination_center,
 .page_links {
   display: table-cell;
   text-align: center;
@@ -1832,6 +1833,16 @@ img {
   border: 2px solid black;
 }
 
+#message_table th.critical > .dt-hdr {
+  font-size: 1.8em;
+  padding-right: 0.5em;
+}
+
+#message_table td.critical {
+  padding-left: 1em;
+  font-weight: bold;
+}
+
 #message_table tr.notice_display {
   border-color: green;
 }

From d36d693fd739fd91527fc5aacc8107b534af5436 Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Wed, 9 Sep 2015 17:13:22 -0400
Subject: [PATCH 39/85] Fix for ambiguous order attribute/column

As the corresponding query has more than one ID column/attribute, a
fully qualified table + column name is required.

This changeset also includes a minor style fix ('old' -> 'ago') for
last_updated message filters.
---
 BrainPortal/app/controllers/tasks_controller.rb                | 2 +-
 BrainPortal/app/views/messages/_message_index_display.html.erb | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/BrainPortal/app/controllers/tasks_controller.rb b/BrainPortal/app/controllers/tasks_controller.rb
index d03426f7a..fff11cb33 100644
--- a/BrainPortal/app/controllers/tasks_controller.rb
+++ b/BrainPortal/app/controllers/tasks_controller.rb
@@ -116,7 +116,7 @@ def batch_list
         .where(:batch_id => params[:batch_id])
     )
       .includes([:bourreau, :user, :group])
-      .order([:rank, :level, :id])
+      .order(['cbrain_tasks.rank', 'cbrain_tasks.level', 'cbrain_tasks.id'])
       .map { |task| { :batch => task.batch_id, :first => task, :count => 1 } }
 
     @bourreau_status = Bourreau
diff --git a/BrainPortal/app/views/messages/_message_index_display.html.erb b/BrainPortal/app/views/messages/_message_index_display.html.erb
index 9694b404e..f1ab783dc 100644
--- a/BrainPortal/app/views/messages/_message_index_display.html.erb
+++ b/BrainPortal/app/views/messages/_message_index_display.html.erb
@@ -166,7 +166,7 @@
           [2.months,   'Two months' ],
           [1.year,     'One year'   ]
         ]).map do |value, label|
-          [value.ago.to_datetime, label + ' old']
+          [value.ago.to_datetime, label + ' ago']
         end
       ) { |m| to_localtime(m.last_sent, :datetime) }
     %>

From cb3e4e004a2ec82663d87db743006206cfb22520 Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Fri, 11 Sep 2015 10:17:48 -0400
Subject: [PATCH 40/85] Messages & projects colors

Messages no longer have a border to indicate their 'unread' status; they
are now of a darker (more vibrant) color instead. Project buttons' color
scheme now colors buttons of a given type similarly (bright red for
system groups, darker red for everyone group, etc.)

Conflicts:

	BrainPortal/public/stylesheets/cbrain.css
---
 BrainPortal/public/stylesheets/cbrain.css | 94 ++++++++++++-----------
 1 file changed, 50 insertions(+), 44 deletions(-)

diff --git a/BrainPortal/public/stylesheets/cbrain.css b/BrainPortal/public/stylesheets/cbrain.css
index 4991e3fb3..02bb2cf03 100644
--- a/BrainPortal/public/stylesheets/cbrain.css
+++ b/BrainPortal/public/stylesheets/cbrain.css
@@ -1104,37 +1104,37 @@ pre {
   right: 5px;
 }
 
-.system_project_point     { color:      #c51700; }
-.system_project           { background: #c51700; }
-.system_project:active    { background: #c51700; }
+.system_project_point     { color:      #d41c1c; }
+.system_project           { background: #d41c1c; }
+.system_project:active    { background: #d41c1c; }
 
-.everyone_project_point   { color:      #960065; }
-.everyone_project         { background: #960065; }
-.everyone_project:active  { background: #960065; }
+.everyone_project_point   { color:      #af0b0b; }
+.everyone_project         { background: #af0b0b; }
+.everyone_project:active  { background: #af0b0b; }
 
-.site_project_point       { color:      #b00035; }
-.site_project             { background: #b00035; }
-.site_project:active      { background: #b00035; }
+.site_project_point       { color:      #8c0953; }
+.site_project             { background: #8c0953; }
+.site_project:active      { background: #8c0953; }
 
-.user_project_point       { color:      #017277; }
-.user_project             { background: #017277; }
-.user_project:active      { background: #017277; }
+.user_project_point       { color:      #500d75; }
+.user_project             { background: #500d75; }
+.user_project:active      { background: #500d75; }
 
-.shared_project_point     { color:      #008b41; }
-.shared_project           { background: #008b41; }
-.shared_project:active    { background: #008b41; }
+.shared_project_point     { color:      #098c09; }
+.shared_project           { background: #098c09; }
+.shared_project:active    { background: #098c09; }
 
-.personal_project_point   { color:      #0a4081; }
-.personal_project         { background: #0a4081; }
-.personal_project:active  { background: #0a4081; }
+.personal_project_point   { color:      #076969; }
+.personal_project         { background: #076969; }
+.personal_project:active  { background: #076969; }
 
-.invisible_project_point  { color:      #c59900; }
-.invisible_project        { background: #c59900; }
-.invisible_project:active { background: #c59900; }
+.invisible_project_point  { color:      #70a30a; }
+.invisible_project        { background: #70a30a; }
+.invisible_project:active { background: #70a30a; }
 
-.empty_project_point      { color:      #c56a00; }
-.empty_project            { background: #c56a00; }
-.empty_project:active     { background: #c56a00; }
+.empty_project_point      { color:      #16a916; }
+.empty_project            { background: #16a916; }
+.empty_project:active     { background: #16a916; }
 
 .giant{
   margin-top: 0.3em;
@@ -2066,40 +2066,46 @@ img {
 /* % Message Index */
 /* % ######################################################### */
 
-#message_table tbody > tr {
-  border: 2px solid black;
+#message_table tr.notice_display.message_read:hover,
+#message_table tr.notice_display.message_unread:hover,
+#message_table tr.system_display.message_read:hover,
+#message_table tr.system_display.message_unread:hover,
+#message_table tr.error_display.message_read:hover,
+#message_table tr.error_display.message_unread:hover {
+  background: #fff3d3;
 }
 
-#message_table tr.notice_display {
-  border-color: green;
+#message_table tr.notice_display.message_read:active,
+#message_table tr.notice_display.message_unread:active,
+#message_table tr.system_display.message_read:active,
+#message_table tr.system_display.message_unread:active,
+#message_table tr.error_display.message_read:active,
+#message_table tr.error_display.message_unread:active {
+  background: #ffe49a;
 }
 
-#message_table tr.error_display {
-  border-color: red;
+#message_table tr.notice_display.message_read {
+  background: #c3f6b3;
 }
 
-#message_table tr.system_display {
-  border-color: blue;
+#message_table tr.notice_display.message_unread {
+  background: #5cdd5c;
 }
 
-#message_table tr.message_read {
-  border-style: none;
+#message_table tr.system_display.message_read {
+  background: #b6c7f0;
 }
 
-#message_table tr.message_unread {
-  border-style: solid;
-}
-
-#message_table tr.notice_display:not(:hover):not(:active) {
-  background-color: #ddffdd;
+#message_table tr.system_display.message_unread {
+  background: #5f7ec6;
 }
 
-#message_table tr.error_display:not(:hover):not(:active) {
-  background-color: #ffeeee;
+#message_table tr.error_display.message_read {
+  background: #ff8f8f;
 }
 
-#message_table tr.system_display:not(:hover):not(:active) {
-  background-color: #ddeeff;
+#message_table tr.error_display.message_unread {
+  background: #ff6b6b;
 }
 
 #message_table td.operations {

From d6f34095c960c40f39fecbfdb231dd241ad76989 Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Fri, 11 Sep 2015 10:43:04 -0400
Subject: [PATCH 41/85] Issue #208 - Search by name should trim whitespace

Each model's matching *_like scope now trims (strip) its argument.
---
 BrainPortal/app/models/group.rb    | 2 +-
 BrainPortal/app/models/user.rb     | 2 +-
 BrainPortal/app/models/userfile.rb | 6 +++---
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/BrainPortal/app/models/group.rb b/BrainPortal/app/models/group.rb
index 2c537584f..f8b9d12b7 100644
--- a/BrainPortal/app/models/group.rb
+++ b/BrainPortal/app/models/group.rb
@@ -62,7 +62,7 @@ class Group < ActiveRecord::Base
 
   attr_accessible         :name, :description, :site_id, :creator_id, :user_ids
 
-  cb_scope                :name_like, lambda { |n| {:conditions => ["groups.name LIKE ?", "%#{n}%"]} }
+  cb_scope                :name_like, lambda { |n| {:conditions => ["groups.name LIKE ?", "%#{n.strip}%"]} }
 
   # Returns the unique and special group 'everyone'
   def self.everyone
diff --git a/BrainPortal/app/models/user.rb b/BrainPortal/app/models/user.rb
index 1974f3e97..c6898e363 100644
--- a/BrainPortal/app/models/user.rb
+++ b/BrainPortal/app/models/user.rb
@@ -111,7 +111,7 @@ class User < ActiveRecord::Base
 
   force_text_attribute_encoding 'UTF-8', :full_name, :city, :country
 
-  cb_scope                   :name_like, lambda { |n| where("users.login LIKE ? OR users.full_name LIKE ?", "%#{n}%", "%#{n}%") }
+  cb_scope                   :name_like, lambda { |n| where("users.login LIKE ? OR users.full_name LIKE ?", "%#{n.strip}%", "%#{n.strip}%") }
 
   # Returns the admin user
   def self.admin
diff --git a/BrainPortal/app/models/userfile.rb b/BrainPortal/app/models/userfile.rb
index 1ac6956b6..b3493bf6e 100644
--- a/BrainPortal/app/models/userfile.rb
+++ b/BrainPortal/app/models/userfile.rb
@@ -78,7 +78,7 @@ class Userfile < ActiveRecord::Base
   attr_accessible         :name, :size, :user_id, :parent_id, :type, :group_id, :data_provider_id, :group_writable,
                           :num_files, :tag_ids, :hidden, :immutable, :description
 
-  cb_scope                :name_like, lambda { |n| {:conditions => ["userfiles.name LIKE ?", "%#{n}%"]} }
+  cb_scope                :name_like, lambda { |n| {:conditions => ["userfiles.name LIKE ?", "%#{n.strip}%"]} }
 
   cb_scope                :has_no_parent, :conditions => {:parent_id => nil}
   cb_scope                :has_no_child,  lambda { |ignored|
@@ -86,12 +86,12 @@ class Userfile < ActiveRecord::Base
                                             parents_ids.blank? ? where({}) : where("userfiles.id NOT IN (?)", parents_ids)
                                           }
   cb_scope                :parent_name_like, lambda { |n|
-                                            matching_parents_ids = Userfile.where("name like ?", "%#{n}%").raw_first_column(:id).uniq
+                                            matching_parents_ids = Userfile.where("name like ?", "%#{n.strip}%").raw_first_column(:id).uniq
                                             where(:parent_id => matching_parents_ids)
                                           }
 
   cb_scope                :child_name_like, lambda { |n|
-                                             matching_children_ids = Userfile.where("name like ?", "%#{n}%").where("parent_id IS NOT NULL").raw_first_column(:id).uniq
+                                             matching_children_ids = Userfile.where("name like ?", "%#{n.strip}%").where("parent_id IS NOT NULL").raw_first_column(:id).uniq
                                              matching_parents_ids  = Userfile.where(:id => matching_children_ids).raw_first_column(:parent_id).uniq
                                              where(:id => matching_parents_ids)
                                             }

From bcba0a16e2e7c8e018e58a630d65130fefc89632 Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Fri, 11 Sep 2015 17:10:28 -0400
Subject: [PATCH 42/85] Port of the DP browsing table to the Scopes API

Possible mainly due to scopes and dynamic table allowing regular Ruby
collections as well as AR models. The newly ported table supports all
features of regular index tables, such as integrated sorting, filtering
and pagination (an improvement over the previous implementation).

This changeset also contains a minor fix for dynamic_scoped_table; the
current page is now reset to 1 when changing per_page.
---
 .../controllers/data_providers_controller.rb  |  55 ++---
 .../app/helpers/dynamic_table_helper.rb       |   1 +
 .../data_providers/_dp_browse_table.html.erb  | 190 +++++++++---------
 .../_view_option_button.html.erb              |  28 ++-
 .../app/views/data_providers/browse.js.erb    |   4 +-
 5 files changed, 147 insertions(+), 131 deletions(-)

diff --git a/BrainPortal/app/controllers/data_providers_controller.rb b/BrainPortal/app/controllers/data_providers_controller.rb
index 083cbc109..0358b6772 100644
--- a/BrainPortal/app/controllers/data_providers_controller.rb
+++ b/BrainPortal/app/controllers/data_providers_controller.rb
@@ -290,12 +290,21 @@ 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 => @scope.custom['as_user_id'] ||= (
+        params['as_user_id'] || current_user.id
+      ))
+      .first
+    @as_user ||= current_user
 
     begin
       # [ base, size, type, mtime ]
@@ -361,21 +370,15 @@ 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)
 
+    scope_to_session(@scope)
     current_session.save_preferences
 
     respond_to do |format|
@@ -398,12 +401,16 @@ 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."
diff --git a/BrainPortal/app/helpers/dynamic_table_helper.rb b/BrainPortal/app/helpers/dynamic_table_helper.rb
index 026e3651c..6ba905a9a 100644
--- a/BrainPortal/app/helpers/dynamic_table_helper.rb
+++ b/BrainPortal/app/helpers/dynamic_table_helper.rb
@@ -1191,6 +1191,7 @@ def dynamic_scoped_table(collection, options = {}, &block)
             url_for(
               :controller => params[:controller],
               :action     => params[:action],
+              :page            => 1,
               :_pag_scope_name => @scope.name
             )
           end
diff --git a/BrainPortal/app/views/data_providers/_dp_browse_table.html.erb b/BrainPortal/app/views/data_providers/_dp_browse_table.html.erb
index 1088f2507..a76f78eb0 100644
--- a/BrainPortal/app/views/data_providers/_dp_browse_table.html.erb
+++ b/BrainPortal/app/views/data_providers/_dp_browse_table.html.erb
@@ -24,109 +24,107 @@
 
 <div name="dataprovider_files" class="index_block">
 
-  <h2>Files Available On Remote Data Provider '<%= @provider.name %>'
-  <% if @as_user != current_user %>
-    (Browsing as user '<%= @as_user.login %>')
-  <% end %>
+  <h2>
+    Files Available On Remote Data Provider '<%= @provider.name %>'
+    <% if @as_user != current_user %>
+      (Browsing as user '<%= @as_user.login %>')
+    <% end %>
   </h2>
 
-  <% if @filter_params["browse_hash"]["name_like"].present? %>
-    <div class="active_status">
-      <span class="active_status_left_side">
-         <span class="active_label">Active Filters:</span>
-         <span class="current_filters_item">
-           Name like: <%=  @filter_params["browse_hash"]["name_like"] %>
-         </span>
-         <%= filter_remove_link delete_icon, "name_like", :parameter => "browse_hash", :ajax => false, :action  => :browse, :id => @provider.id  %>
-      </span>
-    </div>
-  <% end %>
-
   <div class="pagination">
-    <div class="pagination_left_side"></div>
-
-    <div class="page_links">
-      <%= will_paginate @fileinfolist, :container => false %> (<%= pluralize @file_count, "files" %>)
+    <div class="pagination_left_side">
+      Register files as:
+      <%= master_select("file_select", ["..."] + SingleFile.valid_file_classes.map(&:pretty_type)) %>,
+      and directories as:
+      <%= master_select("directory_select", ["..."] + FileCollection.valid_file_classes.map(&:pretty_type)) %>
     </div>
 
     <div class="pagination_right_side">
-      Search by name: <%=  ajax_search_box "name_like", browse_data_provider_path(:update_filter => :browse_hash) %>
+      Search by name: <%= ajax_search_box("name_like", browse_data_provider_path) %>
     </div>
   </div>
 
-  <table class="resource_list" id="dp_browse_table">
-    <tr>
-      <th><%= select_all_checkbox "file_checkbox" %></th>
-      <th>Name</th>
-      <th>Size</th>
-      <th>Type<br>
-        <%= master_select("file_select", ["All files as..."] + SingleFile.valid_file_classes.map(&:pretty_type) ) %><br>
-        <%= master_select("directory_select", ["All directories as..."] + FileCollection.valid_file_classes.map(&:pretty_type) ) %>
-      </th>
-      <th>Last modified</th>
-      <th>Registered?</th>
-      <th>Note</th>
-    </tr>
-
-    <% @fileinfolist.each do |fi| %>
-      <%
-         fi_name     = fi.name
-         fi_size     = fi.size
-         fi_type     = fi.symbolic_type
-         fi_mtime    = fi.mtime
-
-         fi_userfile = fi.userfile
-         fi_ok       = fi.state_ok
-         fi_message  = fi.message
-      %>
-      <tr class="<%= cycle('list-odd', 'list-even') %>  row_highlight">
-
-        <% if fi_ok %>
-          <td><%= check_box_tag("basenames[]",fi_name, false, :class => "file_checkbox") %></td>
-        <% else %>
-          <td></td>
-        <% end %>
-
-        <td class="left"><%= fi_name %></td>
-
-        <td><%= fi_type == :regular ? fi_size : "-" %></td>
-
-        <% if fi_userfile %>
-          <td><%= fi_userfile.class.to_s %></td>
-        <% else %>
-           <% if ! fi_ok %>
-             <td><%= html_colorize("Unacceptable?") %></td>
-           <% elsif fi_type == :regular %>
-             <td>
-               <%=
-                 select_tag("filetypes[]",
-                   options_for_select(SingleFile.valid_file_classes.map{|c| [c.pretty_type, "#{c.name}-#{fi_name}"]}, class_param_for_name(fi_name, SingleFile)),
-                   :class  => "file_select")
-               %>
-             </td>
-           <% elsif fi_type == :directory %>
-             <td>
-              <%=
-                select_tag("filetypes[]",
-                    options_for_select(FileCollection.valid_file_classes.map{|c| [c.pretty_type, "#{c.name}-#{fi_name}"]}, class_param_for_name(fi_name, FileCollection)),
-                    :class  => "directory_select")
-              %>
-             </td>
-           <% end %>
-        <% end %>
-
-        <td><%= to_localtime(Time.at(fi_mtime),:datetime) %></td>
-
-        <% if fi_userfile %>
-          <% to_who = "" %>
-          <% to_who = " (as user #{fi_userfile.user.login})" if (fi_userfile.user_id != @as_user.id) || (fi_userfile.user_id != current_user.id) %>
-          <td><%= link_to "Registered#{to_who}", { :controller => 'userfiles', :action => 'show', :id => fi_userfile.id } %></td>
-        <% else %>
-          <td>No</td>
-        <% end %>
-        <td><%= fi_message %></td>
-      </tr>
-    <% end %> <!-- each fileinfo -->
-  </table>
-</div>
+  <%=
+    render(:partial => 'shared/active_filters', :locals  => {
+      :scope => @scope,
+      :model => nil
+    })
+  %>
+
+  <%=
+    dynamic_scoped_table(@files,
+      :id           => 'dp_browse_table',
+      :class        => [:whole_width],
+      :request_type => 'server_javascript',
+      :scope        => @scope
+    ) do |t|
+  %>
+    <%
+      t.paginate
+
+      t.row do |f|
+        {
+          :select_param => 'basenames[]',
+          :select_value => f.name
+        } if f.state_ok
+      end
+
+      t.column('Name', :name,
+        :sortable => true
+      )
+
+      t.column('Size', :size,
+        :sortable => true
+      ) { |f| f.symbolic_type == :regular ? colored_pretty_size(f.size) : '-' }
+
+      t.column('Type', :symbolic_type,
+        :sortable => true,
+        :filters  => filter_values_for(@fileinfolist, :symbolic_type,
+          format: lambda do |value, label, count|
+            { :value => value.to_s, :label => label.to_s.humanize, :indicator => count }
+          end
+        )
+      ) do |f|
+        next f.userfile.pretty_type if f.userfile
+        next html_colorize('Unacceptable?') unless f.state_ok
+
+        case f.symbolic_type
+        when :regular
+          base       = SingleFile
+          html_class = 'file_select'
+        when :directory
+          base       = FileCollection
+          html_class = 'directory_select'
+        else
+          next f.symbolic_type.to_s.humanize
+        end
+
+        select_tag('filetypes[]',
+          options_for_select(
+            base.valid_file_classes.map do |c|
+              [c.pretty_type, "#{c.name}-#{f.name}"]
+            end,
+            class_param_for_name(f.name, base)
+          ),
+          :class => html_class
+        )
+      end
+
+      t.column('Last modified', :mtime,
+        :sortable => true
+      ) { |f| to_localtime(Time.at(f.mtime), :datetime) }
+
+      t.column('Registered?', :registered) do |f|
+        userfile = f.userfile
+        next 'No' unless userfile
+
+        owner = "(as user #{userfile.user.login})" unless
+          [@as_user.id, current_user.id].include?(userfile.user_id)
+        link_to("Registered #{owner}", { :controller => 'userfiles', :action => 'show', :id => userfile.id })
+      end
+
+      t.column('Note', :message)
+    %>
+  <% end %>
 
+</div>
diff --git a/BrainPortal/app/views/data_providers/_view_option_button.html.erb b/BrainPortal/app/views/data_providers/_view_option_button.html.erb
index 8109d4502..4dc45ea4f 100644
--- a/BrainPortal/app/views/data_providers/_view_option_button.html.erb
+++ b/BrainPortal/app/views/data_providers/_view_option_button.html.erb
@@ -18,27 +18,35 @@
 # 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/>.
 #
 -%>
 
 <%= button_with_dropdown_menu("View Options") do %>
   <div class="view_options">
-
     <% user_list = current_user.available_users.sort_by(&:login) %>
     <% if user_list.size > 1 %>
       Browse as another user:
-      <%= ajax_onchange_select( :as_user_id, browse_data_provider_path(:update_filter => "browse_hash"),
-          options_for_select( user_list.collect { |u| [ u.login, u.id.to_s ] },
-                              @as_user.id.to_s ), :datatype => "script") %>
+      <%=
+        ajax_onchange_select(:as_user_id,
+          browse_data_provider_path,
+          options_for_select(
+            user_list.collect { |u| [ u.login, u.id.to_s ] },
+            @as_user.id.to_s
+          ),
+          :datatype => 'script'
+        )
+      %>
       <br/>
     <% end %>
 
-    <%= ajax_link 'Refresh list of files', browse_data_provider_path(:refresh => true), :datatype  => 'script' %><br/>
-  
-    Number of files per page:
-    <%= ajax_onchange_select( :per_page, browse_data_provider_path(:update_filter => "browse_hash"), options_for_select( [25, 50, 100, 200, 500 ], @per_page ), :datatype => "script") %>
-    
+    <%=
+      ajax_link('Refresh list of files',
+        browse_data_provider_path(:refresh => true),
+        :datatype => 'script'
+      )
+    %>
+    <br/>
   </div>
 <% end %>
 
diff --git a/BrainPortal/app/views/data_providers/browse.js.erb b/BrainPortal/app/views/data_providers/browse.js.erb
index cca6e66a3..c0e4a236e 100644
--- a/BrainPortal/app/views/data_providers/browse.js.erb
+++ b/BrainPortal/app/views/data_providers/browse.js.erb
@@ -22,5 +22,7 @@
 #
 -%>
 
-jQuery("#dp_browse_table").html(<%= html_for_js(render :partial  => 'dp_browse_table') %>);
+jQuery("#dp_browse_table")
+  .html(<%= html_for_js(render :partial  => 'dp_browse_table') %>)
+  .trigger('new_content');
 

From 9dc11e1230dc7a34e4c32a718e54a5f7e7a4b2e7 Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Mon, 14 Sep 2015 15:08:43 -0400
Subject: [PATCH 43/85] Strip off '_options' suffix for scope_*_link helpers,
 minor fixes

URL and link option arguments are now named just 'url' and 'link',
respectively. This helps reduce clutter without sacrificing too much
readability.

This changeset also adds a few missing comments and fixes a minor bug
where an empty filter or order set in a scope sent via scope_params
would not clear the corresponding set (attribute) in the session scope.
---
 .../app/controllers/tasks_controller.rb       |  7 ++-
 BrainPortal/app/helpers/scope_helper.rb       | 44 +++++++++++--------
 .../custom_filters/_custom_filter_li.html.erb |  4 +-
 .../messages/_message_index_display.html.erb  |  4 +-
 .../app/views/shared/_active_filters.html.erb |  8 ++--
 .../app/views/sites/_sites_table.html.erb     |  4 +-
 BrainPortal/app/views/tags/_tag_li.html.erb   |  4 +-
 .../app/views/tasks/_tasks_display.html.erb   |  2 +-
 .../app/views/userfiles/_file_menu.html.erb   |  4 +-
 .../userfiles/_view_option_button.html.erb    |  2 +-
 .../app/views/users/_users_table.html.erb     |  4 +-
 BrainPortal/lib/view_scopes.rb                |  2 +-
 12 files changed, 51 insertions(+), 38 deletions(-)

diff --git a/BrainPortal/app/controllers/tasks_controller.rb b/BrainPortal/app/controllers/tasks_controller.rb
index fff11cb33..110246e2d 100644
--- a/BrainPortal/app/controllers/tasks_controller.rb
+++ b/BrainPortal/app/controllers/tasks_controller.rb
@@ -730,6 +730,8 @@ def update_multiple
   # [*Terminate*] Kill the task, while maintaining its temporary files and its entry in the database.
   # [*Delete*] Kill the task, delete the temporary files and remove its entry in the database.
   def operation
+    @scope      = scope_from_session('tasks')
+
     operation   = params[:operation]
     tasklist    = params[:tasklist]  || []
     tasklist    = [ tasklist ]  unless tasklist.is_a?(Array)
@@ -981,7 +983,10 @@ def resource_class #:nodoc:
     CbrainTask
   end
 
-  def view_scope(base) #:nodoc:
+  # View tasks scope; filtered and sorted list of tasks to display (or currently
+  # displayed). +base+ is expected to be the base scope to filter and sort
+  # (defaults to +base_scope+). Requires a valid @scope object.
+  def view_scope(base)
     base = base.where(:group_id => current_project.id) if current_project
     base = base.where(
       :bourreau_id => Bourreau
diff --git a/BrainPortal/app/helpers/scope_helper.rb b/BrainPortal/app/helpers/scope_helper.rb
index f87b66951..0de3f06d6 100644
--- a/BrainPortal/app/helpers/scope_helper.rb
+++ b/BrainPortal/app/helpers/scope_helper.rb
@@ -52,8 +52,16 @@ module ScopeHelper
   def scope_params(name, scope, compress: true)
     scope = scope.to_hash if scope.is_a?(Scope)
     scope = Scope.compact_hash(scope)
-    scope = ViewScopes.compress_scope(scope) if compress
 
+    # Scope's compact_hash will naturally remove default values (empty arrays
+    # and hashes). They are restored here to allow clearing the corresponding
+    # Scope attributes, as CbrainSession's apply_changes method will only update
+    # an attribute if the corresponding key is present in the input hash.
+    { 'o' => [], 'f' => [], 'c' => {} }.each do |key, default|
+      scope[key] = default unless scope.has_key?(key)
+    end
+
+    scope = ViewScopes.compress_scope(scope) if compress
     { '_scopes' => { name => scope } }
   end
 
@@ -137,38 +145,38 @@ def scope_custom_params(scope, custom)
   # link's URL and thus behave identically to +scope_params+'s corresponding
   # parameters.
   #
-  # +label+ is expected to be the link's text label and +url_options+ and
-  # +link_options+ are expected to be hashes of options to pass to url_for and
-  # link_to (or ajax_link), respectively. Only the special link option :ajax
-  # (whether or not to use ajax_link instead of link_to, defaulting to link_to)
-  # is not passed.
-  def scope_link(label, name, scope, compress: true, url_options: {}, link_options: {})
-    url = url_for(scope_params(name, scope, compress: compress).merge(url_options))
-    generic_scope_link(label, url, link_options)
+  # +label+ is expected to be the link's text label and +url+ and +link+ are
+  # expected to be hashes of options to pass to url_for and link_to
+  # (or ajax_link), respectively. Only the special link option :ajax (whether
+  # or not to use ajax_link instead of link_to, defaulting to link_to) is not
+  # passed.
+  def scope_link(label, name, scope, compress: true, url: {}, link: {})
+    url = url_for(scope_params(name, scope, compress: compress).merge(url))
+    generic_scope_link(label, url, link)
   end
 
   # Link version of +scope_filter_params+. Identical to +scope_link+ but uses
   # +scope_filter_params+ in order to generate the URL. See +scope_link+ for more
   # information.
-  def scope_filter_link(label, scope, operation, filters, url_options: {}, link_options: {})
-    url = url_for(scope_filter_params(scope, operation, filters).merge(url_options))
-    generic_scope_link(label, url, link_options)
+  def scope_filter_link(label, scope, operation, filters, url: {}, link: {})
+    url = url_for(scope_filter_params(scope, operation, filters).merge(url))
+    generic_scope_link(label, url, link)
   end
 
   # Link version of +scope_order_params+. Identical to +scope_link+ but uses
   # +scope_order_params+ in order to generate the URL. See +scope_link+ for more
   # information.
-  def scope_order_link(label, scope, operation, orders, url_options: {}, link_options: {})
-    url = url_for(scope_order_params(scope, operation, orders).merge(url_options))
-    generic_scope_link(label, url, link_options)
+  def scope_order_link(label, scope, operation, orders, url: {}, link: {})
+    url = url_for(scope_order_params(scope, operation, orders).merge(url))
+    generic_scope_link(label, url, link)
   end
 
   # Link version of +scope_custom_params+. Identical to +scope_link+ but uses
   # +scope_custom_params+ in order to generate the URL. See +scope_link+ for more
   # information.
-  def scope_custom_link(label, scope, custom, url_options: {}, link_options: {})
-    url = url_for(scope_custom_params(scope, custom).merge(url_options))
-    generic_scope_link(label, url, link_options)
+  def scope_custom_link(label, scope, custom, url: {}, link: {})
+    url = url_for(scope_custom_params(scope, custom).merge(url))
+    generic_scope_link(label, url, link)
   end
 
   # Generate a pretty string representation of +filter+, optionally using
diff --git a/BrainPortal/app/views/custom_filters/_custom_filter_li.html.erb b/BrainPortal/app/views/custom_filters/_custom_filter_li.html.erb
index 8d54ecbee..b3a4686f4 100644
--- a/BrainPortal/app/views/custom_filters/_custom_filter_li.html.erb
+++ b/BrainPortal/app/views/custom_filters/_custom_filter_li.html.erb
@@ -26,11 +26,11 @@
 <%=
   scope_custom_link(crop_text_to(15, filter.name),
     @scope, { 'custom_filters' => [filter.id] },
-    url_options:  {
+    url:  {
       'controller'  => @custom_filter.filtered_class_controller,
       '_scope_mode' => 'append'
     },
-    link_options: {
+    link: {
       :ajax => true
     }
   )
diff --git a/BrainPortal/app/views/messages/_message_index_display.html.erb b/BrainPortal/app/views/messages/_message_index_display.html.erb
index f1ab783dc..67b8f95d2 100644
--- a/BrainPortal/app/views/messages/_message_index_display.html.erb
+++ b/BrainPortal/app/views/messages/_message_index_display.html.erb
@@ -48,7 +48,7 @@
           scope_filter_link(
             html_colorize("#{@unread_count} unread"),
             @scope, :set, { :a => 'read', :v => 0 },
-            link_options: { :ajax => true }
+            link: { :ajax => true }
           )
         %>
       <% end %>
@@ -57,7 +57,7 @@
           scope_filter_link(
             "#{@read_count} read",
             @scope, :set, { :a => 'read', :v => 1 },
-            link_options: { :ajax => true }
+            link: { :ajax => true }
           )
         %>
       <% end %>
diff --git a/BrainPortal/app/views/shared/_active_filters.html.erb b/BrainPortal/app/views/shared/_active_filters.html.erb
index bfdfd72a8..6f7e3138f 100644
--- a/BrainPortal/app/views/shared/_active_filters.html.erb
+++ b/BrainPortal/app/views/shared/_active_filters.html.erb
@@ -34,7 +34,7 @@
     (<%=
       scope_filter_link('clear',
         scope, :clear, nil,
-        link_options: { :ajax => true }
+        link: { :ajax => true }
       )
     %>)
     <span id="current_filters">
@@ -45,7 +45,7 @@
         <%=
           scope_filter_link(delete_icon,
             scope, :remove, filter,
-            link_options: { :ajax => true }
+            link: { :ajax => true }
           )
         %>
       <% end %>
@@ -56,8 +56,8 @@
         <%=
           scope_custom_link(delete_icon,
             scope, { 'custom_filters' => [id] },
-            url_options:  { '_scope_mode' => 'delete' },
-            link_options: { :ajax         => true     }
+            url:  { '_scope_mode' => 'delete' },
+            link: { :ajax         => true     }
           )
         %>
       <% end %>
diff --git a/BrainPortal/app/views/sites/_sites_table.html.erb b/BrainPortal/app/views/sites/_sites_table.html.erb
index 70dbef511..1e5ea6a76 100644
--- a/BrainPortal/app/views/sites/_sites_table.html.erb
+++ b/BrainPortal/app/views/sites/_sites_table.html.erb
@@ -65,14 +65,14 @@
     t.column("Number of Users", :nusers) do |s|
       scope_filter_link(s.users.count.to_s,
         users_scope, :set, { :a => 'site_id', :v => s.id },
-        url_options: { :controller => :users }
+        url: { :controller => :users }
       )
     end
 
     t.column("Number of Projects", :nprojects) do |s|
       scope_filter_link(s.groups.count.to_s,
         groups_scope, :set, { :a => 'site_id', :v => s.id },
-        url_options: { :controller => :groups }
+        url: { :controller => :groups }
       )
     end
   %>
diff --git a/BrainPortal/app/views/tags/_tag_li.html.erb b/BrainPortal/app/views/tags/_tag_li.html.erb
index 6f10223a3..5197640d6 100644
--- a/BrainPortal/app/views/tags/_tag_li.html.erb
+++ b/BrainPortal/app/views/tags/_tag_li.html.erb
@@ -26,8 +26,8 @@
   <%=
     scope_filter_link(crop_text_to(15, tag.name),
       @scope, :set, { 'type' => 'uf.tags', 'value' => [tag.id] },
-      url_options:  { :controller => :userfiles },
-      link_options: { :ajax       => true       }
+      url:  { :controller => :userfiles },
+      link: { :ajax       => true       }
     )
   %>
 </b>
diff --git a/BrainPortal/app/views/tasks/_tasks_display.html.erb b/BrainPortal/app/views/tasks/_tasks_display.html.erb
index 772722246..79a921a10 100644
--- a/BrainPortal/app/views/tasks/_tasks_display.html.erb
+++ b/BrainPortal/app/views/tasks/_tasks_display.html.erb
@@ -309,7 +309,7 @@
         scope_custom_link(
           "Switch to #{batch_view ? 'List' : 'Batch'} View",
           @scope, { 'batch' => !batch_view },
-          link_options: { :ajax => true }
+          link: { :ajax => true }
         )
       %>
     </div>
diff --git a/BrainPortal/app/views/userfiles/_file_menu.html.erb b/BrainPortal/app/views/userfiles/_file_menu.html.erb
index 51a219113..7f6b67f1f 100644
--- a/BrainPortal/app/views/userfiles/_file_menu.html.erb
+++ b/BrainPortal/app/views/userfiles/_file_menu.html.erb
@@ -178,7 +178,7 @@
           <%=
             scope_filter_link('Has no parent',
               @scope, :add, { 'type' => 'uf.hier', 'operator' => 'no_parent' },
-              link_options: { :ajax => true }
+              link: { :ajax => true }
             )
           %>
         </li>
@@ -186,7 +186,7 @@
           <%=
             scope_filter_link('Has no children',
               @scope, :add, { 'type' => 'uf.hier', 'operator' => 'no_child' },
-              link_options: { :ajax => true }
+              link: { :ajax => true }
             )
           %>
         </li>
diff --git a/BrainPortal/app/views/userfiles/_view_option_button.html.erb b/BrainPortal/app/views/userfiles/_view_option_button.html.erb
index 8389d4b57..b0ef9f7ae 100644
--- a/BrainPortal/app/views/userfiles/_view_option_button.html.erb
+++ b/BrainPortal/app/views/userfiles/_view_option_button.html.erb
@@ -28,7 +28,7 @@
       toggle_link = lambda do |on, off, key|
         scope_custom_link((@scope.custom[key] ? off : on),
           @scope, { key => !@scope.custom[key] },
-          link_options: { :ajax => true }
+          link: { :ajax => true }
         )
       end
     %>
diff --git a/BrainPortal/app/views/users/_users_table.html.erb b/BrainPortal/app/views/users/_users_table.html.erb
index d7879f95f..66dad18ad 100644
--- a/BrainPortal/app/views/users/_users_table.html.erb
+++ b/BrainPortal/app/views/users/_users_table.html.erb
@@ -41,7 +41,7 @@
         <%=
           scope_filter_link("#{@unlocked_users_count} active",
             @scope, :set, { :a => 'account_locked', :v => 0 },
-            link_options: { :ajax => true }
+            link: { :ajax => true }
           )
         %>
       <% end %>
@@ -49,7 +49,7 @@
         <%=
           scope_filter_link("#{@locked_users_count} locked",
             @scope, :set, { :a => 'account_locked', :v => 1 },
-            link_options: { :ajax => true }
+            link: { :ajax => true }
           )
         %>
       <% end %>
diff --git a/BrainPortal/lib/view_scopes.rb b/BrainPortal/lib/view_scopes.rb
index d38b0e168..91ad98aa1 100644
--- a/BrainPortal/lib/view_scopes.rb
+++ b/BrainPortal/lib/view_scopes.rb
@@ -329,7 +329,7 @@ def self.compact_hash(hash)
 
         # Include other attributes
         's'  =>  hash['s']  || hash['selection'],
-        'c'  => (hash['c']  || hash['custom']).stringify_keys.to_h,
+        'c'  => (hash['c']  || hash['custom'] || {}).stringify_keys.to_h,
         'fc' => (hash['fc'] || hash['filter_combination']).to_s,
       }
 

From a7c9771ef11c05817e5626942f9cb060f3549ae4 Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Wed, 16 Sep 2015 10:11:07 -0400
Subject: [PATCH 44/85] Refactor/cleanup of old filter API

basic_filter_helpersi.rb and filter_helper.rb have been removed
(including the dynamic table binding dynamic_index_table), and all
the calls left to the methods they contained replaced with the
corresponding Scope API method calls.

This changeset also contains a minor fix for scope_items_url_params,
and a specialized status filter for tasks (required as part of the port
to the Scope API).
---
 .../controllers/custom_filters_controller.rb  |   5 -
 .../app/controllers/tasks_controller.rb       | 115 ++++++++++-
 .../app/controllers/userfiles_controller.rb   |   1 +
 .../app/helpers/dynamic_table_helper.rb       | 121 +-----------
 BrainPortal/app/helpers/filter_helper.rb      | 154 ---------------
 BrainPortal/app/helpers/scope_helper.rb       |  38 +++-
 BrainPortal/app/models/group.rb               |   2 -
 BrainPortal/app/models/message.rb             |   9 -
 BrainPortal/app/models/user.rb                |   2 -
 BrainPortal/app/views/portal/report.html.erb  |  23 ++-
 BrainPortal/app/views/portal/welcome.html.erb |  25 +--
 .../cb_serializer/views/_show_params.html.erb |   8 +-
 .../parallelizer/views/_show_params.html.erb  |   8 +-
 BrainPortal/lib/basic_filter_helpers.rb       | 184 ------------------
 14 files changed, 198 insertions(+), 497 deletions(-)
 delete mode 100644 BrainPortal/app/helpers/filter_helper.rb
 delete mode 100644 BrainPortal/lib/basic_filter_helpers.rb

diff --git a/BrainPortal/app/controllers/custom_filters_controller.rb b/BrainPortal/app/controllers/custom_filters_controller.rb
index 30e874a2b..7eb2739a0 100644
--- a/BrainPortal/app/controllers/custom_filters_controller.rb
+++ b/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."
diff --git a/BrainPortal/app/controllers/tasks_controller.rb b/BrainPortal/app/controllers/tasks_controller.rb
index 110246e2d..f69e727bf 100644
--- a/BrainPortal/app/controllers/tasks_controller.rb
+++ b/BrainPortal/app/controllers/tasks_controller.rb
@@ -1007,6 +1007,119 @@ def view_scope(base)
     view
   end
 
-  # Warning: private context in effect here.
+  public
+
+  # Tasks-specific status filter; filter by a broad class of statuses: whether
+  # or not a given task's status is within a specific class of statuses. For
+  # example, the 'active' status class contains 'New', 'Standby', 'Configured',
+  # etc.
+  #
+  # Note that this filter uses Scope::Filter's *value* attribute to hold the
+  # status class to check against, and that the *attribute* attribute is
+  # statically set to 'status' (as this filter will only ever filter on a task's
+  # status).
+  class StatusFilter < Scope::Filter
+    # Status classes and their corresponding statuses (possible values for the
+    # *value* attribute). These correspond to CbrainTask's status lists.
+    StatusClasses = {
+      'completed'  => CbrainTask::COMPLETED_STATUS,
+      'running'    => CbrainTask::RUNNING_STATUS,
+      'active'     => CbrainTask::ACTIVE_STATUS,
+      'queued'     => CbrainTask::QUEUED_STATUS,
+      'processing' => CbrainTask::PROCESSING_STATUS,
+      'failed'     => CbrainTask::FAILED_STATUS
+    }
+
+    # Create a new blank StatusFilter. Only present to pre-set *attribute*.
+    def initalize
+      @attribute = 'status'
+    end
+
+    # Nice string representation of this filter for +pretty_scope_filter+.
+    def to_s
+      "Status: #{@value.to_s.humanize}"
+    end
+
+    # The methods below are TagFilter specific versions of the Scope::Filter
+    # interface. See Scope::Filter for more details on how these methods
+    # operate and for detailed parameter information.
+
+    # Type name to recognize this filter when in hash representation
+    # (+type+ (+t+) key).
+    def self.type_name
+      't.sts'
+    end
+
+    # Apply this filter on +collection+, which is expected to be a tasks
+    # model or scope or a collection of CbrainTask objects.
+    #
+    # Note that this filter is specific to CbrainTasks and will not operate
+    # correctly with any other kind of object.
+    def apply(collection)
+      raise "no status to filter with" unless @value.present?
+
+      statuses = StatusClasses[@value.to_s.downcase]
+
+      # With a CbrainTask model (or scope)
+      if (collection <= ActiveRecord::Base rescue nil)
+        collection.where(:status => statuses)
+
+      # With a Ruby Enumerable
+      else
+        collection.select { |t| statuses.include?(t.status) }
+      end
+    end
+
+    # Check if this filter is valid (+apply+ can be used). A StatusFilter only
+    # requires a valid *value* to be useable.
+    def valid?
+      @value.present?
+    end
+
+    # Create a new StatusFilter from a hash representation. The following keys
+    # are recognized in +hash+:
+    #
+    # [+value+ or +v+]
+    #  *value* attribute: a string or symbol denoting which set of statuses to
+    #  match against; one of 'completed', 'running', 'active', 'queued',
+    #  'processing' or 'failed'.
+    #
+    # Note that no other key from Scope::Filter's +from_hash+ is recognized.
+    def self.from_hash(hash)
+      return nil unless hash.is_a?(Hash)
+
+      hash = hash.with_indifferent_access unless
+        hash.is_a?(HashWithIndifferentAccess)
+
+      filter = self.new
+      value = (hash['value'] || hash['v']).to_s.downcase
+      filter.value = value if StatusClasses.keys.include?(value)
+
+      filter
+    end
+
+    # Convert this StatusFilter into a hash representation, doing the exact
+    # opposite of +from_hash+.
+    def to_hash(compact: false)
+      hash = {
+        'type'  => self.class.type_name,
+        'value' => @value
+      }
+
+      compact ? self.class.compact_hash(hash) : hash
+    end
+
+    # Compact +hash+, a hash representation of StatusFilter (matching
+    # +from_hash+'s structure).
+    def self.compact_hash(hash)
+      ViewScopes::Scope.generic_compact_hash(
+        hash,
+        {
+          'type'  => 't',
+          'value' => 'v',
+        }
+      )
+    end
+  end
 
 end
diff --git a/BrainPortal/app/controllers/userfiles_controller.rb b/BrainPortal/app/controllers/userfiles_controller.rb
index fa178d8c5..8d4bef0ae 100644
--- a/BrainPortal/app/controllers/userfiles_controller.rb
+++ b/BrainPortal/app/controllers/userfiles_controller.rb
@@ -1620,6 +1620,7 @@ def view_scope(base = nil)
     custom_filters  = (@scope.custom[:custom_filters] || []).dup
     custom_filters &= current_user.custom_filter_ids
     custom_filters.map! { |id| UserfileCustomFilter.find(id) }
+    custom_filters.compact!
 
     @scope.order << Scope::Order.from_hash({
       :attribute => 'name',
diff --git a/BrainPortal/app/helpers/dynamic_table_helper.rb b/BrainPortal/app/helpers/dynamic_table_helper.rb
index 6ba905a9a..fb0165501 100644
--- a/BrainPortal/app/helpers/dynamic_table_helper.rb
+++ b/BrainPortal/app/helpers/dynamic_table_helper.rb
@@ -57,7 +57,7 @@
 #
 # Dynamic table public API methods:
 # * +dynamic_table+              Create a dynamic table
-# * +dynamic_index_table+        Create a index-specific dynamic table
+# * +dynamic_scoped_table+       Create a dynamic table using the Scope API
 # * +DynamicTable+::+column+     Add a column
 # * +DynamicTable+::+row+        Set row attributes
 # * +DynamicTable+::+selectable+ Make rows selectable
@@ -952,125 +952,6 @@ def dynamic_table(collection, options = {}, &block)
     (options.has_key?(:render) && ! options[:render]) ? table : table.render
   end
 
-  # This method is a simple variation of +dynamic_table+ (and DynamicTable)
-  # to make creating index tables easier. For example, this method supplies
-  # sort_target and filter_target lambda functions mimicking what
-  # index_table (IndexTableHelper) would send.
-  # This method's parameters are the same as +dynamic_table+'s, with the
-  # following additional options:
-  #
-  # [sort_map]
-  #  Mapping (hash) between table column names and the full column definitions
-  #  used for sorting. For example, a column for user logins would have
-  #  name :login and sorting definition 'users.login'. If a map for a given
-  #  column name is not found, it defaults to the column name itself.
-  #
-  # [filter_map]
-  #  Mapping (hash) between table column names and object fields used for
-  #  filtering. For example, a column for user logins would have
-  #  name :login and filtering field 'user_id'. If a map for a given
-  #  column name is not found, it defaults to the column name itself.
-  #
-  # This method gives index_table-like defaults for:
-  # * sort_target and filter_target
-  # * fetching the sorting order and column (@filter_params)
-  # * converting filters to DynamicTable's format ([<value>, <label>, <indicator>])
-  # * sending how many rows per page should be displayed (per_page)
-  def dynamic_index_table(collection, options = {}, &block)
-    sort_map   = options[:sort_map]   || {}
-    filter_map = options[:filter_map] || {}
-
-    # Sorting parameters syntax:
-    #  <controller>[sort_hash][order]=<column>&
-    #  <controller>[sort_hash][dir]=<'ASC'|'DESC'>
-    options[:sort_target] ||= lambda do |column,order|
-      {
-        :controller => params[:controller],
-        :action     => params[:action],
-        params[:controller] => { :sort_hash => {
-          :order => sort_map[column] || column,
-          :dir   => (order == :asc ? :desc : :asc).to_s.upcase
-        } }
-      }
-    end
-
-    # Use the filter_proxy mechanism to add filters
-    options[:filter_target] ||= lambda do |column,filter|
-      filter_column = filter_map[column] || column
-      link = filter_add_link('', { :filters => { filter_column => filter.value } })
-      link.match(/href="(.+?)"/)[1] # FIXME there is no filter_add_url...
-    end
-
-    # We create and cache a subclass of DynamicTable to act as
-    # a compatibility layer for the old 'index_table' framework
-    @@index_table_class ||= Class.new(DynamicTable) do
-      attr_accessor :sort_map
-      attr_accessor :filter_map
-
-      define_method(:column) do |label, name = nil, options = {}, &block| #:nodoc:
-        # If the column is sortable and its order set as :auto, use
-        # filter_params' order value rather than the
-        # params[<column>][:sort_order] default.
-        filter_params = @template.instance_eval { @filter_params }
-        sortable      = [:sortable, :sort_target, :sort_order].any? { |k| options[k] }
-        is_auto       = ! options[:sort_order] || options[:sort_order] == :auto
-        if sortable && is_auto
-          name    = (name || label.to_s.underscore).to_sym
-          order   = :none unless filter_params['sort_hash']['order'] == @sort_map[name]
-          order ||= filter_params['sort_hash']['dir'].downcase.to_sym rescue :asc
-          options[:sort_order] = order
-        end
-
-        # If we have index_table-like filters, convert them to DynamicTable's format
-        options[:filters].map! do |label,hash|
-          value = hash[:filters].first[1]
-          empty = hash[:class].to_s =~ /filter_zero/ # old HTML class convention
-          { :value => value, :label => label, :empty => empty }
-        end if
-          options[:filters] && options[:filters].all? do |filter|
-            filter[1][:filters].first[1] rescue nil
-          end
-
-        super(label, name, options, &block)
-      end
-
-      define_method(:pagination) do |location = nil, options = {}| #:nodoc:
-        # If options are given without a location...
-        if options.blank? && ! [:top, :bottom, :both].include?(location)
-          options  = location || {}
-          location = nil
-        end
-
-        # Pre-set some HTML attributes for the per-page input
-        (options[:input_html] ||= {}).merge!({
-          :name        => 'per_page',
-          :class       => 'search_box',
-          :'data-type' => 'script',
-          :'data-url'  =>  @template.instance_eval do
-            url_for(:controller => params[:controller], :update_filter => true)
-          end
-        }) { |key,old,new| old }
-
-        super(location, options)
-      end
-
-      alias_method :paginated, :pagination
-      alias_method :paginate,  :pagination
-
-    end
-
-    # Alright, let's create an instance of our backwards-compatible index_table object
-    table = @@index_table_class.create(collection, self, options) do |t|
-      # Make the table aware of the sorting and filtering mappings
-      t.sort_map   = sort_map
-      t.filter_map = filter_map
-
-      block.call(t)
-    end
-
-    (options.has_key?(:render) && ! options[:render]) ? table : table.render
-  end
-
   # Specialization of +dynamic_table+ (and DynamicTable) to make creating
   # tables using the view scopes mechanism (see the ViewScopes module) easier
   # by supplying sort_targer and filter_target lambda functions using Scope
diff --git a/BrainPortal/app/helpers/filter_helper.rb b/BrainPortal/app/helpers/filter_helper.rb
deleted file mode 100644
index b29ab8b39..000000000
--- a/BrainPortal/app/helpers/filter_helper.rb
+++ /dev/null
@@ -1,154 +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 <http://www.gnu.org/licenses/>.
-#
-
-#Helpers for creating filter links.
-module FilterHelper
-
-  Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
-
-  # Add to currently active filters. Options include:
-  # [:parameter] which filter parameter to adjust (default to :filter_hash).
-  # [:value]     the value to update it with.
-  def filter_add_link(name, options = {})
-    filter_param = options.delete(:parameter) || :filter_hash
-    values       = options.delete(:value)   if options.has_key?(:value) #Value and filters synonymous but filters takes priority
-    values       = options.delete(:filters) if options.has_key?(:filters)
-    if values.respond_to?(:merge)
-      params_hash  = values.merge :update_filter => filter_param
-    else
-      params_hash  = {filter_param => values}.merge :update_filter => true
-    end
-    options[:pretty] = true
-    build_filter_link name, params_hash, options
-  end
-
-  # Remove a filter from those currently active. +key+ is the filter
-  # attribute to be adjusted.
-  #
-  # Options:
-  # [:parameter] which filter to adjust (defaults to :filter_hash).
-  def filter_remove_link(name, key, options = {})
-    filter_param = options.delete(:parameter) || :filter_hash
-    params_hash = {:remove => {filter_param => key}}
-    build_filter_link name, params_hash, options
-  end
-
-  # Clear a filter. The option :clear_params can be used in two ways.
-  # The first is to set it to the name of a know filter. The second is to
-  # set the value to clear_<x>, where +x+ is the prefix of a 'type' of filter.
-  # In the latter case, all filters with the given prefix will be cleared.
-  def filter_clear_link(name, options = {})
-    cleared_params = options.delete(:clear_params) || :clear_filter
-    if !cleared_params.is_a?(Array) && cleared_params.to_s =~ /^clear_/
-      params_hash = {cleared_params => true}
-    else
-      params_hash = {:clear_all  => cleared_params}
-    end
-    options[:pretty] = true
-    build_filter_link name, params_hash, options
-  end
-
-  # Combines the functionality of filter_add_link and filter_clear_link.
-  # A filter is cleared and than a new value is added to the the empty filter.
-  def filter_reset_link(name, options = {})
-    filter_param = options.delete(:parameter) || :filter_hash
-    values       = options.delete(:value)   if options.has_key?(:value) #Value and filters synonymous but filters takes priority
-    values       = options.delete(:filters) if options.has_key?(:filters)
-    if values.respond_to?(:merge)
-      params_hash  = values.merge :update_filter => filter_param
-    else
-      params_hash  = {filter_param => values}.merge :update_filter => true
-    end
-    cleared_params = options.delete(:clear_params) || :clear_filter
-    if !cleared_params.is_a?(Array) && cleared_params.to_s =~ /^clear_/
-      params_hash.merge! cleared_params => true
-    else
-      params_hash.merge! :clear_all  => cleared_params
-    end
-    options[:pretty] = true
-    build_filter_link name, params_hash, options
-  end
-
-  def build_filter_link(name, params_hash, options = {}) #:nodoc:
-    controller   = options.delete(:controller) || params[:controller]
-    action       = options.delete(:action)     || :index
-    id           = options.delete(:id)
-    if options.has_key?(:ajax)
-      ajax         = options.delete(:ajax)
-    else
-      ajax         = true
-    end
-    unless options.delete(:pretty)
-      params_hash = {controller.to_sym  => params_hash}
-    end
-    url_hash = {:proxy_destination_controller => controller, :proxy_destination_action => action, :proxy_destination_id => id}.merge params_hash
-    url = filter_proxy_path(url_hash)
-    if ajax
-      options[:datatype] ||= :script
-      ajax_link name, url, options
-    else
-      link_to h(name.to_s), url, options
-    end
-  end
-
-  # Will check for associations to display them properly.
-  def display_filter(model, key, value, methods = {})
-    exceptions = {
-      "group" => "project",
-      "bourreau"  => "server"
-    }
-
-    klass = Class.const_get model.to_s.classify
-    association = klass.reflect_on_all_associations(:belongs_to).find { |a| a.foreign_key == key.to_s  }
-    if association
-      association_key   = association.foreign_key
-      association_name  = association.name.to_s
-      association_class = Class.const_get association.class_name
-      name_method = methods[association_key.to_sym] || methods[association_name.to_sym] || :name
-      object = association_class.find_by_id(value)
-      if exceptions[association_name]
-        association_name = exceptions[association_name]
-      end
-      if object
-        "#{association_name.humanize}: #{object.send(name_method)}"
-      else
-        "#{key.to_s.humanize}: #{value}"
-      end
-    else
-      "#{key.to_s.humanize}: #{value}"
-    end
-  end
-
-  # Show count of an association and link to association's page.
-  def index_count_filter(count, controller, filters, options={})
-     count = count.to_i
-     return ""  if count == 0 && ! ( options[:show_zeros] || options[:link_zeros] )
-     return "0" if count == 0 && ! options[:link_zeros]
-     controller = :bourreaux if controller.to_sym == :remote_resources
-     name = options[:name] || count
-     filter_reset_link name,
-                       :controller   => controller,
-                       :filters      => filters,
-                       :ajax         => false,
-                       :clear_params => options[:clear_params]
-  end
-end
diff --git a/BrainPortal/app/helpers/scope_helper.rb b/BrainPortal/app/helpers/scope_helper.rb
index 0de3f06d6..112d1c27e 100644
--- a/BrainPortal/app/helpers/scope_helper.rb
+++ b/BrainPortal/app/helpers/scope_helper.rb
@@ -433,7 +433,7 @@ def assoc_filter_values_for(model, assoc, label: 'name')
   # intended to be used only to implement +scope_filter_params+ and
   # +scope_order_params+ and is most likely unsuitable for anything else.
   def scope_items_url_params(scope, operation, attr, changes) #:nodoc:
-    return if changes.blank? && operation != :clear
+    return {} unless changes.present? || [:clear, :replace].include?(operation)
 
     key   = (attr == :filters ? 'f' : 'o')
     items = (
@@ -479,4 +479,40 @@ def generic_scope_link(label, url, options)
     }))
   end
 
+  # Deprecated/old methods
+
+  # Generate +count+ as a link to +controller+'s index page, with +filters+ as
+  # the only filters applied on +controller+'s scope. +count+ is expected to be
+  # a count (Integer) of some sort (usually a count of elements on one end of
+  # an association), :controller a controller name as a symbol or string, and
+  # +filters+ a set of old-style filters (hash of <attribute> => <value> pairs,
+  # each equivalent to a { :a => <attribute>, :v => <value>, :o => '==' }
+  # Filter).
+  #
+  # The available options in +options+ are:
+  # [:show_zeros]
+  #  By default, +index_count_filter+ will return an empty string if +count+
+  #  is 0. If this option is specified, '0' will be returned instead.
+  # [:scope_name]
+  #  Scope name to update with the generated link. Defaults to +controller+,
+  #  the same as the controller name.
+  #
+  # This method more-or-less behaves as a clunky, if sightly less wordy,
+  # alternative to using scope_filter_link (:replace operation) directly with
+  # a few quirks added.
+  def index_count_filter(count, controller, filters, options = {})
+    return (options[:show_zeros] ? '0' : '') if (count = count.to_i) == 0
+
+    controller = controller.to_s.downcase
+    controller = 'bourreaux' if controller == 'remote_resources'
+
+    scope_filter_link(count,
+      (options[:scope_name] || controller),
+      :replace, filters.map do |attr, value|
+        { :a => attr, :v => value }
+      end,
+      url: { :controller => controller }
+    )
+  end
+
 end
diff --git a/BrainPortal/app/models/group.rb b/BrainPortal/app/models/group.rb
index 2c537584f..a60356639 100644
--- a/BrainPortal/app/models/group.rb
+++ b/BrainPortal/app/models/group.rb
@@ -62,8 +62,6 @@ class Group < ActiveRecord::Base
 
   attr_accessible         :name, :description, :site_id, :creator_id, :user_ids
 
-  cb_scope                :name_like, lambda { |n| {:conditions => ["groups.name LIKE ?", "%#{n}%"]} }
-
   # Returns the unique and special group 'everyone'
   def self.everyone
     @everyone ||= EveryoneGroup.find_by_name('everyone')
diff --git a/BrainPortal/app/models/message.rb b/BrainPortal/app/models/message.rb
index 17573c85d..af60988fe 100644
--- a/BrainPortal/app/models/message.rb
+++ b/BrainPortal/app/models/message.rb
@@ -42,15 +42,6 @@ class Message < ActiveRecord::Base
 
   attr_accessible :header, :description, :variable_text, :message_type, :read, :user_id, :expiry, :last_sent, :critical, :display, :send_email, :group_id, :sender_id
 
-  cb_scope :time_interval, lambda { |s, e|
-                                    bef = s.to_i
-                                    aft = e.to_i
-                                    bef,aft = aft,bef if aft < bef
-                                    bef = bef < 1 ? 1.day.from_now : bef.ago
-                                    aft = aft.ago
-                                    { :conditions => [ "messages.last_sent < TIMESTAMP(?) AND messages.last_sent > TIMESTAMP(?)", bef, aft ] }
-                                  }
-
   # Send a new message to a user, the users of a group, or a site.
   #
   # The +destination+ argument can be a User, a Group, a Site,
diff --git a/BrainPortal/app/models/user.rb b/BrainPortal/app/models/user.rb
index 1974f3e97..be44d288e 100644
--- a/BrainPortal/app/models/user.rb
+++ b/BrainPortal/app/models/user.rb
@@ -111,8 +111,6 @@ class User < ActiveRecord::Base
 
   force_text_attribute_encoding 'UTF-8', :full_name, :city, :country
 
-  cb_scope                   :name_like, lambda { |n| where("users.login LIKE ? OR users.full_name LIKE ?", "%#{n}%", "%#{n}%") }
-
   # Returns the admin user
   def self.admin
     @@admin ||= self.find_by_login("admin")
diff --git a/BrainPortal/app/views/portal/report.html.erb b/BrainPortal/app/views/portal/report.html.erb
index 26104fd3f..5d37202a2 100644
--- a/BrainPortal/app/views/portal/report.html.erb
+++ b/BrainPortal/app/views/portal/report.html.erb
@@ -152,8 +152,16 @@ in a tabular layout. Proceed as follow:
 
          # Standard proc for TD content (and totals too).
          td_content_proc = Proc.new do |vector,td_filters|
-           pretty_cell_value = @filter_show_proc ? @filter_show_proc.call(vector) : vector[0].to_s
-           index_count_filter(vector[0], @filter_model, @filter_fixed.merge( td_filters || {} ), :name => pretty_cell_value)
+           next '' if vector[0].to_i == 0
+
+           scope_filter_link(
+             (@filter_show_proc ? @filter_show_proc.call(vector) : vector[0].to_s),
+             @filter_model.to_s, :replace,
+             @filter_fixed.merge(td_filters).map do |attr, value|
+               { :a => attr, :v => value }
+             end,
+             url: { :controller => @filter_model }
+           )
          end
       %>
 
@@ -169,10 +177,13 @@ in a tabular layout. Proceed as follow:
                <%= disk_space_info_display(size || 0) do %>
                  <%= pretty_size(size) %></br>
                  <%=
-                   filter_reset_link (pluralize(num_entries,"entry") + " / " + pluralize(sum_files,"file")),
-                                     :controller => :userfiles,
-                                     :filters => @filter_fixed.merge(td_filters || {}),
-                                     :ajax => false
+                   scope_filter_link("#{pluralize(num_entries,"entry")} / #{pluralize(sum_files,"file")}",
+                     'userfiles', :replace,
+                     @filter_fixed.merge(td_filters).map do |attr, value|
+                       { :a => attr, :v => value }
+                     end,
+                     url: { :controller => :userfiles }
+                   )
                  %>
                  <% if num_size_unk > 0 %>
                    </br><%= html_colorize(pluralize(num_size_unk," file") + " w/ unk size") %>
diff --git a/BrainPortal/app/views/portal/welcome.html.erb b/BrainPortal/app/views/portal/welcome.html.erb
index f6dc803a5..b98ccd716 100644
--- a/BrainPortal/app/views/portal/welcome.html.erb
+++ b/BrainPortal/app/views/portal/welcome.html.erb
@@ -175,15 +175,19 @@
     <% if @tasks.size > 0 %>
       <h1>
         <%=
-          link_to "Latest Updated Tasks",
-            :controller   => :tasks,
-            :action       => :index,
-            :tasks        => { :sort_hash => { :order => 'cbrain_tasks.updated_at', :dir => 'DESC' } },
-            :clear_filter => true
+          scope_link('Latest Updated Tasks',
+            'tasks', { :order => [{ :a => 'updated_at', :d => 'desc' }], },
+            url: { :controller => :tasks, :action => :index }
+          )
         %>
         <% active_count = CbrainTask.active.count rescue 0 %>
         <% if active_count > 0 %>
-          <%= filter_reset_link "(#{active_count} active)", :controller => :tasks, :filters  => { :status => :active }, :ajax => false %>
+          <%=
+            scope_filter_link("(#{active_count} active)",
+              'tasks', :replace, { :t => 't.sts', :v => 'active' },
+              url: { :controller => :tasks }
+            )
+          %>
         <% else %>
           (None active)
         <% end %>
@@ -203,11 +207,10 @@
     <% if @files.size > 0 %>
       <h1>
         <%=
-          link_to "Latest Updated Files",
-            :controller   => :userfiles,
-            :action       => :index,
-            :userfiles    => { :sort_hash => { :order => 'userfiles.updated_at', :dir => 'DESC' } },
-            :clear_filter => true
+          scope_link('Latest Updated Files',
+            'userfiles', { :order => [{ :a => 'updated_at', :d => 'desc' }], },
+            url: { :controller => :userfiles, :action => :index }
+          )
         %>
       </h1>
       <table class="latest_summary_table">
diff --git a/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/cb_serializer/views/_show_params.html.erb b/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/cb_serializer/views/_show_params.html.erb
index a02032f48..79af51460 100644
--- a/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/cb_serializer/views/_show_params.html.erb
+++ b/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/cb_serializer/views/_show_params.html.erb
@@ -49,7 +49,13 @@
 
   <p>
   In the task manager, you can view the full
-  <%= filter_reset_link "list of tasks", :controller => :tasks, :filters  => { :batch_id => @task.batch_id }, :ajax => false %> 
+  <%=
+    scope_filter_link('list of tasks',
+      'tasks', :replace, { :a => 'batch_id', :v => @task.batch_id },
+      url:  { :controller => :tasks },
+      link: { :ajax       => false  }
+    )
+  %>
   in this batch.
   </p>
 
diff --git a/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/parallelizer/views/_show_params.html.erb b/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/parallelizer/views/_show_params.html.erb
index 121d95b2d..f93f2fb9c 100644
--- a/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/parallelizer/views/_show_params.html.erb
+++ b/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/parallelizer/views/_show_params.html.erb
@@ -49,7 +49,13 @@
 
   <p>
   In the task manager, you can view the full
-  <%= filter_reset_link "list of tasks", :controller => :tasks, :filters  => { :batch_id => @task.batch_id }, :ajax => false %>
+  <%=
+    scope_filter_link('list of tasks',
+      'tasks', :replace, { :a => 'batch_id', :v => @task.batch_id },
+      url:  { :controller => :tasks },
+      link: { :ajax       => false  }
+    )
+  %>
   in this batch.
   </p>
 
diff --git a/BrainPortal/lib/basic_filter_helpers.rb b/BrainPortal/lib/basic_filter_helpers.rb
deleted file mode 100644
index 7f1a64453..000000000
--- a/BrainPortal/lib/basic_filter_helpers.rb
+++ /dev/null
@@ -1,184 +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 <http://www.gnu.org/licenses/>.
-#
-
-# Helpers to create filter lists for index tables
-# (see index_table_helper.rb).
-module BasicFilterHelpers
-
-  Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
-
-  def self.included(includer) #:nodoc:
-    includer.class_eval do
-      helper_method :basic_filters_for, :association_filters_for
-      # To improve performance update_filters should be called only in certain case in:
-      before_filter :update_filters,             :only => [
-          :index,                  # for all controllers
-          :filter_proxy,           # in application controller
-          :row_data,               # in bourreaux controller
-          :browse, :register,      # in data_providers controller
-          :operation, :batch_list, :update_multiple, # in tasks controller
-          :manage_persistent,      # in userfiles controller
-          ]
-      before_filter :validate_pagination_values, :only => [ :index, :filter_proxy ]
-    end
-  end
-
-  # Easy and safe filtering based on individual attributes or named scopes.
-  # Simply adding <att>=<val> to a URL on an index page that uses this method
-  # will automatically filter as long as <att> is a valid attribute or named
-  # scope.
-  def base_filtered_scope(filtered_scope = resource_class.scoped({}))
-    @filter_params["filter_hash"].each do |att, val|
-      if filtered_scope.cb_scopes[att.to_sym] && att.to_sym != :scoped
-        filtered_scope = filtered_scope.send(att, *val)
-      elsif table_column?(resource_class, att)
-        filtered_scope = filtered_scope.where(att => val)
-      else
-        @filter_params["filter_hash"].delete att
-      end
-    end
-    filtered_scope
-  end
-
-  # Apply currently active sort parameters to a scope
-  def base_sorted_scope(sorted_scope = resource_class.scoped)
-    if @filter_params["sort_hash"] && @filter_params["sort_hash"]["order"] && table_column?(*@filter_params["sort_hash"]["order"].split("."))
-      sorted_scope = sorted_scope.order("#{@filter_params["sort_hash"]["order"]} #{@filter_params["sort_hash"]["dir"]}")
-    end
-    sorted_scope
-  end
-
-  # Convenience method to determine wether a given model has the provided attribute.
-  # Note: mainly for security reasons; this allows easy sanitization of parameters related
-  # to attributes.
-  def table_column?(model, attribute)
-    column = attribute
-    klass = Class.const_get model.to_s.classify
-
-    klass.columns_hash[column]
-  rescue
-    false
-  end
-
-  # Create filtered array to be used by TableBuilder for
-  # basic attribute filters.
-  def basic_filters_for(filtered_scope, header_scope, tab, col, &formatter)
-    table         = tab.to_s.underscore.pluralize
-    column        = col.to_sym
-    column_object = ActiveRecord::Base.connection.columns(table).find { |c| c.name == column.to_s }
-    table_column  = "#{table}.#{column}"
-
-    filt_counts = filtered_scope.undo_where(table_column).group(table_column).count
-
-    header_scope.
-      where( "#{table_column} IS NOT NULL" ).
-      group( table_column ).
-      order( table_column ).
-      raw_rows(table_column, "COUNT(#{table_column})").
-      reject { |pair| pair[0].blank? }.
-      map { |pair|
-        raw_name, count = pair     # [ 'CbrainTask::Civet', 45 ]
-        name            = column_object.type_cast(raw_name)
-        pretty_name     = column == :type ? name.constantize.pretty_type : name
-        formatted_name  = formatter ? formatter.call(pretty_name) : pretty_name
-        filt_count      = filt_counts[name].to_i
-
-        [ formatted_name, filt_count, count, raw_name ]
-      }.
-      sort_by { |tuple| tuple[0] }.
-      map { |tuple|
-        formatted_name, filt_count, count, raw_name = tuple
-        [ "#{formatted_name} (#{filt_count}/#{count})",
-            :filters => { column => raw_name },
-            :class   => filt_count == 0 ? "filter_zero" : nil
-        ]
-      }
-  end
-
-  # Create filtered array to be used by TableBuilder for
-  # basic association filters.
-  def association_filters_for(filtered_scope, header_scope, tab, assoc, options = {}, &formatter)
-    table       = tab.to_s.underscore.pluralize
-    association = assoc.to_s.underscore.singularize
-    assoc_table = options[:association_table] || association.pluralize
-    name_method = options[:name_method] || "name"
-    foreign_key = options[:foreign_key] || "#{association}_id"
-
-    table_fkey  = "#{table}.#{foreign_key}"
-    assoc_name  = "#{assoc_table}.#{name_method}"
-
-    filt_counts = filtered_scope.undo_where(table_fkey).joins(association.to_sym).group(table_fkey).count
-
-    header_scope.
-      joins(association.to_sym).
-      order(assoc_name).
-      group(table_fkey).
-      raw_rows( table_fkey, assoc_name, "COUNT(#{table_fkey})").
-      map do |triplet|
-        fkey, name, count = triplet
-        filt_count        = filt_counts[fkey].to_i
-        formatted_name    = formatter ? formatter.call(name) : name
-
-        [ "#{formatted_name} (#{filt_count}/#{count})",
-            :filters => { foreign_key => fkey },
-            :class   => filt_count == 0 ? "filter_zero" : nil
-        ]
-      end
-  end
-
-  # Set up the current_session variable. Mainly used to set up the filter hash to be
-  # used by index actions.
-  def update_filters
-    Rails.logger.warn(
-      'WARNING: BasicFilterHelpers::update_filters has been ' +
-      'stubbed pending a rewrite of the filtering subsystem'
-    )
-
-    controller = params[:proxy_destination_controller] || params[:controller]
-    current_session.update({ :controllers => { controller => params } })
-    @filter_params = current_session.params_for(controller)
-  end
-
-  ########################################################################
-  # CBRAIN Helper for pagination
-  ########################################################################
-
-  # This prevents users to give wrong number page for example -1 or 999_999_999_9999_999
-  # and limit the per_page variable in order to be in a certain range.
-  # If the values for @per_page or @current_page are already set, you can
-  # use this method to sanitize them.
-  def validate_pagination_values #:nodoc:
-    # Validate per_page
-    @per_page     ||= @filter_params["per_page"]
-    @per_page       = @per_page.to_i
-    @per_page       = 25   if @per_page < 25
-    @per_page       = 1000 if @per_page > 1000
-
-    # Validate page
-    @current_page ||= params[:page]
-    @current_page   = @current_page.to_i
-    @current_page   = 1      if @current_page < 1
-    @current_page   = 99_999 if @current_page > 99_999
-  end
-
-end
-

From df574b1252666d1d1e67e55d7cb3b5e2b542c2f9 Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Wed, 16 Sep 2015 17:26:35 -0400
Subject: [PATCH 45/85] Simple URL filtering format

The new URL parameter, _simple_filters, enables a simplified format
(attribute=value) for specifying scope filters when creating URLs
outside of CBRAIN's codebase (by hand or on another platform, for
example).
---
 BrainPortal/lib/view_scopes.rb | 74 ++++++++++++++++++++++++++++++----
 1 file changed, 66 insertions(+), 8 deletions(-)

diff --git a/BrainPortal/lib/view_scopes.rb b/BrainPortal/lib/view_scopes.rb
index 91ad98aa1..52102e438 100644
--- a/BrainPortal/lib/view_scopes.rb
+++ b/BrainPortal/lib/view_scopes.rb
@@ -1186,6 +1186,33 @@ def default_scope_name
   #  Name of the scope to update with the page and per-page/per_page parameters.
   #  Defaults to the current route's default scope name (+default_scope_name+).
   #
+  # [_simple_filters]
+  #  Special flag to indicate that the remaining query parameters are to be
+  #  interpreted as simple attribute => value filters (each corresponding to a
+  #  { :a => <attribute>, :v => <value>, :o => '==' } Scope::Filter).
+  #  This simplified interface is meant to be used when manually composing URLs
+  #  without aid from the Scope API (such as in applications outside CBRAIN
+  #  or when composing by hand). For example, an URL to filter userfiles on a
+  #  certain data provider could look like:
+  #    http://portal.cbrain.ca/userfiles?_simple_filters=1&data_provider_id=4
+  #  instead of the full version required by the +_scopes+ parameter.
+  #
+  #  To specify which scope to update, have +_simple_filters+'s value be the
+  #  name of the target scope. If such a scope is not found (+_simple_filters+
+  #  is '1' or 'true', for example), +update_session_scopes+ will fall back
+  #  to the controller's name (common convention for index pages) then to
+  #  +default_scope_name+. For example, doing:
+  #    http://portal.cbrain.ca/userfiles?_simple_filters=tasks&...
+  #  would update the 'tasks' scope, if it exists, while:
+  #    http://portal.cbrain.ca/userfiles?_simple_filters=1&...
+  #  would try to update the 'userfiles' scope, falling back to
+  #  +default_scope_name+ if there is no 'userfiles' scope.
+  #
+  #  Note that this option cannot be used in conjunction with +_scopes+ or
+  #  +_default_scope+, and that every query parameter (other than
+  #  +_simple_filters+, +_scope_mode+ and pagination parameters) is considered
+  #  to be a filter.
+  #
   # Note that the scopes in +_default_scope+ and +_scopes+ can be in
   # compressed format (see the +compress_scope+ and +decompress_scope+ utility
   # methods).
@@ -1194,15 +1221,46 @@ def update_session_scopes
         [ 'append', 'delete', 'replace' ].include?(params['_scope_mode'])
     mode ||= :replace
 
-    # Decompress (if required) and merge _scopes and _default_scope
-    scopes = (params['_scopes'] || {}).deep_dup
-    scopes.merge!({ default_scope_name => params['_default_scope'] }) if
-      params['_default_scope']
-    scopes = scopes.map do |n, s|
-      return [n, s] if s.is_a?(Hash)
-      [ n, ViewScopes.decompress_scope(s) ]
-    end.to_h
+    # Special _simple_filters filter syntax
+    if (simple = params['_simple_filters'])
+      # Determine which scope to update
+      known      = (current_session['scopes'] ||= {})
+      controller = params[:controller].to_s.downcase
+      name   = simple     if known.has_key?(simple)
+      name ||= controller if known.has_key?(controller)
+      name ||= default_scope_name
+
+      # Then convert other query parameters to Scope::Filter hashes
+      excluded = [
+        'action', 'controller',
+        '_simple_filters', '_scope_mode',
+        'page', 'per-page', 'per_page'
+      ]
+      scopes   = { name => { 'f' =>
+        params.to_h
+          .reject { |key| excluded.include?(key) }
+          .map    { |attr,value| { 'a' => attr.to_s, 'v' => value.to_s } }
+      } }
+
+    # Generic scopes updates through '_scopes' or '_default_scope'
+    elsif params['_scopes'] || params['_default_scope']
+      # Merge _scopes and _default_scope
+      scopes = (params['_scopes'] || {}).deep_dup
+      scopes.merge!({ default_scope_name => params['_default_scope'] }) if
+        params['_default_scope']
+
+      # Then decompress, if required
+      scopes = scopes.map do |n, s|
+        return [n, s] if s.is_a?(Hash)
+        [ n, ViewScopes.decompress_scope(s) ]
+      end.to_h
+
+    # No scopes updates requested
+    else
+      scopes = nil
+    end
 
+    # Apply the scope changes, if any
     current_session.apply_changes([mode, { 'scopes' => scopes }]) unless scopes.blank?
 
     # Pagination parameters (which override _scopes and _default_scope)

From ce73793c3f22c8d7d2b2c4be3238d4a4ae3a1fec Mon Sep 17 00:00:00 2001
From: glatard <glatard@creatis.insa-lyon.fr>
Date: Thu, 17 Sep 2015 13:00:11 -0400
Subject: [PATCH 46/85] Fixes in Docker script: now supports bash variables ;
 now uses login shell.

---
 BrainPortal/app/models/cluster_task.rb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/BrainPortal/app/models/cluster_task.rb b/BrainPortal/app/models/cluster_task.rb
index 6a95d3617..6e8aafc4a 100644
--- a/BrainPortal/app/models/cluster_task.rb
+++ b/BrainPortal/app/models/cluster_task.rb
@@ -1645,8 +1645,8 @@ def docker_commands
 
     cache_dir=RemoteResource.current_resource.dp_cache_dir;
     task_dir=self.bourreau.cms_shared_dir;
-    docker_commands = "cat << DOCKERJOB > .dockerjob.sh
-#!/bin/bash\n
+    docker_commands = "cat << \"DOCKERJOB\" > .dockerjob.sh
+#!/bin/bash -l\n
 #{commands_joined}\n
 DOCKERJOB\n
 chmod 755 ./.dockerjob.sh\n

From 3a42fd7db2bf64ee3acc7c9163de6c8ac376343b Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Mon, 21 Sep 2015 15:27:17 -0400
Subject: [PATCH 47/85] Pre/post scoping filter counts

Filters generated by filter_values_for now more closely mimic the old
filtering system's double count feature; a scope can now be specified,
and an extra count pass is performed with this scope applied.

This changeset also includes a complete refactor of wrapper/helper
filter methods to a single one, default_filters_for, which should handle
almost all simple cases. Most uses of filter_values_for and old helpers
have been replaced by this new helper in index views.
---
 .../app/controllers/bourreaux_controller.rb   |   9 +-
 .../controllers/data_providers_controller.rb  |   9 +-
 .../controllers/exception_logs_controller.rb  |   3 +-
 .../app/controllers/feedbacks_controller.rb   |   3 +-
 .../app/controllers/groups_controller.rb      |   3 +-
 .../app/controllers/messages_controller.rb    |   9 +-
 .../app/controllers/tasks_controller.rb       |  71 ++--
 .../app/controllers/tools_controller.rb       |   3 +-
 .../app/controllers/users_controller.rb       |   3 +-
 BrainPortal/app/helpers/scope_helper.rb       | 335 +++++++++++++-----
 .../bourreaux/_bourreaux_display.html.erb     |   8 +-
 .../_one_data_provider_table.html.erb         |   6 +-
 .../_exception_logs_table.html.erb            |   6 +-
 .../views/feedbacks/_feedbacks_table.html.erb |   2 +-
 .../app/views/groups/_groups_table.html.erb   |   8 +-
 .../messages/_message_index_display.html.erb  |  30 +-
 .../app/views/tasks/_tasks_display.html.erb   |  16 +-
 .../app/views/tools/_tools_table.html.erb     |   6 +-
 .../userfiles/_userfiles_display.html.erb     |  13 +-
 .../app/views/users/_users_table.html.erb     |  25 +-
 20 files changed, 359 insertions(+), 209 deletions(-)

diff --git a/BrainPortal/app/controllers/bourreaux_controller.rb b/BrainPortal/app/controllers/bourreaux_controller.rb
index 84de2a1e2..717170024 100644
--- a/BrainPortal/app/controllers/bourreaux_controller.rb
+++ b/BrainPortal/app/controllers/bourreaux_controller.rb
@@ -41,11 +41,10 @@ def index #:nodoc:
     @scope = scope_from_session('bourreaux')
     scope_default_order(@scope, 'type')
 
-    @bourreaux = @scope.apply(
-      RemoteResource
-        .find_all_accessible_by_user(current_user)
-        .includes(:user, :group)
-    )
+    @base_scope = RemoteResource
+      .find_all_accessible_by_user(current_user)
+      .includes(:user, :group)
+    @bourreaux = @scope.apply(@base_scope)
 
     respond_to do |format|
       format.html
diff --git a/BrainPortal/app/controllers/data_providers_controller.rb b/BrainPortal/app/controllers/data_providers_controller.rb
index 0358b6772..6aff3e09e 100644
--- a/BrainPortal/app/controllers/data_providers_controller.rb
+++ b/BrainPortal/app/controllers/data_providers_controller.rb
@@ -39,11 +39,10 @@ def index #:nodoc:
     @scope = scope_from_session('data_providers')
     scope_default_order(@scope, 'name')
 
-    @data_providers = @scope.apply(
-      DataProvider
-        .find_all_accessible_by_user(current_user)
-        .includes(:user, :group)
-    )
+    @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
diff --git a/BrainPortal/app/controllers/exception_logs_controller.rb b/BrainPortal/app/controllers/exception_logs_controller.rb
index 1129b140a..fa4967656 100644
--- a/BrainPortal/app/controllers/exception_logs_controller.rb
+++ b/BrainPortal/app/controllers/exception_logs_controller.rb
@@ -32,7 +32,8 @@ def index #:nodoc:
     @scope = scope_from_session('exception_logs')
     scope_default_order(@scope, 'created_at', :desc)
 
-    @view_scope = @scope.apply(ExceptionLog)
+    @base_scope = ExceptionLog
+    @view_scope = @scope.apply(@base_scope)
 
     @scope.pagination ||= Scope::Pagination.from_hash({ :per_page => 50 })
     @exception_logs = @scope.pagination.apply(@view_scope)
diff --git a/BrainPortal/app/controllers/feedbacks_controller.rb b/BrainPortal/app/controllers/feedbacks_controller.rb
index d3af05021..f9bee88c7 100644
--- a/BrainPortal/app/controllers/feedbacks_controller.rb
+++ b/BrainPortal/app/controllers/feedbacks_controller.rb
@@ -32,7 +32,8 @@ def index #:nodoc:
     @scope = scope_from_session('feedbacks')
     scope_default_order(@scope, 'created_at', :desc)
 
-    @feedbacks = @scope.apply(Feedback.includes(:user))
+    @base_scope = Feedback.includes(:user)
+    @feedbacks  = @scope.apply(@base_scope)
 
     respond_to do |format|
       format.js
diff --git a/BrainPortal/app/controllers/groups_controller.rb b/BrainPortal/app/controllers/groups_controller.rb
index b6ff1ca74..4ce43e8cb 100644
--- a/BrainPortal/app/controllers/groups_controller.rb
+++ b/BrainPortal/app/controllers/groups_controller.rb
@@ -42,7 +42,8 @@ def index  #:nodoc:
     @scope.custom[:button] = true if
       current_user.has_role?(:normal_user) && @scope.custom[:button].nil?
 
-    @view_scope = @scope.apply(current_user.available_groups.includes(:site))
+    @base_scope = current_user.available_groups.includes(:site)
+    @view_scope = @scope.apply(@view_scope)
 
     @scope.pagination ||= Scope::Pagination.from_hash({ :per_page => 50 })
     @groups = @scope.pagination.apply(@view_scope)
diff --git a/BrainPortal/app/controllers/messages_controller.rb b/BrainPortal/app/controllers/messages_controller.rb
index 416f351c5..3900209a5 100644
--- a/BrainPortal/app/controllers/messages_controller.rb
+++ b/BrainPortal/app/controllers/messages_controller.rb
@@ -34,11 +34,10 @@ def index #:nodoc:
     @scope = scope_from_session('messages')
     scope_default_order(@scope, 'last_sent', :desc)
 
-    @view_scope = @messages = @scope.apply(
-      Message.where(current_user.has_role?(:admin_user) ?
-        {} : { :user_id => current_user.available_users.map(&:id) }
-      )
-    )
+    @base_scope = Message
+    @base_scope = @base_scope.where(:user_id => current_user.available_users.map(&:id)) unless
+      current_user.has_role?(:admin_user)
+    @view_scope = @messages = @scope.apply(@base_scope)
 
     @read_count   = @view_scope.where(:read => true).count
     @unread_count = @view_scope.count - @read_count
diff --git a/BrainPortal/app/controllers/tasks_controller.rb b/BrainPortal/app/controllers/tasks_controller.rb
index f69e727bf..b67553fd1 100644
--- a/BrainPortal/app/controllers/tasks_controller.rb
+++ b/BrainPortal/app/controllers/tasks_controller.rb
@@ -42,8 +42,9 @@ def index #:nodoc:
     end
 
     @scope.pagination ||= Scope::Pagination.from_hash({ :per_page => 25 })
-    @view_scope = view_scope(current_user.available_tasks)
+    @base_scope = user_scope(current_user.available_tasks)
       .includes([:bourreau, :user, :group])
+    @view_scope = view_scope(@base_scope)
 
     # Display totals
     @total_tasks       = @view_scope.count
@@ -109,13 +110,14 @@ def index #:nodoc:
   # Renders a set of tasks associated with a batch.
   def batch_list
     @scope = scope_from_session('tasks')
-    @tasks = view_scope(
+    @base_scope = user_scope(
       current_user
         .available_tasks
         .real_tasks
         .where(:batch_id => params[:batch_id])
+        .includes([:bourreau, :user, :group])
     )
-      .includes([:bourreau, :user, :group])
+    @tasks = view_scope(@base_scope)
       .order(['cbrain_tasks.rank', 'cbrain_tasks.level', 'cbrain_tasks.id'])
       .map { |task| { :batch => task.batch_id, :first => task, :count => 1 } }
 
@@ -570,14 +572,11 @@ def update #:nodoc:
   def update_multiple
 
     # Construct task_ids and batch_ids
-    task_ids    = Array(params[:tasklist]  || [])
-    batch_ids   = Array(params[:batch_ids] || [])
-
-    if batch_ids.delete "nil"
-      task_ids += view_scope(CbrainTask.real_tasks.where( :batch_id => nil )).select("id").raw_first_column
-    end
-    task_ids   += view_scope(CbrainTask.real_tasks.where( :batch_id => batch_ids )).select("id").raw_first_column
-    task_ids    = task_ids.map(&:to_i).uniq
+    task_ids   = Array(params[:tasklist]  || [])
+    batch_ids  = Array(params[:batch_ids] || [])
+    batch_ids << nil if batch_ids.delete('nil')
+    task_ids  += view_scope(user_scope(CbrainTask.where(:batch_id => batch_ids))).select(:id).raw_first_column
+    task_ids   = task_ids.map(&:to_i).uniq
 
     commit_name = extract_params_key([ :update_user_id, :update_group_id, :update_results_data_provider_id, :update_tool_config_id ])
 
@@ -732,18 +731,14 @@ def update_multiple
   def operation
     @scope      = scope_from_session('tasks')
 
-    operation   = params[:operation]
-    tasklist    = params[:tasklist]  || []
-    tasklist    = [ tasklist ]  unless tasklist.is_a?(Array)
-    batch_ids   = params[:batch_ids] || []
-    batch_ids   = [ batch_ids ] unless batch_ids.is_a?(Array)
-
-    if batch_ids.delete "nil"
-      tasklist += view_scope(CbrainTask.where( :batch_id => nil )).select("id").raw_first_column
-    end
-
-    tasklist   += view_scope(CbrainTask.where( :batch_id => batch_ids )).select("id").raw_first_column
-    tasklist    = tasklist.map(&:to_i).uniq
+    operation  = params[:operation]
+    tasklist   = params[:tasklist]  || []
+    tasklist   = [ tasklist ]  unless tasklist.is_a?(Array)
+    batch_ids  = params[:batch_ids] || []
+    batch_ids  = [ batch_ids ] unless batch_ids.is_a?(Array)
+    batch_ids << nil if batch_ids.delete('nil')
+    tasklist  += view_scope(user_scope(CbrainTask.where(:batch_id => batch_ids))).select(:id).raw_first_column
+    tasklist   = tasklist.map(&:to_i).uniq
 
     flash[:error]  ||= ""
     flash[:notice] ||= ""
@@ -983,28 +978,30 @@ def resource_class #:nodoc:
     CbrainTask
   end
 
+  # User task scope; tasks from +base+ currently visible/accessible to the
+  # user, respecting project and bourreau restrictions.
+  def user_scope(base)
+    base
+      .where(current_project ? { :group_id => current_project.id } : {})
+      .where(
+        :bourreau_id => Bourreau
+          .find_all_accessible_by_user(current_user)
+          .raw_rows("#{Bourreau.quoted_table_name}.id")
+          .flatten
+      )
+  end
+
   # View tasks scope; filtered and sorted list of tasks to display (or currently
-  # displayed). +base+ is expected to be the base scope to filter and sort
-  # (defaults to +base_scope+). Requires a valid @scope object.
+  # displayed). +base+ is expected to be the base scope to filter and sort.
+  # Requires a valid @scope object.
   def view_scope(base)
-    base = base.where(:group_id => current_project.id) if current_project
-    base = base.where(
-      :bourreau_id => Bourreau
-        .find_all_accessible_by_user(current_user)
-        .raw_rows("#{Bourreau.quoted_table_name}.id")
-        .flatten
-    )
-
     custom_filters  = (@scope.custom[:custom_filters] || []).dup
     custom_filters &= current_user.custom_filter_ids
     custom_filters.map! { |id| TaskCustomFilter.find(id) }
 
-    view = @scope.apply(base)
-    view = custom_filters.inject(view) do |scope, filter|
+    custom_filters.inject(@scope.apply(base)) do |scope, filter|
       filter.filter_scope(scope)
     end
-
-    view
   end
 
   public
diff --git a/BrainPortal/app/controllers/tools_controller.rb b/BrainPortal/app/controllers/tools_controller.rb
index d7370a76e..7f0bb4c47 100644
--- a/BrainPortal/app/controllers/tools_controller.rb
+++ b/BrainPortal/app/controllers/tools_controller.rb
@@ -34,7 +34,8 @@ def index #:nodoc:
     @scope = scope_from_session('tools')
     scope_default_order(@scope, 'name')
 
-    @tools = @scope.apply(current_user.available_tools.includes(:user, :group))
+    @base_scope = current_user.available_tools.includes(:user, :group)
+    @tools = @scope.apply(@base_scope)
 
     respond_to do |format|
       format.js
diff --git a/BrainPortal/app/controllers/users_controller.rb b/BrainPortal/app/controllers/users_controller.rb
index c5445f0f8..b84fbc052 100644
--- a/BrainPortal/app/controllers/users_controller.rb
+++ b/BrainPortal/app/controllers/users_controller.rb
@@ -44,7 +44,8 @@ def index #:nodoc:
       :operator  => 'match'
     })
 
-    @view_scope = @scope.apply(current_user.available_users.includes(:groups, :site))
+    @base_scope = current_user.available_users.includes(:groups, :site)
+    @view_scope = @scope.apply(@base_scope)
 
     @scope.pagination ||= Scope::Pagination.from_hash({ :per_page => 50 })
     @users = @scope.pagination.apply(@view_scope) if
diff --git a/BrainPortal/app/helpers/scope_helper.rb b/BrainPortal/app/helpers/scope_helper.rb
index 112d1c27e..a9a3d8ce2 100644
--- a/BrainPortal/app/helpers/scope_helper.rb
+++ b/BrainPortal/app/helpers/scope_helper.rb
@@ -293,7 +293,7 @@ def pretty_scope_filter(filter, model: nil)
   # As this method is intended as a view helper to create the list of values to
   # filter a collection/model with, the possible values are returned as a list
   # of hashes matching +DynamicTable+'s filter format (unless +format+ is
-  # specified. See below), containing:
+  # specified; see below), containing:
   # [:value]
   #  Possible value for +attribute+.
   # [:label]
@@ -303,114 +303,146 @@ def pretty_scope_filter(filter, model: nil)
   #  Count of how many times this specific +:value: was found for +attribute+ in
   #  +collection+.
   #
-  # If +label+ is specified, it is expected to be an attribute name as a string
-  # or symbol (like +attribute+), representing which +collection+ attribute to
-  # use as value labels.
+  # This method accepts following optional (named) arguments:
+  # [label]
+  #  Attribute name (as a string or symbol) representing which +collection+
+  #  attribute to use as value labels. Defaults to the value of +attribute+ if
+  #  left unspecified.
   #
-  # If +association+ is specified, it is expected to be in the same format as
-  # +Scope+::+Filter+'s *association* attribute, and fulfills roughly the same
-  # purpose; allow +attribute+ and +label+ to refer to attributes on the joined
-  # model (only applicable if +collection+ is an ActiveRecord model).
+  # [association]
+  #  Association to join on +collection+. Expected to be in the same format as
+  #  +Scope+::+Filter+'s *association* attribute, it roughly fulfills the same
+  #  purpose; allow +attribute+ and +label+ to refer to attributes on the joined
+  #  model (only applicable if +collection+ is an ActiveRecord model).
   #
-  # If +format+ is specified, it is expected to be a lambda (or proc) accepting
-  # three arguments; a possible value for +attribute+, a label for the value,
-  # and a count of how many times this value was present and will be used to
-  # format the list of filter values, overriding the default +DynamicTable+
-  # format specified above. Specifying +format+ is roughly equivalent to using
-  # map on the  the generated filter values but without having to unpack the
-  # +DynamicTable+'s filter format hash.
+  #  If :association is specified and is an AR model, +attribute+ is also
+  #  allowed to be nil to indicate that it should automatically be selected as
+  #  the foreign key of the first association on +collection+ matching the given
+  #  +association+ model. The +label+ option will also default to the 'name'
+  #  attribute on the given +association+ (and will refer to the association
+  #  model unless qualified by a table name). This behavior allows generating
+  #  association filters without explicitly specifying the association join
+  #  attributes. For example,
+  #    filter_values_for(@userfiles, nil, :association => DataProvider)
+  #  is equivalent to the more verbose
+  #    filter_values_for(@userfiles, 'data_provider_id',
+  #      :label       => 'data_providers.name',
+  #      :association => DataProvider
+  #    )
   #
-  # TODO Unscoped/base scope/total item count.
-  def filter_values_for(collection, attribute, label: nil, association: nil, format: nil)
+  # [format]
+  #  Lambda (or proc) accepting three arguments; a possible value for
+  #  +attribute+, a label for the value, and a count of how many times this
+  #  value was present. This lambda will be used to format the list of filter
+  #  values, overriding the default +DynamicTable+ format specified above.
+  #  Specifying +format+ is roughly equivalent to using map on the generated
+  #  filter values but without having to unpack the +DynamicTable+'s filter
+  #  format hash.
+  #
+  # [scope]
+  #  Generate a separate set of filter value counts (how many times a given
+  #  filter value is found) for +collection+ when scoped under +scope+. For
+  #  example, if a given userfile collection has 30 TextFiles out of 40 and
+  #  10 of those 30 belong to a given user, the unscoped TextFile filter count
+  #  would be 30 and the user-scoped count 10. When this option is specified,
+  #  +format+ takes a fourth argument; the corresponding scoped count, and,
+  #  if +format+ is unspecified, the two counts (normal and scoped) are appended
+  #  to the default label value. For example, in the above TextFile example,
+  #  the label would look like 'TextFile (10/30)'.
+  #
+  #  Note that any Filter filtering on +attribute+ in +scope+ will be skipped to
+  #  avoid generating empty filter values (while this behavior is
+  #  counter-intuitive and clunky, it is required for table filtering).
+  def filter_values_for(collection, attribute, label: nil, association: nil, format: nil, scope: nil)
     return [] if collection.blank?
 
-    # DynamicTable's filter hashes are the default output format
-    format ||= lambda do |value, label, count|
-      { :value => value, :label => label, :indicator => count }
+    # Remove any +attribute+ filter on +scope+
+    if scope
+      scope = scope.dup
+      scope.filters.reject! do |f|
+        f.attribute.to_s.downcase == attribute.to_s.downcase
+      end
     end
 
+    # Invoke the model/collection specific method
     if (collection <= ActiveRecord::Base rescue nil)
-      # Resolve and validate the main +attribute+ to fetch the values of
-      attribute, model = ViewScopes.resolve_model_attribute(attribute, collection, association)
-
-      # And +label+, if provided
-      if label
-        label, model = ViewScopes.resolve_model_attribute(label, model, association)
-      else
-        label = attribute
-      end
-
-      # NOTE: The 'AS' specifier bypasses Rails' uniq on the column names, which
-      # would remove the label column if label happens to have the same value
-      # as attribute.
-      label_alias = model.connection.quote_column_name('label')
-
-      model
-        .where("#{attribute} IS NOT NULL")
-        .order(attribute, label)
-        .group(attribute, label)
-        .raw_rows(attribute, "#{label} AS #{label_alias}", "COUNT(#{attribute})")
-        .reject { |r| r.first.blank? }
-        .map(&format)
-
+      filters = model_filter_values(
+        collection, attribute, label,
+        association: association,
+        scope: scope
+      )
     else
-      # Make sure +attribute+ and +label+ can be accessed in
-      # +collection+'s items.
-      attr_get = ViewScopes.generate_getter(collection.first, attribute)
-      raise "no way to get '#{attribute}' out of collection items" unless attr_get
-
-      if label == attribute
-        lbl_get = attr_get
-      else
-        lbl_get = ViewScopes.generate_getter(collection.first, label || attribute)
-        raise "no way to get '#{label}' out of collection items" unless lbl_get
-      end
+      filters = collection_filter_values(
+        collection, attribute, label,
+        scope: scope
+      )
+    end
 
-      collection
-        .map     { |i| [attr_get.(i), lbl_get.(i)].freeze }
-        .reject  { |v, l| v.blank? }
-        .sort_by { |v, l| v }
-        .inject(Hash.new(0)) { |h, i| h[i] += 1; h }
-        .map { |(v, l), c| format.(v, l, c) }
+    # No need to use the default format if one is specified
+    return filters.map(&format) if format
+
+    # Format the generated filter arrays as DynamicTable's filter hashes
+    filters.map do |value, label, count, *rest|
+      scoped = rest.first
+      label  = "#{label} (#{scoped}/#{count})" if scoped
+      {
+        :value     => value,
+        :label     => label,
+        :indicator => scoped || count,
+        :empty     => (scoped || count) == 0
+      }
     end
   end
 
-  # Fetch the possible values (and their count) for +model+'s (an ActiveRecord
-  # model) association +assoc+ (again an ActiveRecord model), using the
-  # attribute +label+ as labels. This method is a small wrapper around
-  # +filter_values_for+ to make generating association filters easier. For
-  # example, to get group filters for a given @view_scope, one can do:
-  #   assoc_filter_values_for(@view_scope, Group)
-  # which is equivalent to
-  #   filter_values_for(
-  #     @view_scope, :group_id,
-  #     label: 'groups.name',
-  #     association: Group
-  #   )
+  # Fetch the possible values for +attribute+ within +collection+.
+  # A simple wrapper around +filter_values_for+, this method offers a set
+  # of commonly used defaults to +filter_values_for+ when generating simple
+  # attribute filters.
   #
-  # Note that +assoc_filter_values_for+ will take the first association on
-  # +model+ matching +assoc+. For a more flexible version of this method (to
-  # use the full association format (which supports arbitrary joins), for
-  # example), use +filter_values_for+ instead.
-  def assoc_filter_values_for(model, assoc, label: 'name')
-    return [] unless (model <= ActiveRecord::Base rescue nil)
-
-    assoc = assoc.klass if assoc.respond_to?(:klass)
-    reflection = model
-      .reflect_on_all_associations
-      .find { |r| r.klass == assoc }
-    raise "no associations on '#{model.table_name}' matching '#{assoc.table_name}'" unless
-      reflection
-
-    filter_values_for(
-      model, reflection.foreign_key,
-      label: ("#{reflection.table_name}.#{label}" if label),
-      association: [
-        assoc,
-        reflection.association_primary_key,
-        reflection.association_foreign_key
-      ]
-    )
+  # +collection+ and +attribute+ are passed directly to +filter_values_for+,
+  # with one exception; if both +collection+ and +attribute+ are AR models
+  # (or scopes), +default_filters_for+ will pass +attribute+ as an association
+  # on +collection+ instead:
+  #   default_filters_for(some_scope, SomeModel)
+  # corresponds to:
+  #   filter_values_for(scope_scope, nil, association: SomeModel)
+  #
+  # For more information on how filter values are generated,
+  # see +filter_values_for+.
+  def default_filters_for(collection, attribute)
+    # Generate a formatting lambda which will call +block+ to format a filter
+    # value's label.
+    formatter = lambda do |block|
+      return unless block
+
+      lambda do |args|
+        value, label, count, scoped = args
+        label = block.(label) rescue label
+        label = "#{label} (#{scoped}/#{count})" if scoped
+        {
+          :value     => value,
+          :label     => label,
+          :indicator => scoped || count,
+          :empty     => (scoped || count) == 0
+        }
+      end
+    end
+
+    # Is +attribute+ an association?
+    if (attribute <= ActiveRecord::Base rescue nil)
+      filter_values_for(collection, nil, association: attribute,
+        scope: @scope,
+        label: ('login' if attribute <= User)
+      )
+    else
+      filter_values_for(collection, attribute,
+        scope:  @scope,
+        format: formatter.((
+          proc { |l| l.constantize.pretty_type } if
+            attribute.to_s.downcase == 'type'
+        ))
+      )
+    end
   end
 
   # Internal methods
@@ -479,6 +511,119 @@ def generic_scope_link(label, url, options)
     }))
   end
 
+  # Fetch the possible values (and their count) for +attribute+ within +model+,
+  # an ActiveRecord model. Internal model-specific implementation of
+  # +filter_values_for+ for AR models; see +filter_values_for+ for more
+  # information on this method's arguments (which are handled just like
+  # +filter_values_for+'s, save for +scope+).
+  #
+  # Note that the filter values returned by this method are in array format,
+  # ([value, label, count, (scoped_count)]) as this method is intended for
+  # internal use by +filter_values_for+ which will perform final formatting.
+  def model_filter_values(model, attribute, label, association: nil, scope: nil)
+    # Handle the special case where +attribute+ is nil and corresponds to
+    # +model+'s foreign key for +association+
+    if ! attribute && association
+      # Find the matching +association+ reflection on +model+
+      assoc = association.respond_to?(:klass) ? association.klass : association
+      reflection = model
+        .reflect_on_all_associations
+        .find { |r| r.klass == assoc }
+      raise "no associations on '#{model.table_name}' matching '#{assoc.table_name}'" unless
+        reflection
+
+      # Use +association+'s reflection to set missing argument values
+      attribute   = reflection.foreign_key
+      label       = "#{reflection.table_name}.#{label || 'name'}"
+      association = [
+        assoc,
+        reflection.association_primary_key,
+        reflection.association_foreign_key
+      ]
+    end
+
+    # Resolve and validate the main +attribute+ to fetch the values of
+    attribute, model = ViewScopes.resolve_model_attribute(attribute, model, association)
+
+    # And +label+, if provided
+    if label
+      label, model = ViewScopes.resolve_model_attribute(label, model, association)
+    else
+      label = attribute
+    end
+
+    # NOTE: The 'AS' specifier bypasses Rails' uniq on column names, which
+    # would remove the label column if +label+ happens to have the same value
+    # as +attribute+.
+    label_alias = model.connection.quote_column_name('label')
+
+    # Fetch the main filter values as an array of arrays:
+    # [[value, label, count], [...]]
+    filters = model
+      .where("#{attribute} IS NOT NULL")
+      .order(attribute, label)
+      .group(attribute, label)
+      .raw_rows(attribute, "#{label} AS #{label_alias}", "COUNT(#{attribute})")
+      .reject { |r| r.first.blank? }
+      .map(&:to_a)
+      .to_a
+
+    # No +scope+? Then +filters+ is ready
+    return filters unless scope
+
+    # Add in the scoped counts
+    scoped = scope.apply(model)
+      .where("#{attribute} IS NOT NULL")
+      .group(attribute)
+      .raw_rows(attribute, "COUNT(#{attribute})")
+      .to_h
+
+    filters.map { |f| f << (scoped[f.first] || 0) }
+  end
+
+  # Fetch the possible values (and their count) for +attribute+ within
+  # +collection+, a generic Ruby collection. Internal collection-specific
+  # implementation of +filter_values_for+ for Ruby collections; see
+  # +filter_values_for+ for more information on this method's arguments
+  # (which are handled just like +filter_values_for+'s, save for +scope+).
+  #
+  # Note that the filter values returned by this method are in array format,
+  # ([value, label, count, (scoped_count)]) as this method is intended for
+  # internal use by +filter_values_for+ which will perform final formatting.
+  def collection_filter_values(collection, attribute, label, scope: nil)
+    # Make sure +attribute+ and +label+ can be accessed in
+    # +collection+'s items.
+    attr_get = ViewScopes.generate_getter(collection.first, attribute)
+    raise "no way to get '#{attribute}' out of collection items" unless attr_get
+
+    if label == attribute
+      lbl_get = attr_get
+    else
+      lbl_get = ViewScopes.generate_getter(collection.first, label || attribute)
+      raise "no way to get '#{label}' out of collection items" unless lbl_get
+    end
+
+    # Generate the main filter values as a hash; [value, label] => count
+    count_values = lambda do |collection|
+      collection
+        .map     { |i| [attr_get.(i), lbl_get.(i)].freeze }
+        .reject  { |v, l| v.blank? }
+        .sort_by { |v, l| v }
+        .inject(Hash.new(0)) { |h, i| h[i] += 1; h }
+    end
+
+    filters = count_values.(collection)
+
+    # Add in the scoped counts, if required, then flatten the hash into
+    # array format
+    if scope
+      scoped = count_values.(scope.apply(collection))
+      filters.map { |i, c| [*i, c, scoped[i] || 0] }
+    else
+      filters.map { |(v, l), c| [v, l, c] }
+    end
+  end
+
   # Deprecated/old methods
 
   # Generate +count+ as a link to +controller+'s index page, with +filters+ as
diff --git a/BrainPortal/app/views/bourreaux/_bourreaux_display.html.erb b/BrainPortal/app/views/bourreaux/_bourreaux_display.html.erb
index 7ba98227e..5f0377122 100644
--- a/BrainPortal/app/views/bourreaux/_bourreaux_display.html.erb
+++ b/BrainPortal/app/views/bourreaux/_bourreaux_display.html.erb
@@ -50,7 +50,7 @@
 
     t.column("Server Type", :type,
       :sortable => true,
-      :filters  => filter_values_for(@bourreaux, :type)
+      :filters  => default_filters_for(@base_scope, :type)
     ) { |r| r.is_a?(Bourreau) ? "Execution" : "Portal" }
 
     t.column("Server Name", :name,
@@ -75,12 +75,12 @@
     t.column("Owner", :owner,
       :hidden   => true,
       :sortable => true,
-      :filters  => assoc_filter_values_for(@bourreaux, User, label: 'login')
+      :filters  => default_filters_for(@base_scope, User)
     ) { |r| link_to_user_with_tooltip(r.user) }
 
     t.column("Project", :group,
       :sortable => true,
-      :filters  => assoc_filter_values_for(@bourreaux, Group)
+      :filters  => default_filters_for(@base_scope, Group)
     ) { |r| link_to_group_if_accessible(r.group) }
 
     t.column("Site", :site,
@@ -90,7 +90,7 @@
     t.column("Time Zone", :time_zone,
       :hidden   => true,
       :sortable => true,
-      :filters  => filter_values_for(@bourreaux, :time_zone)
+      :filters  => default_filters_for(@base_scope, :time_zone)
     ) { |r| r.time_zone || "(Unset)" }
 
     t.column("Online?", :online,
diff --git a/BrainPortal/app/views/data_providers/_one_data_provider_table.html.erb b/BrainPortal/app/views/data_providers/_one_data_provider_table.html.erb
index 8cff9bf10..0152bc77c 100644
--- a/BrainPortal/app/views/data_providers/_one_data_provider_table.html.erb
+++ b/BrainPortal/app/views/data_providers/_one_data_provider_table.html.erb
@@ -47,18 +47,18 @@
     t.column("Type", :type,
       :sortable => true,
       :hidden   => true,
-      :filters  => filter_values_for(@data_providers, :type)
+      :filters  => default_filters_for(@base_scope, :type)
     ) { |dp| dp.class.to_s } if current_user.has_role? :admin_user
 
     t.column("Owner", :owner,
       :hidden   => true,
       :sortable => true,
-      :filters  => assoc_filter_values_for(@data_providers, User, label: 'login')
+      :filters  => default_filters_for(@base_scope, User)
     ) { |dp| link_to_user_with_tooltip(dp.user) }
 
     t.column("Project", :group,
       :sortable => true,
-      :filters  => assoc_filter_values_for(@data_providers, Group)
+      :filters  => default_filters_for(@base_scope, Group)
     ) { |dp| link_to_group_if_accessible(dp.group) }
 
     t.column("Site", :site,
diff --git a/BrainPortal/app/views/exception_logs/_exception_logs_table.html.erb b/BrainPortal/app/views/exception_logs/_exception_logs_table.html.erb
index f2277291b..706f58a28 100644
--- a/BrainPortal/app/views/exception_logs/_exception_logs_table.html.erb
+++ b/BrainPortal/app/views/exception_logs/_exception_logs_table.html.erb
@@ -57,7 +57,7 @@
       generic_column = lambda do |label,field|
         t.column(label, field,
           :sortable => true,
-          :filters  => filter_values_for(@view_scope, field)
+          :filters  => default_filters_for(@base_scope, field)
         )
       end
 
@@ -66,7 +66,7 @@
 
       t.column("Exception", :exception_class,
         :sortable => true,
-        :filters  => filter_values_for(@view_scope, :exception_class)
+        :filters  => default_filters_for(@base_scope, :exception_class)
       ) { |e| link_to e.exception_class, e }
 
       t.column("Message", :message) { |e| crop_text_to(75, e.message) }
@@ -78,7 +78,7 @@
 
       t.column("User", :user,
         :sortable => true,
-        :filters  => assoc_filter_values_for(@view_scope, User, label: 'login')
+        :filters  => default_filters_for(@view_scope, User)
       ) { |e| link_to_user_with_tooltip(e.user) }
 
       generic_column.("Revision",   :revision_no)
diff --git a/BrainPortal/app/views/feedbacks/_feedbacks_table.html.erb b/BrainPortal/app/views/feedbacks/_feedbacks_table.html.erb
index f34c73cdf..67bcc8eaa 100644
--- a/BrainPortal/app/views/feedbacks/_feedbacks_table.html.erb
+++ b/BrainPortal/app/views/feedbacks/_feedbacks_table.html.erb
@@ -53,7 +53,7 @@
 
     t.column("Author", :author,
       :sortable => true,
-      :filters  => assoc_filter_values_for(@feedbacks, User, label: 'login')
+      :filters  => default_filters_for(@base_scope, User)
     ) { |f| link_to_user_with_tooltip(f.user) }
 
     t.column("Posted at", :created_at,
diff --git a/BrainPortal/app/views/groups/_groups_table.html.erb b/BrainPortal/app/views/groups/_groups_table.html.erb
index 7ce07a12f..fa95e25d8 100644
--- a/BrainPortal/app/views/groups/_groups_table.html.erb
+++ b/BrainPortal/app/views/groups/_groups_table.html.erb
@@ -85,12 +85,12 @@
 
         t.column("Project Type", :type,
           :sortable => true,
-          :filters  => filter_values_for(@view_scope, :type)
+          :filters  => default_filters_for(@base_scope, :type)
         )
 
         t.column("Site", :site,
           :sortable => true,
-          :filters  => assoc_filter_values_for(@view_scope, Site)
+          :filters  => default_filters_for(@base_scope, Site)
         )
       end
     %>
@@ -174,12 +174,12 @@
 
       t.column("Project Type", :type,
         :sortable => true,
-        :filters  => filter_values_for(@view_scope, :type)
+        :filters  => default_filters_for(@base_scope, :type)
       ) { |g| g.pretty_category_name(current_user) }
 
       t.column("Site", :site,
         :sortable => true,
-        :filters  => assoc_filter_values_for(@view_scope, Site)
+        :filters  => default_filters_for(@base_scope, Site)
       ) { |g| link_to_site_if_accessible(g.site) }
 
       t.column("Users", :users) do |g|
diff --git a/BrainPortal/app/views/messages/_message_index_display.html.erb b/BrainPortal/app/views/messages/_message_index_display.html.erb
index 67b8f95d2..c118e3630 100644
--- a/BrainPortal/app/views/messages/_message_index_display.html.erb
+++ b/BrainPortal/app/views/messages/_message_index_display.html.erb
@@ -101,10 +101,16 @@
         :pretty_name => 'Critical',
         :hidden      => true,
         :filters     => filter_values_for(
-          @view_scope, :critical,
-          format: lambda do |value, label, count|
+          @base_scope, :critical,
+          scope:  @scope,
+          format: lambda do |value, label, count, scoped|
             label = (! value || value == 0) ? 'Not critical' : 'Critical'
-            { :value => value, :label => label, :indicator => count }
+            {
+              :value     => value,
+              :label     => "#{label} (#{scoped}/#{count})",
+              :indicator => scoped,
+              :empty     => scoped == 0
+            }
           end
         )
       ) { |m| html_colorize("!!!") if m.critical }
@@ -113,9 +119,15 @@
         :hidden   => true,
         :sortable => true,
         :filters  => filter_values_for(
-          @view_scope, :message_type,
-          format: lambda do |value, label, count|
-            { :value => value, :label => label.humanize, :indicator => count }
+          @base_scope, :message_type,
+          scope:  @scope,
+          format: lambda do |value, label, count, scoped|
+            {
+              :value     => value,
+              :label     => "#{label.humanize} (#{scoped}/#{count})",
+              :indicator => scoped,
+              :empty     => scoped == 0
+            }
           end
         )
       ) { |m| m.message_type.humanize }
@@ -132,7 +144,8 @@
       t.column("Sender", :sender,
         :sortable => true,
         :filters  => filter_values_for(
-          @view_scope, :sender_id,
+          @base_scope, :sender_id,
+          scope: @scope,
           label: 'users.login',
           association: [User, 'id', 'sender_id'],
         ) + [{
@@ -147,7 +160,8 @@
       t.column("Recipient", :recipient,
         :sortable => true,
         :filters  => filter_values_for(
-          @view_scope, :user_id,
+          @base_scope, :user_id,
+          scope: @scope,
           label: 'users.login',
           association: [User, 'id', 'user_id']
         )
diff --git a/BrainPortal/app/views/tasks/_tasks_display.html.erb b/BrainPortal/app/views/tasks/_tasks_display.html.erb
index f0b8fafc9..ff03c9897 100644
--- a/BrainPortal/app/views/tasks/_tasks_display.html.erb
+++ b/BrainPortal/app/views/tasks/_tasks_display.html.erb
@@ -125,12 +125,7 @@
   <%
     t.column("Task Type", :type,
       :sortable => true,
-      :filters  => filter_values_for(@view_scope, :type,
-        format: lambda do |value, label, count|
-          label = label.constantize.pretty_type rescue label
-          { :value => value, :label => label, :indicator => count }
-        end
-      )
+      :filters  => default_filters_for(@base_scope, :type)
     ) do |type,id,count,task|
   %>
     <% case type %>
@@ -151,14 +146,14 @@
 
     t.column("Owner", :owner,
       :sortable => true,
-      :filters  => assoc_filter_values_for(@view_scope, User, label: 'login')
+      :filters  => default_filters_for(@base_scope, User)
     ) do |type,id,count,task|
       link_to_user_if_accessible(task.user) unless type == :loaded_batch
     end
 
     t.column("Project", :project,
       :sortable => true,
-      :filters  => assoc_filter_values_for(@view_scope, Group)
+      :filters  => default_filters_for(@base_scope, Group)
     ) do |type,id,count,task|
       link_to_group_if_accessible(task.group) unless type == :loaded_batch
     end unless current_project
@@ -166,7 +161,8 @@
     t.column("Execution Server", :server,
       :sortable => true,
       :filters  => filter_values_for(
-        @view_scope, :bourreau_id,
+        @base_scope, :bourreau_id,
+        scope: @scope,
         label: 'remote_resources.name',
         association: [Bourreau, 'id', 'bourreau_id']
       )
@@ -178,7 +174,7 @@
   <%
     t.column("Current Status", :status,
       :sortable => true,
-      :filters  => filter_values_for(@view_scope, :status)
+      :filters  => default_filters_for(@base_scope, :status)
     ) do |type,id,count,task|
   %>
     <%
diff --git a/BrainPortal/app/views/tools/_tools_table.html.erb b/BrainPortal/app/views/tools/_tools_table.html.erb
index 2f350e8a5..d9d919778 100644
--- a/BrainPortal/app/views/tools/_tools_table.html.erb
+++ b/BrainPortal/app/views/tools/_tools_table.html.erb
@@ -71,17 +71,17 @@
 
     t.column("Category", :category,
       :sortable => true,
-      :filters  => filter_values_for(@tools, :category)
+      :filters  => default_filters_for(@base_scope, :category)
     )
 
     t.column("Owner", :owner,
       :sortable => true,
-      :filters  => assoc_filter_values_for(@tools, User, label: 'login')
+      :filters  => default_filters_for(@base_scope, User)
     ) { |tool| link_to_user_with_tooltip(tool.user) }
 
     t.column("Project", :group,
       :sortable => true,
-      :filters  => assoc_filter_values_for(@tools, Group)
+      :filters  => default_filters_for(@base_scope, Group)
     ) { |tool| link_to_group_if_accessible(tool.group) }
 
     t.column("Execution & Versions", :exec) do |tool|
diff --git a/BrainPortal/app/views/userfiles/_userfiles_display.html.erb b/BrainPortal/app/views/userfiles/_userfiles_display.html.erb
index 6b68a1572..f082c173c 100644
--- a/BrainPortal/app/views/userfiles/_userfiles_display.html.erb
+++ b/BrainPortal/app/views/userfiles/_userfiles_display.html.erb
@@ -115,17 +115,12 @@
     t.column("File Type", :type,
       :field_name => :pretty_type,
       :sortable   => true,
-      :filters    => filter_values_for(@view_scope, :type,
-        format: lambda do |value, label, count|
-          label = label.constantize.pretty_type rescue label
-          { :value => value, :label => label, :indicator => count }
-        end
-      )
+      :filters    => default_filters_for(@base_scope, :type)
     )
 
     t.column("Owner", :login,
       :sortable => true,
-      :filters  => assoc_filter_values_for(@view_scope, User, label: 'login')
+      :filters  => default_filters_for(@base_scope, User)
     ) { |u| link_to_user_if_accessible(u.user) }
 
     t.column("Creation Date", :creation_date,
@@ -190,7 +185,7 @@
     unless current_project
       t.column("Project", :group,
         :sortable => true,
-        :filters  => assoc_filter_values_for(@view_scope, Group)
+        :filters  => default_filters_for(@base_scope, Group)
       ) do |u|
         link_to_group_if_accessible(u.group) if u.group
       end
@@ -204,7 +199,7 @@
 
     t.column("Provider", :data_provider,
       :sortable => true,
-      :filters  => assoc_filter_values_for(@view_scope, DataProvider)
+      :filters  => default_filters_for(@base_scope, DataProvider)
     ) do |u|
       link_to_data_provider_if_accessible(u.data_provider)
     end
diff --git a/BrainPortal/app/views/users/_users_table.html.erb b/BrainPortal/app/views/users/_users_table.html.erb
index 66dad18ad..96c9d7404 100644
--- a/BrainPortal/app/views/users/_users_table.html.erb
+++ b/BrainPortal/app/views/users/_users_table.html.erb
@@ -80,10 +80,16 @@
 
     t.column("Login", :login,
       :sortable => true,
-      :filters  => filter_values_for(@view_scope, :account_locked,
-        format: lambda do |value, label, count|
+      :filters  => filter_values_for(@base_scope, :account_locked,
+        scope:  @scope,
+        format: lambda do |value, label, count, scoped|
           label = (!value || value == 0 ? 'Unlocked' : 'Locked')
-          { :value => value, :label => label, :indicator => count }
+          {
+            :value     => value,
+            :label     => "#{label} (#{scoped}/#{count})",
+            :indicator => scoped,
+            :empty     => scoped == 0
+          }
         end
       )
     ) do |u|
@@ -121,27 +127,22 @@
 
     t.column("Role", :type,
       :sortable => true,
-      :filters  => filter_values_for(@view_scope, :type,
-        format: lambda do |value, label, count|
-          label = label.constantize.pretty_type rescue label
-          { :value => value, :label => label, :indicator => count }
-        end
-      )
+      :filters  => default_filters_for(@base_scope, :type)
     ) { |u| u.type.underscore.titleize }
 
     t.column("Site", :site,
       :sortable => true,
-      :filters  => assoc_filter_values_for(@view_scope, Site)
+      :filters  => default_filters_for(@base_scope, Site)
     ) { |u| link_to_site_if_accessible(u.site) }
 
     t.column("City", :city,
       :sortable => true,
-      :filters  => filter_values_for(@view_scope, :city)
+      :filters  => default_filters_for(@base_scope, :city)
     )
 
     t.column("Country", :country,
       :sortable => true,
-      :filters  => filter_values_for(@view_scope, :country)
+      :filters  => default_filters_for(@base_scope, :country)
     )
 
     t.column("Time Zone", :time_zone,

From 02cb4903d2b6c28d27f374f6af66e65bd379164d Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Mon, 21 Sep 2015 15:35:25 -0400
Subject: [PATCH 48/85] Various small fixes to scopes and dynamic table

This changeset fixes:
- Several documentation typos (thanks to Natacha)
- Missing scope_default_order helper invocation
- Unset attribute field for HierarchyFilter
- Missing server-side-JS update for userfiles' Other Filters panel
- Filter display for the match operator is now 'like'
- Restored CSS styles for critical messages
- Small CSS tweak to dynamic tables
---
 .../app/controllers/userfiles_controller.rb   | 11 +++--
 .../app/helpers/dynamic_table_helper.rb       |  2 +-
 BrainPortal/app/helpers/scope_helper.rb       |  2 +-
 .../app/views/userfiles/_file_menu.html.erb   | 22 ++--------
 .../views/userfiles/_other_filters.html.erb   | 43 +++++++++++++++++++
 BrainPortal/app/views/userfiles/index.js.erb  |  2 +-
 BrainPortal/lib/view_scopes.rb                |  7 +--
 BrainPortal/public/stylesheets/cbrain.css     | 10 +++++
 .../public/stylesheets/dynamic-table.css      |  2 +-
 9 files changed, 69 insertions(+), 32 deletions(-)
 create mode 100644 BrainPortal/app/views/userfiles/_other_filters.html.erb

diff --git a/BrainPortal/app/controllers/userfiles_controller.rb b/BrainPortal/app/controllers/userfiles_controller.rb
index 7e9701dff..a12d2abed 100644
--- a/BrainPortal/app/controllers/userfiles_controller.rb
+++ b/BrainPortal/app/controllers/userfiles_controller.rb
@@ -1623,10 +1623,7 @@ def view_scope(base = nil)
     custom_filters.map! { |id| UserfileCustomFilter.find(id) }
     custom_filters.compact!
 
-    @scope.order << Scope::Order.from_hash({
-      :attribute => 'name',
-      :direction => 'asc'
-    }) if @scope.order.blank?
+    scope_default_order(@scope, 'name')
 
     view = @scope.apply(base)
     view = custom_filters.inject(view) do |scope, filter|
@@ -1749,7 +1746,8 @@ def self.compact_hash(hash)
   # whether or not a given userfile has children or a parent.
   #
   # Note that this filter uses Scope::Filter's *operator* attribute to hold
-  # which condition to filter on. The following conditions (values for
+  # which condition to filter on, and that the *attribute* attribute is set
+  # accordingly to avoid duplication. The following conditions (values for
   # *operator*) are available:
   # [+no_child+]  Userfiles without any children (shortened to 'c').
   # [+no_parent+] Userfiles without a parent (shortened to 'p').
@@ -1829,7 +1827,8 @@ def self.from_hash(hash)
       filter = self.new
 
       operator = (hash['operator'] || hash['o'] || 'no_child').to_s.downcase
-      filter.operator = operator if ['no_child', 'no_parent'].include?(operator)
+      filter.operator  = operator if ['no_child', 'no_parent'].include?(operator)
+      filter.attribute = "##{filter.operator}" if filter.operator
 
       filter
     end
diff --git a/BrainPortal/app/helpers/dynamic_table_helper.rb b/BrainPortal/app/helpers/dynamic_table_helper.rb
index fb0165501..57a4e3810 100644
--- a/BrainPortal/app/helpers/dynamic_table_helper.rb
+++ b/BrainPortal/app/helpers/dynamic_table_helper.rb
@@ -954,7 +954,7 @@ def dynamic_table(collection, options = {}, &block)
 
   # Specialization of +dynamic_table+ (and DynamicTable) to make creating
   # tables using the view scopes mechanism (see the ViewScopes module) easier
-  # by supplying sort_targer and filter_target lambda functions using Scope
+  # by supplying sort_target and filter_target lambda functions using Scope
   # filtering and ordering rules.
   # This method's parameters are the same as +dynamic_table+'s, with the
   # following additional options:
diff --git a/BrainPortal/app/helpers/scope_helper.rb b/BrainPortal/app/helpers/scope_helper.rb
index a9a3d8ce2..b51d1b470 100644
--- a/BrainPortal/app/helpers/scope_helper.rb
+++ b/BrainPortal/app/helpers/scope_helper.rb
@@ -281,7 +281,7 @@ def pretty_scope_filter(filter, model: nil)
       '<='    => 'under ',
       'in'    => 'one of ',
       'out'   => 'anything except ',
-      'match' => '~',
+      'match' => 'like ',
       'range' => 'between '
     })[filter.operator.to_s]
 
diff --git a/BrainPortal/app/views/userfiles/_file_menu.html.erb b/BrainPortal/app/views/userfiles/_file_menu.html.erb
index 7f6b67f1f..3aeada886 100644
--- a/BrainPortal/app/views/userfiles/_file_menu.html.erb
+++ b/BrainPortal/app/views/userfiles/_file_menu.html.erb
@@ -172,25 +172,9 @@
         <%= render :partial => 'userfiles/tag_table_sidebar' %>
       </div>
 
-      <h4>Other Filters</h4>
-      <ul class="filter_menu">
-        <li>
-          <%=
-            scope_filter_link('Has no parent',
-              @scope, :add, { 'type' => 'uf.hier', 'operator' => 'no_parent' },
-              link: { :ajax => true }
-            )
-          %>
-        </li>
-        <li>
-          <%=
-            scope_filter_link('Has no children',
-              @scope, :add, { 'type' => 'uf.hier', 'operator' => 'no_child' },
-              link: { :ajax => true }
-            )
-          %>
-        </li>
-      </ul>
+      <div id="userfiles_other_filters">
+        <%= render :partial => 'userfiles/other_filters' %>
+      </div>
     <% end %>
     <span id="view_option_button">
       <%= render :partial => "userfiles/view_option_button" %>
diff --git a/BrainPortal/app/views/userfiles/_other_filters.html.erb b/BrainPortal/app/views/userfiles/_other_filters.html.erb
new file mode 100644
index 000000000..b497f1bdc
--- /dev/null
+++ b/BrainPortal/app/views/userfiles/_other_filters.html.erb
@@ -0,0 +1,43 @@
+
+<%-
+#
+# 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 <http://www.gnu.org/licenses/>.  
+#
+-%>
+
+<h4>Other Filters</h4>
+<ul class="filter_menu">
+  <li>
+    <%=
+      scope_filter_link('Has no parent',
+        @scope, :set, { 'type' => 'uf.hier', 'operator' => 'no_parent' },
+        link: { :ajax => true }
+      )
+    %>
+  </li>
+  <li>
+    <%=
+      scope_filter_link('Has no children',
+        @scope, :set, { 'type' => 'uf.hier', 'operator' => 'no_child' },
+        link: { :ajax => true }
+      )
+    %>
+  </li>
+</ul>
diff --git a/BrainPortal/app/views/userfiles/index.js.erb b/BrainPortal/app/views/userfiles/index.js.erb
index fad2c927e..89feef32e 100644
--- a/BrainPortal/app/views/userfiles/index.js.erb
+++ b/BrainPortal/app/views/userfiles/index.js.erb
@@ -26,4 +26,4 @@
 jQuery("#userfiles_display").html(<%= html_for_js(render(:partial => 'userfiles_display')) %>);
 jQuery("#userfiles_display").trigger("new_content");
 jQuery("#view_option_button").html(<%= html_for_js(render(:partial => 'view_option_button')) %>).trigger("new_content");
-
+jQuery("#userfiles_other_filters").html(<%= html_for_js(render(:partial => 'other_filters')) %>).trigger("new_content");
diff --git a/BrainPortal/lib/view_scopes.rb b/BrainPortal/lib/view_scopes.rb
index 52102e438..5dbbe9a3e 100644
--- a/BrainPortal/lib/view_scopes.rb
+++ b/BrainPortal/lib/view_scopes.rb
@@ -252,7 +252,7 @@ def apply(collection, paginate: false)
     #  *filter_combination* attribute: either +and+/+intersection+ or
     #  +or+/+union+ (defaults to +and+).
     #
-    # Any missing key will lead to a nil attribute and be handled appriately;
+    # Any missing key will lead to a nil attribute and be handled accordingly;
     # arrays will default to empty and absent components will be ignored.
     #
     # Returns the newly created Scope (just like new would)
@@ -752,7 +752,7 @@ class Order
       # Name of the collection/model attribute to order/sort the
       # collection/model with, as a string or symbol. Must be present as an
       # attribute on in collection/model elements and correspond to a comparable
-      # value (anything that supports <, >), or no sorting/orderin will be
+      # value (anything that supports <, >), or no sorting/ordering will be
       # performed on the collection/model at all.
       #
       # Note that it can also be an attribute on the matching association
@@ -1263,7 +1263,8 @@ def update_session_scopes
     # Apply the scope changes, if any
     current_session.apply_changes([mode, { 'scopes' => scopes }]) unless scopes.blank?
 
-    # Pagination parameters (which override _scopes and _default_scope)
+    # Pagination parameters (which override _scopes, _default_scope
+    # and _simple_filters)
     pagination = {}
     pagination['i'] = params['page']     if params['page']
     pagination['p'] = params['per-page'] if params['per-page']
diff --git a/BrainPortal/public/stylesheets/cbrain.css b/BrainPortal/public/stylesheets/cbrain.css
index 59d8773c6..2dd8502b7 100644
--- a/BrainPortal/public/stylesheets/cbrain.css
+++ b/BrainPortal/public/stylesheets/cbrain.css
@@ -2067,6 +2067,16 @@ img {
 /* % Message Index */
 /* % ######################################################### */
 
+#message_table th.critical > .dt-hdr {
+  font-size: 1.8em;
+  padding-right: 0.5em;
+}
+
+#message_table td.critical {
+  font-weight: bold;
+  padding-left: 1em;
+}
+
 #message_table tr.notice_display.message_read:hover,
 #message_table tr.notice_display.message_unread:hover,
 #message_table tr.system_display.message_read:hover,
diff --git a/BrainPortal/public/stylesheets/dynamic-table.css b/BrainPortal/public/stylesheets/dynamic-table.css
index d3b62439e..6197aa4bd 100644
--- a/BrainPortal/public/stylesheets/dynamic-table.css
+++ b/BrainPortal/public/stylesheets/dynamic-table.css
@@ -248,7 +248,7 @@ td.dt-sel > .dt-sel-lbl > .dt-sel-icon {
 }
 
 .dt-popup > .dt-fpop-table {
-  padding: 0.6em 0.8em 0.6em 0.3em;
+  padding: 0.6em 0.8em 0.6em 0.5em;
 }
 
 .dt-fpop-head > tr > .dt-fpop-find-icon {

From 2fa60c7afe2c0ab74860c720286325f1267a845e Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Wed, 23 Sep 2015 14:04:05 -0400
Subject: [PATCH 49/85] Fix for incorrect group scope application

A small oversight; to initialize @view_scope, the scope was applied to
@view_scope (itself!) instead of @base_scope.
---
 BrainPortal/app/controllers/groups_controller.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/BrainPortal/app/controllers/groups_controller.rb b/BrainPortal/app/controllers/groups_controller.rb
index 4ce43e8cb..0226b9011 100644
--- a/BrainPortal/app/controllers/groups_controller.rb
+++ b/BrainPortal/app/controllers/groups_controller.rb
@@ -43,7 +43,7 @@ def index  #:nodoc:
       current_user.has_role?(:normal_user) && @scope.custom[:button].nil?
 
     @base_scope = current_user.available_groups.includes(:site)
-    @view_scope = @scope.apply(@view_scope)
+    @view_scope = @scope.apply(@base_scope)
 
     @scope.pagination ||= Scope::Pagination.from_hash({ :per_page => 50 })
     @groups = @scope.pagination.apply(@view_scope)

From 0618dd2000bdefe2200657a268345880ea499ef1 Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Wed, 23 Sep 2015 15:37:20 -0400
Subject: [PATCH 50/85] Issue #190 - Document show table helper (Redmine 2654)

The new documentation should cover all options and arguments, although
not as clearly as if it was created along with the source it documents
(missing the original design insight).
---
 BrainPortal/app/helpers/show_table_helper.rb | 159 +++++++++++++++++--
 1 file changed, 147 insertions(+), 12 deletions(-)

diff --git a/BrainPortal/app/helpers/show_table_helper.rb b/BrainPortal/app/helpers/show_table_helper.rb
index 71c2f613d..4b391a172 100644
--- a/BrainPortal/app/helpers/show_table_helper.rb
+++ b/BrainPortal/app/helpers/show_table_helper.rb
@@ -40,10 +40,23 @@ module ShowTableHelper
 
   Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
 
-  # Class that actually builds the table.
+  # Helper class to represent the show table properties required for rendering.
+  # This object is the one passed to +show_table+'s block, and it keeps
+  # track of each cell (field) to be rendered.
   class TableBuilder
-    attr_accessor :cells, :width
+    # Cells to be rendered to form the table, as an array of pairs
+    # (cell HTML markup, individual cell width).
+    attr_accessor :cells
 
+    # Table width, in cells. This property holds how many cells should be
+    # displayed per row, as show tables are mainly cell-based, rather than
+    # column/row-based.
+    attr_accessor :width
+
+    # Create a new TableBuilder for +object+ using +template+ for rendering.
+    # Available +options+ are the same as for the +show_table+ helper method.
+    # Internal method; use +show_table+ (which uses this class) to create and
+    # render show tables.
     def initialize(object, template, options = {}) #:nodoc:
       @object          = object
       @template        = template
@@ -54,29 +67,79 @@ def initialize(object, template, options = {}) #:nodoc:
       @edit_cell_count = 0
     end
 
-    # Returns true if the content is editable
+    # Whether or not this table has editable content. An editable table will
+    # have a toggle button to switch to edition mode.
     def editable?
       !@edit_disabled && @edit_cell_count > 0
     end
 
-    # Generates a cell
+    # Generate a single cell for the table, optionally along with a header cell
+    # containing +header+. Expects a block taking no arguments to generate
+    # the contents of the cell.
+    # Note that cells are placed from left to right in rows of *width* (width
+    # attribute) cells.
+    #
+    # The available +options+ are:
+    # [:no_header]
+    #  Do not generate a header cell with the main content one. +head+ is
+    #  ignored.
+    #
+    # [:show_width]
+    #  Width (in cells or columns) of this cell in the table. For example,
+    #  if a table has 2 cells per row, a show_width of 2 would make the
+    #  generated cell as wide as the entire table. Defaults to 1.
+    #
+    # [:th_options]
+    #  HTML attributes to tackle on the generated header cell. Note that
+    #  +build_cell+ does not have any default attributes for header cells.
+    #
+    # [:td_options]
+    #  Same as :th_options, but for the content cell. Note that +build_cell+
+    #  may override any colspan attribute given in +td_options+, if required.
+    #
+    # [<...>]
+    #  All other options are added as HTML attributes to both the generated
+    #  header and content cells.
     def cell(header = "", options = {}, &block)
       build_cell(ERB::Util.html_escape(header), @template.capture(&block), options)
     end
 
-    # Generates a row
+    # Generate a new table row containing a single cell as wide as the table.
+    # Expects a block taking no arguments to generate the contents of the cell.
+    # The available +options+ are the same as for +cell+ (and will apply to the
+    # single cell filling the row) except for +no_header+ and +show_width+,
+    # which are respectively set to true (as there is no header for full-row
+    # cells) and the width of the table. Note that this method will also pad the
+    # last row with blanks before adding the new row
+    # (see +pad_row_with_blank_cells+).
     def row(options = {}, &block)
       pad_row_with_blank_cells(options)
       build_cell("", @template.capture(&block), options.dup.merge( { :no_header => true, :show_width => @width } ) )
     end
 
-    # Generates the attribute of a cell
+    # Generate a cell for a field named +field+ inside the table's source
+    # object. This method has the same +options+ as the +cell+ method, with
+    # one addition:
+    # [:header]
+    #  Contents for the header cell to generate along with the field cell.
+    #  Defaults to +field+ (field name).
     def attribute_cell(field, options = {})
       header = options[:header] || field.to_s.humanize
       build_cell(ERB::Util.html_escape(header), ERB::Util.html_escape(@object.send(field)), options)
     end
 
-    # Generates an editable cell
+    # Generate an editable cell for a field named +field+ inside the table's
+    # source object. Expects a block taking no arguments to generate HTML
+    # markup for editing +field+ (use +inline_edit_field+'s +content+ option
+    # to specify the cell's contents in display mode).
+    # Unless edition is disabled, the generated cell will toggle between display
+    # and edition mode when the table's edition toggle button is used.
+    #
+    # This method supports both +cell+ and +inline_edit_field+'s
+    # options, with one addition:
+    # [:header]
+    #  Contents for the header cell to generate along with the field cell.
+    #  Defaults to +field+ (field name).
     def edit_cell(field, options = {}, &block)
       header    = options.delete(:header) || field.to_s.humanize
       object    = @object
@@ -85,7 +148,19 @@ def edit_cell(field, options = {}, &block)
       build_cell(ERB::Util.html_escape(header), @template.instance_eval{ inline_edit_field(object, field, options, &block) }, options)
     end
 
-    # Generates an editable checkbox
+    # Generates an editable checkbox cell for +field+, of which the current
+    # value is expected to be +cur_value+, a checked checkbox corresponding to
+    # +checked_value+ and an unchecked one to +unchecked_value+.
+    #
+    # A specialization of +edit_cell+, this method provides some useful
+    # defaults when generating checkbox cells:
+    # - The cell's contents in display mode default to a disabled checkbox
+    # - If no block is given, the edition mode markup defaults to an hidden
+    #   field for +unchecked_value+ and a checkbox for +checked_value+.
+    #
+    # As +boolean_edit_cell+ is a specialization of +edit_cell+, +field+,
+    # +&block+ and +options+ are handled the same way (save for the defaults
+    # outlined above).
     def boolean_edit_cell(field, cur_value, checked_value = "1", unchecked_value = "0", options = {}, &block)
       options[:content] ||= @template.disabled_checkbox(cur_value == checked_value)
       if block_given?
@@ -95,23 +170,32 @@ def boolean_edit_cell(field, cur_value, checked_value = "1", unchecked_value = "
       end
     end
 
-    # Generates an empty cell
+    # Generate +n+ empty cells (blank content and header), each with the same
+    # +options+. Available +options+ are the same as the ones for +cell+.
+    #
+    # FIXME: +options+ is destructively modified in +build_cell+, meaning only
+    # the first cell will have +options+ applied.
     def empty_cell(n = 1, options = {})
       n.times { build_cell("","",options) }
     end
 
-    # Generates X empty cells
+    # Alias for +empty_cell+ (see +empty_cell+).
     def empty_cells(n, options = {})
       empty_cell(n, options)
     end
 
-    # Generates a blank row
+    # Generate a new blank/empty table row. A simple wrapper around +row+, this
+    # method takes the same arguments save for the block, which isn't required
+    # as there is no content to display. See +row+ for more information on how
+    # rows are generated.
     def blank_row(options = {})
       pad_row_with_blank_cells(options)
       row(options) { "&nbsp;".html_safe }
     end
 
-    # Generates a row with empty cells
+    # Fill the last table row with empty cells (+empty_cell+). Each generated
+    # empty cell is generated with the same +options+, which are the same as
+    # the ones for +cell+.
     def pad_row_with_blank_cells(options = {})
       in_current_row = (@cells.inject(0) { |tot,c| tot += c[1]; tot } ) % @width  # c[1] is the show_width of each cell
       empty_cell(@width - in_current_row, options) if in_current_row > 0
@@ -119,6 +203,10 @@ def pad_row_with_blank_cells(options = {})
 
     private
 
+    # Generate a single show table cell containing +content+, usually along with
+    # another header cell containing +head+. Internal method backing most
+    # cell-generating methods in TableBuilder. Available +options+ are the
+    # same as those specified for the +cell+ method.
     def build_cell(head = "", content = "", options = {}) #:nodoc:
       no_header      = options.delete(:no_header)
       header_options = options.delete(:th_options) || {}
@@ -139,6 +227,24 @@ def build_cell(head = "", content = "", options = {}) #:nodoc:
     end
   end # class TableBuilder
 
+  # Generate an input field for +attribute+ within +object+ which can be
+  # toggled by the user into either display or edition mode. This helper method
+  # is designed to be used within a show table, as the table's layout will
+  # provide the toggle button it requires. Expects a block taking no arguments
+  # to generate the HTML markup to render when in edition mode. In display mode,
+  # the field just shows +attribute+'s value.
+  #
+  # The available +options+ are:
+  # [:content]
+  #  Content to show in display mode instead of +attribute+'s value.
+  #
+  # [:disabled]
+  #  Disable edition; this field will always stay in display mode and will
+  #  ignore the show table's toggle button.
+  #
+  # Note that +object+ needs to look like an AR record, as it is expected to
+  # have an errors method. If it has one and it contains +attribute+, the
+  # display mode's text will reflect the erroneous state of the attribute.
   def inline_edit_field(object, attribute, options = {}, &block)
     default_text = h(options.delete(:content) || object.send(attribute))
     return default_text if options.delete(:disabled)
@@ -157,6 +263,35 @@ def inline_edit_field(object, attribute, options = {}, &block)
     return html
   end
 
+  # Create a show (and edition) table for +object+, which is expected to be
+  # an AR record (or a similar object) to use for most table values.
+  # Expects a block taking a single argument, a TableBuilder object, to specify
+  # which fields of +object+ to display (see TableBuilder's methods for more
+  # information).
+  #
+  # The available +options+ are:
+  # [header]
+  #  Title (header), to place on top of the table. Defaults to "Info".
+  #
+  # [url]
+  #  URL (as a string) to perform the edition request on should +object+ be
+  #  editable using this table. Defaults to an URL to the current controller
+  #  for the +create+ action if +object+ does not exist yet in the DB, or
+  #  +update+ with +object+'s ID otherwise.
+  #
+  # [method]
+  #  HTTP method to perform the edition request with, should +object+ be
+  #  editable using this table. Defaults to POST if the object has not been
+  #  saved yet, PUT otherwise.
+  #
+  # [width]
+  #  Table row width, in cells (in other words, the column count).
+  #  Defaults to 2 cells per row.
+  #
+  # [edit_condition]
+  #  Whether or not to make the table's fields editable by the user. If the
+  #  table is editable (+edit_condition+ is specified as true), an edit toggle
+  #  will be added next to the header/title to switch into edition mode.
   def show_table(object, options = {})
     header = options.delete(:header) || "Info"
     url    = options.delete :url

From 7332fad19ccd33d6a098382e58c114bf62516c04 Mon Sep 17 00:00:00 2001
From: Pierre Rioux <pierre.rioux@mcgill.ca>
Date: Fri, 25 Sep 2015 15:05:31 -0400
Subject: [PATCH 51/85] Tiny esthetic code changes.

---
 BrainPortal/app/models/admin_user.rb   | 14 +++++++-------
 BrainPortal/app/models/normal_user.rb  | 18 +++++++++---------
 BrainPortal/app/models/site_manager.rb | 20 ++++++++++----------
 BrainPortal/config/console_rc.rb       |  4 ++--
 4 files changed, 28 insertions(+), 28 deletions(-)

diff --git a/BrainPortal/app/models/admin_user.rb b/BrainPortal/app/models/admin_user.rb
index bc54fe642..33cd10fab 100644
--- a/BrainPortal/app/models/admin_user.rb
+++ b/BrainPortal/app/models/admin_user.rb
@@ -17,7 +17,7 @@
 # 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 <http://www.gnu.org/licenses/>.  
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 
 # Model representing a user with adminstrative rights.
@@ -25,25 +25,25 @@
 class AdminUser < User
 
   Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
-  
+
   def available_tools  #:nodoc:
     Tool.scoped
   end
-  
+
   def available_groups  #:nodoc:
     Group.scoped
   end
-  
+
   def available_tasks  #:nodoc:
     CbrainTask.scoped
   end
-  
+
   def available_users  #:nodoc:
     User.scoped
   end
-  
+
   def visible_users #:nodoc:
     User.scoped
   end
-  
+
 end
diff --git a/BrainPortal/app/models/normal_user.rb b/BrainPortal/app/models/normal_user.rb
index ceac5072b..b30acea9a 100644
--- a/BrainPortal/app/models/normal_user.rb
+++ b/BrainPortal/app/models/normal_user.rb
@@ -17,34 +17,34 @@
 # 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/>.
 #
 
 # Model representing a user with normal rights.
 # Normal users only have access to resources they own or those
 # of projects they are members of.
 class NormalUser < User
-  
+
   Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
 
   def available_tools  #:nodoc:
     Tool.where( ["tools.user_id = ? OR tools.group_id IN (?)", self.id, self.group_ids])
   end
-  
-  def available_groups  #:nodoc:              
-    self.groups.where("groups.name <> 'everyone'").where(invisible: false)
+
+  def available_groups  #:nodoc:
+    self.groups.where("groups.type <> 'EveryoneGroup'").where(:invisible => false)
   end
-  
+
   def available_tasks  #:nodoc:
     CbrainTask.where( ["cbrain_tasks.user_id = ? OR cbrain_tasks.group_id IN (?)", self.id, self.group_ids] )
   end
-  
+
   def available_users  #:nodoc:
     User.where( :id => self.id )
   end
-  
+
   def visible_users #:nodoc:
     User.where("users.type <> 'AdminUser'")
   end
-  
+
 end
diff --git a/BrainPortal/app/models/site_manager.rb b/BrainPortal/app/models/site_manager.rb
index de627db4b..98ec22d05 100644
--- a/BrainPortal/app/models/site_manager.rb
+++ b/BrainPortal/app/models/site_manager.rb
@@ -17,7 +17,7 @@
 # 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 <http://www.gnu.org/licenses/>.  
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 
 # Model representing a user with site manager rights.
@@ -26,30 +26,30 @@
 class SiteManager < User
 
   Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
-  
+
   validates_presence_of :site_id, :message => "must be set for site managers"
-  
+
   def available_tools  #:nodoc:
     Tool.where( ["tools.group_id IN (?) OR tools.user_id IN (?)", self.group_ids, self.site.user_ids])
   end
-  
+
   def available_groups  #:nodoc:
     group_scope = Group.where(["groups.id IN (select groups_users.group_id from groups_users where groups_users.user_id=?) OR groups.site_id=?", self.id, self.site_id])
-    group_scope = group_scope.where("groups.name <> 'everyone'").where(invisible: false)      
-    
+    group_scope = group_scope.where("groups.type <> 'EveryoneGroup'").where(:invisible => false)
+
     group_scope
   end
-  
+
   def available_tasks  #:nodoc:
     CbrainTask.where( ["cbrain_tasks.group_id IN (?) OR cbrain_tasks.user_id IN (?)", self.group_ids, self.site.user_ids] )
   end
-  
+
   def available_users  #:nodoc:
     self.site.users
   end
-  
+
   def visible_users #:nodoc:
     User.where("users.type <> 'AdminUser'")
   end
-  
+
 end
diff --git a/BrainPortal/config/console_rc.rb b/BrainPortal/config/console_rc.rb
index fc855bfce..2b6bfbc7a 100644
--- a/BrainPortal/config/console_rc.rb
+++ b/BrainPortal/config/console_rc.rb
@@ -205,12 +205,12 @@ def cycle_bb(*bb)
 
 # Show bourreau worker processes on given bourreau(x).
 def ps_work(*arg)
-  bb_bash(*arg){ |b| "ps ax -o ruser,pid,%cpu,%mem,vsize,state,stime,time,command | grep 'Worker #{b.name}' | grep -v grep | sed -e 's/  *$//'" }
+  bb_bash(*arg){ |b| "ps -u $USER -o user,pid,%cpu,%mem,vsize,state,stime,time,command | grep 'Worker #{b.name}' | grep -v grep | sed -e 's/  *$//'" }
 end
 
 # Show all processes on given bourreau(x).
 def ps_bb(*arg)
-  bb_bash(*arg){ |b| "ps ax -o ruser,pid,%cpu,%mem,vsize,state,stime,time,command | grep ^$USER | sed -e 's/  *$//'" }
+  bb_bash(*arg){ |b| "ps -u $USER -o user,pid,%cpu,%mem,vsize,state,stime,time,command | sed -e 's/  *$//'" }
 end
 
 # Disable AR logging (actually, just sets logging level to ERROR)

From bda151cb8199441f5c20bee2776156d76c2c6e66 Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Fri, 25 Sep 2015 15:36:28 -0400
Subject: [PATCH 52/85] Scope fixes following further review and testing

This changeset fixes the following issues:
- Broken 'as user' DP browsing
- Filter count format: (34/100) -> (of 100)
- Odd filter menu order (now somewhat ordered by label)
- Broken user & group ordering on bourreaux
- Odd 'register all files' select box order
- Broken custom filters for tasks
- Spurious scopes with only pagination parameters
- Invalid scope filters/ordering rules cannot be removed and
  make the target page inaccessible.
---
 .../controllers/data_providers_controller.rb  |  9 ++--
 BrainPortal/app/helpers/scope_helper.rb       |  8 +--
 .../bourreaux/_bourreaux_display.html.erb     |  2 +-
 .../data_providers/_dp_browse_table.html.erb  |  4 +-
 .../messages/_message_index_display.html.erb  |  4 +-
 .../app/views/shared/_active_filters.html.erb |  2 +-
 .../app/views/users/_users_table.html.erb     |  2 +-
 BrainPortal/lib/view_scopes.rb                | 52 ++++++++++++++++---
 8 files changed, 61 insertions(+), 22 deletions(-)

diff --git a/BrainPortal/app/controllers/data_providers_controller.rb b/BrainPortal/app/controllers/data_providers_controller.rb
index 6aff3e09e..ea6bc4896 100644
--- a/BrainPortal/app/controllers/data_providers_controller.rb
+++ b/BrainPortal/app/controllers/data_providers_controller.rb
@@ -297,13 +297,16 @@ def browse
     })
 
     # Browsing as a different user? Make sure the target user is set.
-    @as_user   = current_user
+    @as_user = current_user
       .available_users
-      .where(:id => @scope.custom['as_user_id'] ||= (
-        params['as_user_id'] || current_user.id
+      .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 ]
diff --git a/BrainPortal/app/helpers/scope_helper.rb b/BrainPortal/app/helpers/scope_helper.rb
index b51d1b470..4cfa73260 100644
--- a/BrainPortal/app/helpers/scope_helper.rb
+++ b/BrainPortal/app/helpers/scope_helper.rb
@@ -384,7 +384,7 @@ def filter_values_for(collection, attribute, label: nil, association: nil, forma
     # Format the generated filter arrays as DynamicTable's filter hashes
     filters.map do |value, label, count, *rest|
       scoped = rest.first
-      label  = "#{label} (#{scoped}/#{count})" if scoped
+      label  = "#{label} (of #{count})" if scoped
       {
         :value     => value,
         :label     => label,
@@ -418,7 +418,7 @@ def default_filters_for(collection, attribute)
       lambda do |args|
         value, label, count, scoped = args
         label = block.(label) rescue label
-        label = "#{label} (#{scoped}/#{count})" if scoped
+        label = "#{label} (of #{count})" if scoped
         {
           :value     => value,
           :label     => label,
@@ -561,7 +561,7 @@ def model_filter_values(model, attribute, label, association: nil, scope: nil)
     # [[value, label, count], [...]]
     filters = model
       .where("#{attribute} IS NOT NULL")
-      .order(attribute, label)
+      .order(label, attribute)
       .group(attribute, label)
       .raw_rows(attribute, "#{label} AS #{label_alias}", "COUNT(#{attribute})")
       .reject { |r| r.first.blank? }
@@ -608,7 +608,7 @@ def collection_filter_values(collection, attribute, label, scope: nil)
       collection
         .map     { |i| [attr_get.(i), lbl_get.(i)].freeze }
         .reject  { |v, l| v.blank? }
-        .sort_by { |v, l| v }
+        .sort_by { |v, l| l }
         .inject(Hash.new(0)) { |h, i| h[i] += 1; h }
     end
 
diff --git a/BrainPortal/app/views/bourreaux/_bourreaux_display.html.erb b/BrainPortal/app/views/bourreaux/_bourreaux_display.html.erb
index 5f0377122..c558a30c3 100644
--- a/BrainPortal/app/views/bourreaux/_bourreaux_display.html.erb
+++ b/BrainPortal/app/views/bourreaux/_bourreaux_display.html.erb
@@ -28,7 +28,7 @@
     :class      => [ :resource_list ],
     :scope      => @scope,
     :render     => false,
-    :sort_map   => {
+    :order_map  => {
       :owner => { :a => 'users.login', :j => User  },
       :group => { :a => 'groups.name', :j => Group }
     },
diff --git a/BrainPortal/app/views/data_providers/_dp_browse_table.html.erb b/BrainPortal/app/views/data_providers/_dp_browse_table.html.erb
index a76f78eb0..3a5f1f8f4 100644
--- a/BrainPortal/app/views/data_providers/_dp_browse_table.html.erb
+++ b/BrainPortal/app/views/data_providers/_dp_browse_table.html.erb
@@ -34,9 +34,9 @@
   <div class="pagination">
     <div class="pagination_left_side">
       Register files as:
-      <%= master_select("file_select", ["..."] + SingleFile.valid_file_classes.map(&:pretty_type)) %>,
+      <%= master_select("file_select", ["..."] + SingleFile.valid_file_classes.map(&:pretty_type).sort) %>,
       and directories as:
-      <%= master_select("directory_select", ["..."] + FileCollection.valid_file_classes.map(&:pretty_type)) %>
+      <%= master_select("directory_select", ["..."] + FileCollection.valid_file_classes.map(&:pretty_type).sort) %>
     </div>
 
     <div class="pagination_right_side">
diff --git a/BrainPortal/app/views/messages/_message_index_display.html.erb b/BrainPortal/app/views/messages/_message_index_display.html.erb
index c118e3630..84d5f443a 100644
--- a/BrainPortal/app/views/messages/_message_index_display.html.erb
+++ b/BrainPortal/app/views/messages/_message_index_display.html.erb
@@ -107,7 +107,7 @@
             label = (! value || value == 0) ? 'Not critical' : 'Critical'
             {
               :value     => value,
-              :label     => "#{label} (#{scoped}/#{count})",
+              :label     => "#{label} (of #{count})",
               :indicator => scoped,
               :empty     => scoped == 0
             }
@@ -124,7 +124,7 @@
           format: lambda do |value, label, count, scoped|
             {
               :value     => value,
-              :label     => "#{label.humanize} (#{scoped}/#{count})",
+              :label     => "#{label.humanize} (of #{count})",
               :indicator => scoped,
               :empty     => scoped == 0
             }
diff --git a/BrainPortal/app/views/shared/_active_filters.html.erb b/BrainPortal/app/views/shared/_active_filters.html.erb
index 6f7e3138f..922e353fb 100644
--- a/BrainPortal/app/views/shared/_active_filters.html.erb
+++ b/BrainPortal/app/views/shared/_active_filters.html.erb
@@ -51,7 +51,7 @@
       <% end %>
       <% Array(scope.custom[:custom_filters]).uniq.each do |id| %>
         <span class="current_filters_item">
-          <%= crop_text_to(30, UserfileCustomFilter.find(id).name) %>
+          <%= crop_text_to(30, CustomFilter.find(id).name) %>
         </span>
         <%=
           scope_custom_link(delete_icon,
diff --git a/BrainPortal/app/views/users/_users_table.html.erb b/BrainPortal/app/views/users/_users_table.html.erb
index 96c9d7404..4c054bcfa 100644
--- a/BrainPortal/app/views/users/_users_table.html.erb
+++ b/BrainPortal/app/views/users/_users_table.html.erb
@@ -86,7 +86,7 @@
           label = (!value || value == 0 ? 'Unlocked' : 'Locked')
           {
             :value     => value,
-            :label     => "#{label} (#{scoped}/#{count})",
+            :label     => "#{label} (of #{count})",
             :indicator => scoped,
             :empty     => scoped == 0
           }
diff --git a/BrainPortal/lib/view_scopes.rb b/BrainPortal/lib/view_scopes.rb
index 5dbbe9a3e..de478cc41 100644
--- a/BrainPortal/lib/view_scopes.rb
+++ b/BrainPortal/lib/view_scopes.rb
@@ -187,25 +187,54 @@ def initialize_copy(other)
     # was a model or a new Ruby Enumerable matching the rules if +collection+
     # was a Ruby Enumerable.
     #
+    # If a rule application fails (a filter's target attribute does not exist on
+    # +collection+, for example), +on_failure+ specifies how to handle the
+    # failure. Three failure resolution methods are available:
+    # [:ignore] The erroneous rule is skipped (default).
+    # [:empty]  An empty collection is returned.
+    # [:raise]  The erroneous rule's raised exception is re-thrown/re-raised.
+    # This parameter is mainly used to avoid raising filtering/sorting rule
+    # exceptions to callers which might just want to ignore the erroneous filter
+    # rather than directly handling the issue (as Scopes are mainly used for
+    # views).
+    #
     # Note that pagination is not applied by default; specify +paginate+ to
     # paginate +collection+.
-    def apply(collection, paginate: false)
+    def apply(collection, on_failure: :ignore, paginate: false)
+      # Wrap a filtering or sorting rule application to handle exceptions,
+      # using +fallback+ as a fall-back value for :ignore.
+      empty = (collection <= ActiveRecord::Base rescue nil) ?
+        collection.where('1 = 0') : []
+      wrap = lambda do |fallback, &block|
+        begin
+          block.call()
+        rescue => e
+          case on_failure
+          when :ignore then next fallback
+          when :empty  then return empty
+          when :raise  then raise
+          end
+        end
+      end
+
       # Apply all filtering rules
       collection = @filters.inject(collection) do |collection, filter|
-        filter.apply(collection)
+        wrap.(collection) { filter.apply(collection) }
       end
 
       # Apply sorting rules
       if (collection <= ActiveRecord::Base rescue nil)
         collection = @order.inject(collection) do |collection, order|
-          order.apply(collection)
+          wrap.(collection) { order.apply(collection) }
         end
       else
-        collection = @order.first.apply(collection) unless @order.empty?
+        collection = wrap.(collection) { @order.first.apply(collection) } unless
+          @order.empty?
       end
 
       # Paginate
-      collection = @pagination.apply(collection) if paginate && @pagination
+      collection = wrap.(collection) { @pagination.apply(collection) } if
+        paginate && @pagination
 
       collection
     end
@@ -1269,10 +1298,17 @@ def update_session_scopes
     pagination['i'] = params['page']     if params['page']
     pagination['p'] = params['per-page'] if params['per-page']
     pagination['p'] = params['per_page'] if params['per_page']
+    pag_scope = params['_pag_scope_name'] || default_scope_name
+
+    # FIXME: the per_page parameter is often passed in many requests where it
+    # doesn't belong, creating spurious Scopes in the session. A workaround is
+    # to require the target scope to already exist:
+    pagination.delete('p') unless
+      (current_session['scopes'] || {}).has_key?(pag_scope)
 
-    current_session.apply_changes({ 'scopes' => {
-      (params['_pag_scope_name'] || default_scope_name) => { 'p' => pagination }
-    } }) unless
+    current_session.apply_changes(
+      { 'scopes' => { pag_scope => { 'p' => pagination } } }
+    ) unless
       pagination.empty?
   end
 

From a5bafa8c01b857e358d6cbad182e6f9e0cf66a3b Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Mon, 28 Sep 2015 14:16:46 -0400
Subject: [PATCH 53/85] Port of DP report table, more small fixes

Same principle as the DP browse table port, as a DP report is a
collection of hashes. Note that compared to most index and report
tables, the DP report is a little shy on features.

This changeset also fixes:
- Incorrect filter counts when used with custom filters
- Missing @scope initialization
- Missing userfiles size total
- Broken dynamic table automatic pagination
- Broken dynamic_scoped_table default scope resolution
- Warning & default_filters_for default for Symbol-valued attributes
- Stale filter menus (now updated through server-side JS)
---
 .../controllers/data_providers_controller.rb  |  8 +-
 .../app/controllers/tasks_controller.rb       | 45 ++++++-----
 .../app/controllers/userfiles_controller.rb   | 48 +++++-------
 .../app/helpers/dynamic_table_helper.rb       | 29 +++----
 BrainPortal/app/helpers/scope_helper.rb       | 45 +++++++----
 .../data_providers/_dp_report_table.html.erb  | 75 +++++++++++++++++++
 .../app/views/data_providers/report.html.erb  | 40 +---------
 .../report.js.erb}                            | 23 +-----
 .../app/views/tasks/_task_menu.html.erb       |  2 +-
 BrainPortal/app/views/tasks/index.js.erb      | 13 +++-
 .../app/views/userfiles/_file_menu.html.erb   |  9 +--
 .../app/views/userfiles/_filters.html.erb     | 23 ++++++
 .../userfiles/_userfiles_display.html.erb     | 10 +--
 BrainPortal/app/views/userfiles/index.js.erb  |  2 +-
 BrainPortal/public/stylesheets/cbrain.css     | 28 +------
 15 files changed, 223 insertions(+), 177 deletions(-)
 create mode 100644 BrainPortal/app/views/data_providers/_dp_report_table.html.erb
 rename BrainPortal/app/views/{userfiles/_other_filters.html.erb => data_providers/report.js.erb} (64%)

diff --git a/BrainPortal/app/controllers/data_providers_controller.rb b/BrainPortal/app/controllers/data_providers_controller.rb
index ea6bc4896..b8ccb53f8 100644
--- a/BrainPortal/app/controllers/data_providers_controller.rb
+++ b/BrainPortal/app/controllers/data_providers_controller.rb
@@ -656,11 +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
diff --git a/BrainPortal/app/controllers/tasks_controller.rb b/BrainPortal/app/controllers/tasks_controller.rb
index b67553fd1..745cdc3bf 100644
--- a/BrainPortal/app/controllers/tasks_controller.rb
+++ b/BrainPortal/app/controllers/tasks_controller.rb
@@ -42,9 +42,10 @@ def index #:nodoc:
     end
 
     @scope.pagination ||= Scope::Pagination.from_hash({ :per_page => 25 })
-    @base_scope = user_scope(current_user.available_tasks)
-      .includes([:bourreau, :user, :group])
-    @view_scope = view_scope(@base_scope)
+    @base_scope = custom_scope(user_scope(
+      current_user.available_tasks.includes([:bourreau, :user, :group])
+    ))
+    @view_scope = @scope.apply(@base_scope)
 
     # Display totals
     @total_tasks       = @view_scope.count
@@ -110,14 +111,14 @@ def index #:nodoc:
   # Renders a set of tasks associated with a batch.
   def batch_list
     @scope = scope_from_session('tasks')
-    @base_scope = user_scope(
+    @base_scope = custom_scope(user_scope(
       current_user
         .available_tasks
         .real_tasks
         .where(:batch_id => params[:batch_id])
         .includes([:bourreau, :user, :group])
-    )
-    @tasks = view_scope(@base_scope)
+    ))
+    @tasks = @scope.apply(@base_scope)
       .order(['cbrain_tasks.rank', 'cbrain_tasks.level', 'cbrain_tasks.id'])
       .map { |task| { :batch => task.batch_id, :first => task, :count => 1 } }
 
@@ -570,12 +571,13 @@ def update #:nodoc:
 
   # Allows user to update attributes of multiple tasks.
   def update_multiple
+    @scope = scope_from_session('tasks')
 
     # Construct task_ids and batch_ids
     task_ids   = Array(params[:tasklist]  || [])
     batch_ids  = Array(params[:batch_ids] || [])
     batch_ids << nil if batch_ids.delete('nil')
-    task_ids  += view_scope(user_scope(CbrainTask.where(:batch_id => batch_ids))).select(:id).raw_first_column
+    task_ids  += filtered_scope(CbrainTask.where(:batch_id => batch_ids)).select(:id).raw_first_column
     task_ids   = task_ids.map(&:to_i).uniq
 
     commit_name = extract_params_key([ :update_user_id, :update_group_id, :update_results_data_provider_id, :update_tool_config_id ])
@@ -729,7 +731,7 @@ def update_multiple
   # [*Terminate*] Kill the task, while maintaining its temporary files and its entry in the database.
   # [*Delete*] Kill the task, delete the temporary files and remove its entry in the database.
   def operation
-    @scope      = scope_from_session('tasks')
+    @scope = scope_from_session('tasks')
 
     operation  = params[:operation]
     tasklist   = params[:tasklist]  || []
@@ -737,7 +739,7 @@ def operation
     batch_ids  = params[:batch_ids] || []
     batch_ids  = [ batch_ids ] unless batch_ids.is_a?(Array)
     batch_ids << nil if batch_ids.delete('nil')
-    tasklist  += view_scope(user_scope(CbrainTask.where(:batch_id => batch_ids))).select(:id).raw_first_column
+    tasklist  += filtered_scope(CbrainTask.where(:batch_id => batch_ids)).select(:id).raw_first_column
     tasklist   = tasklist.map(&:to_i).uniq
 
     flash[:error]  ||= ""
@@ -991,17 +993,22 @@ def user_scope(base)
       )
   end
 
-  # View tasks scope; filtered and sorted list of tasks to display (or currently
-  # displayed). +base+ is expected to be the base scope to filter and sort.
-  # Requires a valid @scope object.
-  def view_scope(base)
-    custom_filters  = (@scope.custom[:custom_filters] || []).dup
-    custom_filters &= current_user.custom_filter_ids
-    custom_filters.map! { |id| TaskCustomFilter.find(id) }
+  # Custom filters scope; filtered list of tasks respecting currently active
+  # custom filters. +base+ is expected to be the initial scope to apply custom
+  # filters to. Requires a valid @scope object.
+  def custom_scope(base)
+    ((@scope.custom[:custom_filters] || []) & current_user.custom_filter_ids)
+      .map { |id| TaskCustomFilter.find_by_id(id) }
+      .compact
+      .inject(base) { |scope, filter| filter.filter_scope(scope) }
+  end
 
-    custom_filters.inject(@scope.apply(base)) do |scope, filter|
-      filter.filter_scope(scope)
-    end
+  # Combination of +user_scope+, +custom_scope+ and @scope object; returns a
+  # scoped list of tasks fitlered/ordered by all three. +base+ is expected to
+  # be the base scope to start with (passed directly to +user_scope+).
+  # Requires a valid @scope object.
+  def filtered_scope(base)
+    @scope.apply(custom_scope(user_scope(base)))
   end
 
   public
diff --git a/BrainPortal/app/controllers/userfiles_controller.rb b/BrainPortal/app/controllers/userfiles_controller.rb
index a12d2abed..38b012ced 100644
--- a/BrainPortal/app/controllers/userfiles_controller.rb
+++ b/BrainPortal/app/controllers/userfiles_controller.rb
@@ -51,10 +51,12 @@ def index #:nodoc:
       :operator  => 'match'
     })
 
-    # Base userfiles scope, without any filtering or ordering
-    @base_scope = base_scope
-    # Ordered, filtered view scope
-    @view_scope = view_scope(@base_scope)
+    # Apply basic and @scope-based scoping
+    scope_default_order(@scope, 'name')
+    @base_scope = custom_scope(
+      base_scope.includes([:user, :data_provider, :sync_status, :tags, :group])
+    )
+    @view_scope = @scope.apply(@base_scope)
 
     # Generate tag filters
     tag_counts   = @view_scope.joins(:tags).group('tags.name').count
@@ -71,17 +73,13 @@ def index #:nodoc:
         }
       end
 
-    # Join in other models to display additional view information
-    @view_scope = @view_scope.includes([
-      :user, :data_provider, :sync_status, :tags, :group
-    ])
-
     # Generate display totals
     @userfiles_total = @view_scope.count('distinct userfiles.id')
     @archived_total  = @view_scope.where(:archived => true).count
     @immutable_total = @view_scope.where(:immutable => true).count
     @hidden_total    = @view_scope.undo_where(:hidden).where(:hidden => true).count unless
       @scope.custom[:view_hidden]
+    @userfiles_total_size = @view_scope.sum(:size)
 
     # Prepare the Pagination object
     @scope.pagination ||= Scope::Pagination.from_hash({ :per_page => 25 })
@@ -1592,8 +1590,9 @@ def all_tree_children_by_pairs(top,level = nil) #:nodoc:
     result
   end
 
-  # Base userfiles scope; all userfiles currently visible to the user, without any
-  # filtering yet. Requires a valid @scope object.
+  # Base userfiles scope; all userfiles currently visible to the user,
+  # respecting view options, user and project restrictions.
+  # Requires a valid @scope object.
   def base_scope
     base = Userfile.scoped
 
@@ -1612,25 +1611,14 @@ def base_scope
     base
   end
 
-  # View userfiles scope; filtered and sorted list of userfiles to display.
-  # +base+ is expected to be the base scope to filter and sort (defaults to
-  # +base_scope+). Requires a valid @scope object.
-  def view_scope(base = nil)
-    base ||= base_scope
-
-    custom_filters  = (@scope.custom[:custom_filters] || []).dup
-    custom_filters &= current_user.custom_filter_ids
-    custom_filters.map! { |id| UserfileCustomFilter.find(id) }
-    custom_filters.compact!
-
-    scope_default_order(@scope, 'name')
-
-    view = @scope.apply(base)
-    view = custom_filters.inject(view) do |scope, filter|
-      filter.filter_scope(scope)
-    end
-
-    view
+  # Custom filters scope; filtered list of userfiles respecting currently active
+  # custom filters. +base+ is expected to be the initial scope to apply custom
+  # filters to (defaults to +base_scope+). Requires a valid @scope object.
+  def custom_scope(base = nil)
+    ((@scope.custom[:custom_filters] || []) & current_user.custom_filter_ids)
+      .map { |id| UserfileCustomFilter.find_by_id(id) }
+      .compact
+      .inject(base || base_scope) { |scope, filter| filter.filter_scope(scope) }
   end
 
   # Userfiles-specific tag Scope filter; filter by a set of tags which must
diff --git a/BrainPortal/app/helpers/dynamic_table_helper.rb b/BrainPortal/app/helpers/dynamic_table_helper.rb
index 57a4e3810..9cfcd93fd 100644
--- a/BrainPortal/app/helpers/dynamic_table_helper.rb
+++ b/BrainPortal/app/helpers/dynamic_table_helper.rb
@@ -694,19 +694,21 @@ def initialize(location, collection, options = {})
           collection.respond_to?(:current_page) &&
           collection.current_page
         )
-          # Is there a paginate method available?
-          if collection.respond_to?(:paginate)
-            collection.paginate(
-              :page          => page,
-              :per_page      => per_page,
-              :total_entries => total_entries
-            )
-          # Otherwise, just manually create a WillPaginate::Collection
-          else
-            WillPaginate::Collection.create(page, per_page, total_entries) do |pager|
-              pager.replace(collection[pager.offset, pager.per_page].to_a)
+          collection = (
+            # Is there a paginate method available?
+            if collection.respond_to?(:paginate)
+              collection.paginate(
+                :page          => page,
+                :per_page      => per_page,
+                :total_entries => total_entries
+              )
+            # Otherwise, just manually create a WillPaginate::Collection
+            else
+              WillPaginate::Collection.create(page, per_page, total_entries) do |pager|
+                pager.replace(collection[pager.offset, pager.per_page].to_a)
+              end
             end
-          end
+          )
         end
 
         @collection = collection
@@ -1064,6 +1066,7 @@ def dynamic_scoped_table(collection, options = {}, &block)
         end
 
         # Pre-set some HTML attributes for the per-page input
+        scope = @scope
         (options[:input_html] ||= {}).reverse_merge!({
           :name        => 'per_page',
           :class       => 'search_box',
@@ -1073,7 +1076,7 @@ def dynamic_scoped_table(collection, options = {}, &block)
               :controller => params[:controller],
               :action     => params[:action],
               :page            => 1,
-              :_pag_scope_name => @scope.name
+              :_pag_scope_name => scope.name
             )
           end
         })
diff --git a/BrainPortal/app/helpers/scope_helper.rb b/BrainPortal/app/helpers/scope_helper.rb
index 4cfa73260..5da5eb26a 100644
--- a/BrainPortal/app/helpers/scope_helper.rb
+++ b/BrainPortal/app/helpers/scope_helper.rb
@@ -353,6 +353,14 @@ def pretty_scope_filter(filter, model: nil)
   #  Note that any Filter filtering on +attribute+ in +scope+ will be skipped to
   #  avoid generating empty filter values (while this behavior is
   #  counter-intuitive and clunky, it is required for table filtering).
+  #
+  #  NOTE: The filters generated by this method are commonly used with the Scope
+  #  and DynamicTable APIs, which impose an hidden restriction on the values
+  #  that can be taken for +attribute+'s values; they must be safely
+  #  deserializable from YAML. This is the case for almost all common value
+  #  types with the notable exception of Symbols. If +attribute+'s values are
+  #  symbols, consider converting them the resulting filter values to strings
+  #  before using them to construct filtering URLs.
   def filter_values_for(collection, attribute, label: nil, association: nil, format: nil, scope: nil)
     return [] if collection.blank?
 
@@ -428,21 +436,28 @@ def default_filters_for(collection, attribute)
       end
     end
 
-    # Is +attribute+ an association?
-    if (attribute <= ActiveRecord::Base rescue nil)
-      filter_values_for(collection, nil, association: attribute,
-        scope: @scope,
-        label: ('login' if attribute <= User)
-      )
-    else
-      filter_values_for(collection, attribute,
-        scope:  @scope,
-        format: formatter.((
-          proc { |l| l.constantize.pretty_type } if
-            attribute.to_s.downcase == 'type'
-        ))
-      )
-    end
+    filters = (
+      # Is +attribute+ an association?
+      if (attribute <= ActiveRecord::Base rescue nil)
+        filter_values_for(collection, nil, association: attribute,
+          scope: @scope,
+          label: ('login' if attribute <= User)
+        )
+      else
+        filter_values_for(collection, attribute,
+          scope:  @scope,
+          format: formatter.((
+            proc { |l| l.constantize.pretty_type } if
+              attribute.to_s.downcase == 'type'
+          ))
+        )
+      end
+    )
+
+    # Convert all symbol values to strings to avoid deserialization issues
+    # when used in scope URLs.
+    filters.each { |f| f[:value] = f[:value].to_s if f[:value].is_a?(Symbol) }
+    filters
   end
 
   # Internal methods
diff --git a/BrainPortal/app/views/data_providers/_dp_report_table.html.erb b/BrainPortal/app/views/data_providers/_dp_report_table.html.erb
new file mode 100644
index 000000000..0ced3c231
--- /dev/null
+++ b/BrainPortal/app/views/data_providers/_dp_report_table.html.erb
@@ -0,0 +1,75 @@
+
+<%-
+#
+# 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 <http://www.gnu.org/licenses/>.
+#
+-%>
+
+<%=
+  render(:partial => 'shared/active_filters', :locals  => {
+    :scope => @scope,
+    :model => nil
+  })
+%>
+
+<%
+  @issues.each do |issue|
+    issue[:userfile] = Userfile.find_by_id(issue[:userfile_id]) if issue[:userfile_id]
+    issue[:user]   = User.find_by_id(issue[:user_id]) if issue[:user_id]
+    issue[:user] ||= issue[:userfile].user if issue[:userfile]
+  end
+%>
+
+<%=
+  dynamic_scoped_table(@view_scope,
+    :id    => 'data_provider_issues',
+    :scope => @scope
+  ) do |t|
+%>
+  <%
+    t.paginate
+    t.selectable('issue_ids[]')
+
+    t.row { |issue| { :class => "severity-#{issue[:severity]}" } }
+
+    t.column('Issue', :message,
+      :sortable => true
+    )
+
+    t.column('Severity', :severity,
+      :sortable => true,
+      :filters  => default_filters_for(@issues, :severity)
+    ) { |issue| issue[:severity].to_s.titleize }
+
+    t.column('Action', :action,
+      :sortable => true
+    ) { |issue| issue[:action] ? issue[:action].to_s.titleize : '-' }
+
+    t.column('File', :userfile) do |issue|
+      next '-' unless issue[:userfile]
+      link_to_userfile_if_accessible(issue[:userfile], current_user)
+    end
+
+    t.column('User', :user) do |issue|
+      next '-' unless issue[:user]
+      link_to_user_with_tooltip(issue[:user])
+    end
+  %>
+<% end %>
diff --git a/BrainPortal/app/views/data_providers/report.html.erb b/BrainPortal/app/views/data_providers/report.html.erb
index cd0026a88..2d5825306 100644
--- a/BrainPortal/app/views/data_providers/report.html.erb
+++ b/BrainPortal/app/views/data_providers/report.html.erb
@@ -34,41 +34,7 @@
     <% end %>
   </div>
 
-  <table id="data_provider_issues">
-    <tbody>
-      <tr>
-        <th><%= select_all_checkbox("issue_checkbox") %></th>
-        <th>Issue</th>
-        <th>Severity</th>
-        <th>Action</th>
-        <th>File</th>
-        <th>User</th>
-      </tr>
-      <% unless @issues.empty? %>
-        <% @issues.each do |issue| %>
-          <%
-            userfile   = Userfile.find_by_id(issue[:userfile_id]) if issue[:userfile_id]
-            user       = User.find_by_id(issue[:user_id])         if issue[:user_id]
-            user     ||= userfile.user if userfile
-          %>
-          <tr class="severity-<%= issue[:severity].to_s %>">
-            <td><%= check_box_tag("issue_ids[]", issue[:id], false, :class => "issue_checkbox") %></td>
-            <td class="left shrinkable"><%= issue[:message] %></td>
-            <td><%= issue[:severity].to_s.titleize %></td>
-            <td><%= issue[:action] ? issue[:action].to_s.titleize : '-' %></td>
-            <% if userfile %>
-              <td class="left"><%= link_to_userfile_if_accessible(userfile, current_user) %></td>
-            <% else %>
-              <td> - </td>
-            <% end %>
-            <td><%= user ? link_to_user_with_tooltip(user) : '-' %></td>
-          </tr>
-        <% end %>
-      <% else %>
-        <tr>
-          <td colspan="6"><em>No issues to report</em></td>
-        </tr>
-      <% end %>
-    </tbody>
-  </table>
+  <div class="resource_list" id="dp_report_table">
+    <%= render :partial => 'dp_report_table' %>
+  </div>
 <% end %>
diff --git a/BrainPortal/app/views/userfiles/_other_filters.html.erb b/BrainPortal/app/views/data_providers/report.js.erb
similarity index 64%
rename from BrainPortal/app/views/userfiles/_other_filters.html.erb
rename to BrainPortal/app/views/data_providers/report.js.erb
index b497f1bdc..067dbe550 100644
--- a/BrainPortal/app/views/userfiles/_other_filters.html.erb
+++ b/BrainPortal/app/views/data_providers/report.js.erb
@@ -22,22 +22,7 @@
 #
 -%>
 
-<h4>Other Filters</h4>
-<ul class="filter_menu">
-  <li>
-    <%=
-      scope_filter_link('Has no parent',
-        @scope, :set, { 'type' => 'uf.hier', 'operator' => 'no_parent' },
-        link: { :ajax => true }
-      )
-    %>
-  </li>
-  <li>
-    <%=
-      scope_filter_link('Has no children',
-        @scope, :set, { 'type' => 'uf.hier', 'operator' => 'no_child' },
-        link: { :ajax => true }
-      )
-    %>
-  </li>
-</ul>
+jQuery("#dp_report_table")
+  .html(<%= html_for_js(render :partial  => 'dp_report_table') %>)
+  .trigger('new_content');
+
diff --git a/BrainPortal/app/views/tasks/_task_menu.html.erb b/BrainPortal/app/views/tasks/_task_menu.html.erb
index 098bd5dbd..272d495bd 100644
--- a/BrainPortal/app/views/tasks/_task_menu.html.erb
+++ b/BrainPortal/app/views/tasks/_task_menu.html.erb
@@ -195,7 +195,7 @@
     <p/>
   <% end %>
 
-  <%= button_with_dropdown_menu("Filters") do %>
+  <%= button_with_dropdown_menu("Filters", :content_id => 'tasks_filters') do %>
     <%= render :partial => 'tasks/filters' %>
   <% end %>
 
diff --git a/BrainPortal/app/views/tasks/index.js.erb b/BrainPortal/app/views/tasks/index.js.erb
index 8a4568bbc..4e5b6396d 100644
--- a/BrainPortal/app/views/tasks/index.js.erb
+++ b/BrainPortal/app/views/tasks/index.js.erb
@@ -18,11 +18,16 @@
 # 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/>.
 #
 -%>
 
 <%= render :partial  => "shared/flash_update" %>
-var new_table = jQuery(<%= html_for_js(render(:partial => 'tasks_display')) %>);
-jQuery("#tasks_display").html(new_table);
-new_table.trigger("new_content");
+
+jQuery("#tasks_display")
+  .html(<%= html_for_js(render(:partial => 'tasks_display')) %>)
+  .trigger("new_content");
+
+jQuery("#tasks_filters")
+  .html(<%= html_for_js(render(:partial => 'filters')) %>)
+  .trigger("new_content");
diff --git a/BrainPortal/app/views/userfiles/_file_menu.html.erb b/BrainPortal/app/views/userfiles/_file_menu.html.erb
index 3aeada886..c066d542b 100644
--- a/BrainPortal/app/views/userfiles/_file_menu.html.erb
+++ b/BrainPortal/app/views/userfiles/_file_menu.html.erb
@@ -166,15 +166,8 @@
       <% end %>
       </p>
     <% end %>
-    <%= button_with_dropdown_menu("Filters", :content_id => 'userfiles_filters_dropdown_menu') do %>
+    <%= button_with_dropdown_menu("Filters", :content_id => 'userfiles_filters') do %>
       <%= render :partial => 'userfiles/filters' %>
-      <div id="tag_table_sidebar">
-        <%= render :partial => 'userfiles/tag_table_sidebar' %>
-      </div>
-
-      <div id="userfiles_other_filters">
-        <%= render :partial => 'userfiles/other_filters' %>
-      </div>
     <% end %>
     <span id="view_option_button">
       <%= render :partial => "userfiles/view_option_button" %>
diff --git a/BrainPortal/app/views/userfiles/_filters.html.erb b/BrainPortal/app/views/userfiles/_filters.html.erb
index 3523f660f..0cc504f7f 100644
--- a/BrainPortal/app/views/userfiles/_filters.html.erb
+++ b/BrainPortal/app/views/userfiles/_filters.html.erb
@@ -27,3 +27,26 @@
   <%= render :partial => 'custom_filters/custom_filter_list' %>
 </div>
 
+<div id="tag_table_sidebar">
+  <%= render :partial => 'userfiles/tag_table_sidebar' %>
+</div>
+
+<h4>Other Filters</h4>
+<ul class="filter_menu">
+  <li>
+    <%=
+      scope_filter_link('Has no parent',
+        @scope, :set, { 'type' => 'uf.hier', 'operator' => 'no_parent' },
+        link: { :ajax => true }
+      )
+    %>
+  </li>
+  <li>
+    <%=
+      scope_filter_link('Has no children',
+        @scope, :set, { 'type' => 'uf.hier', 'operator' => 'no_child' },
+        link: { :ajax => true }
+      )
+    %>
+  </li>
+</ul>
diff --git a/BrainPortal/app/views/userfiles/_userfiles_display.html.erb b/BrainPortal/app/views/userfiles/_userfiles_display.html.erb
index f082c173c..ddc565f80 100644
--- a/BrainPortal/app/views/userfiles/_userfiles_display.html.erb
+++ b/BrainPortal/app/views/userfiles/_userfiles_display.html.erb
@@ -49,11 +49,11 @@
             total.present? && (total.is_a?(String) || total > 0)
         end
       %>
-      <%= pluralize(@userfiles_total," entry") -%>,
-      <%= colored_pretty_size(@userfiles_total_size) -%>
-      <%= show_total.(@hidden_total,    'hidden',    hidden_icon) -%>
-      <%= show_total.(@archived_total,  'archived',  archived_icon) -%>
-      <%= show_total.(@immutable_total, 'immutable', immutable_icon) -%>
+      <%= pluralize(@userfiles_total," entry") %> ,
+      <%= colored_pretty_size(@userfiles_total_size) %>
+      <%= show_total.(@hidden_total,    'hidden',    hidden_icon) %>
+      <%= show_total.(@archived_total,  'archived',  archived_icon) %>
+      <%= show_total.(@immutable_total, 'immutable', immutable_icon) %>
     )
   </div>
   <div class="pagination_right_side">
diff --git a/BrainPortal/app/views/userfiles/index.js.erb b/BrainPortal/app/views/userfiles/index.js.erb
index 89feef32e..5c0c77eb8 100644
--- a/BrainPortal/app/views/userfiles/index.js.erb
+++ b/BrainPortal/app/views/userfiles/index.js.erb
@@ -26,4 +26,4 @@
 jQuery("#userfiles_display").html(<%= html_for_js(render(:partial => 'userfiles_display')) %>);
 jQuery("#userfiles_display").trigger("new_content");
 jQuery("#view_option_button").html(<%= html_for_js(render(:partial => 'view_option_button')) %>).trigger("new_content");
-jQuery("#userfiles_other_filters").html(<%= html_for_js(render(:partial => 'other_filters')) %>).trigger("new_content");
+jQuery("#userfiles_filters").html(<%= html_for_js(render(:partial => 'filters')) %>).trigger("new_content");
diff --git a/BrainPortal/public/stylesheets/cbrain.css b/BrainPortal/public/stylesheets/cbrain.css
index 2dd8502b7..65ee13df3 100644
--- a/BrainPortal/public/stylesheets/cbrain.css
+++ b/BrainPortal/public/stylesheets/cbrain.css
@@ -1924,39 +1924,19 @@ img {
 /* % Styles for Data Provider Report page */
 /* % ######################################################### */
 
-#data_provider_issues {
-  width: 100%;
-  margin-top: 10px;
-  border: 0;
-}
-
-#data_provider_issues td {
-  border: 1px solid gray;
-  border-width: 1px 0 0 0;
-}
-
-#data_provider_issues td.shrinkable {
-  display: table;
-  overflow: hidden;
-  table-layout: fixed;
-  text-overflow: ellipsis;
-  white-space: nowrap;
-  width: 100%;
-}
-
-#data_provider_issues tr.severity-trivial {
+#dp_report_table tr.severity-trivial {
   background-color: #c9f3f3;
 }
 
-#data_provider_issues tr.severity-minor {
+#dp_report_table tr.severity-minor {
   background-color: #cef9ce;
 }
 
-#data_provider_issues tr.severity-major {
+#dp_report_table tr.severity-major {
   background-color: #fff1e6;
 }
 
-#data_provider_issues tr.severity-critical {
+#dp_report_table tr.severity-critical {
   background-color: #ffd3d3;
 }
 

From 4e7790424151b7d85cad5ce5a6fd70cd99c049b8 Mon Sep 17 00:00:00 2001
From: Pierre Rioux <pierre.rioux@mcgill.ca>
Date: Mon, 28 Sep 2015 14:46:56 -0400
Subject: [PATCH 54/85] Added 'search for anything' feature

---
 .../app/controllers/portal_controller.rb      |  21 +++
 BrainPortal/app/models/admin_user.rb          |   4 +
 BrainPortal/app/models/normal_user.rb         |   4 +
 BrainPortal/app/models/site_manager.rb        |   4 +
 BrainPortal/app/models/user.rb                |   5 +
 .../app/views/layouts/_section_menu.html.erb  |  94 ++++++++------
 BrainPortal/app/views/portal/search.html.erb  | 120 ++++++++++++++++++
 .../config/initializers/validation_portal.rb  |   2 +-
 BrainPortal/config/routes.rb                  |   1 +
 BrainPortal/lib/models_report.rb              |  68 ++++++++++
 BrainPortal/public/stylesheets/cbrain.css     |   7 +
 11 files changed, 289 insertions(+), 41 deletions(-)
 create mode 100644 BrainPortal/app/views/portal/search.html.erb

diff --git a/BrainPortal/app/controllers/portal_controller.rb b/BrainPortal/app/controllers/portal_controller.rb
index 98f83570f..25d9d1e95 100644
--- a/BrainPortal/app/controllers/portal_controller.rb
+++ b/BrainPortal/app/controllers/portal_controller.rb
@@ -356,6 +356,27 @@ def report #:nodoc:
     @filter_show_proc  = (table_op =~ /sum.*size/) ? (Proc.new { |vector| colored_pretty_size(vector[0]) }) : nil
   end
 
+  # This action searches among all sorts of models for IDs or strings,
+  # and reports links to the matches found.
+  def search
+
+    @search = params[:search]
+    @limit  = 20 # used by interface only
+
+    results = @search.present? ? ModelsReport.search_for_token(@search, current_user) : {}
+
+    @users  = results[:users]  || []
+    @tasks  = results[:tasks]  || []
+    @groups = results[:groups] || []
+    @files  = results[:files]  || []
+    @rrs    = results[:rrs]    || []
+    @dps    = results[:dps]    || []
+    @sites  = results[:sites]  || []
+    @tools  = results[:tools]  || []
+    @tcs    = results[:tcs]    || []
+
+  end
+
   private
 
   def merge_vals_as_array(*sub_reports) #:nodoc:
diff --git a/BrainPortal/app/models/admin_user.rb b/BrainPortal/app/models/admin_user.rb
index 33cd10fab..05484c7d0 100644
--- a/BrainPortal/app/models/admin_user.rb
+++ b/BrainPortal/app/models/admin_user.rb
@@ -42,6 +42,10 @@ def available_users  #:nodoc:
     User.scoped
   end
 
+  def accessible_sites #:nodoc:
+    Site.scoped
+  end
+
   def visible_users #:nodoc:
     User.scoped
   end
diff --git a/BrainPortal/app/models/normal_user.rb b/BrainPortal/app/models/normal_user.rb
index b30acea9a..49268c443 100644
--- a/BrainPortal/app/models/normal_user.rb
+++ b/BrainPortal/app/models/normal_user.rb
@@ -43,6 +43,10 @@ def available_users  #:nodoc:
     User.where( :id => self.id )
   end
 
+  def accessible_sites #:nodoc:
+    Site.where( :id => (self.site_id || -1) )
+  end
+
   def visible_users #:nodoc:
     User.where("users.type <> 'AdminUser'")
   end
diff --git a/BrainPortal/app/models/site_manager.rb b/BrainPortal/app/models/site_manager.rb
index 98ec22d05..e322dc891 100644
--- a/BrainPortal/app/models/site_manager.rb
+++ b/BrainPortal/app/models/site_manager.rb
@@ -48,6 +48,10 @@ def available_users  #:nodoc:
     self.site.users
   end
 
+  def accessible_sites #:nodoc:
+    Site.where( :id => self.site_id )
+  end
+
   def visible_users #:nodoc:
     User.where("users.type <> 'AdminUser'")
   end
diff --git a/BrainPortal/app/models/user.rb b/BrainPortal/app/models/user.rb
index be44d288e..69e29fbc3 100644
--- a/BrainPortal/app/models/user.rb
+++ b/BrainPortal/app/models/user.rb
@@ -322,6 +322,11 @@ def available_users
     cb_error "#available_users called from User base class! Method must be implement in a subclass."
   end
 
+  # Return the list of sites accessible to the user
+  def accessible_sites
+    cb_error "#accessible_sites called from User base class! Method must be implement in a subclass."
+  end
+
   # Can this user be accessed by +user+?
   def can_be_accessed_by?(user, access_requested = :read) #:nodoc:
     return true if user.has_role? :admin_user
diff --git a/BrainPortal/app/views/layouts/_section_menu.html.erb b/BrainPortal/app/views/layouts/_section_menu.html.erb
index 73766d5b1..4b7d7efc1 100644
--- a/BrainPortal/app/views/layouts/_section_menu.html.erb
+++ b/BrainPortal/app/views/layouts/_section_menu.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 <http://www.gnu.org/licenses/>.  
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 -%>
 
@@ -27,10 +27,11 @@
 <!-- ********************* -->
 
 <div id="header">
+
   <h1>
     <%= link_to_if(current_user, RemoteResource.current_resource.name.presence || "CBRAIN", start_page_path) %>
     <% if current_user && current_project && !(params[:controller] == "groups" && params[:action] == "index") %>
-      - 
+      -
       <%= hover_dropdown(link_to(current_project.name, group_path(current_project)), :dropdown_class => "project_select_dropdown") do %>
         <div style="margin-right:0.2em">
           <% current_user.groups.where(:type => "WorkGroup", :invisible => false).limit(20).all.each do |g| %>
@@ -39,46 +40,59 @@
           <%= link_to "All Projects", {:controller => :groups, :action => :switch, :id  => "all"}, :method => :post %><br>
           <%= link_to "More Projects", groups_path %>
         </div>
-      <% end %>  
+      <% end %>
     <% end %>
     <%= yield(:title) %>
   </h1>
+
   <%= image_tag "ajax-loader.gif", :style => "display:none", :id => "loading_image" %>
-    <% if current_user %>
-      <div id="main-menu" class="main_menu_left">
-           <ul>
-             <% if !current_user.has_role?(:normal_user) || (current_session[:active_group_id] && !(params[:controller] == "groups" && params[:action] == "index")) %>
-               <li <%= set_selected(params[:controller], :userfiles) %>>
-                 <%= link_to 'Files', userfiles_path %>
-               </li>
-               <li <%= set_selected(params[:controller], :tasks) %>>
-                 <%= link_to 'Tasks', :controller => :tasks, :action => :index %>
-               </li>
-             <% end %>
-             <% unless current_user.has_role?(:normal_user) %>
-               <li <%= set_selected(params[:controller], :data_providers) %>>
-                 <%= link_to 'Data Providers', data_providers_path %>
-               </li>
-               <li <%= set_selected(params[:controller], :bourreaux) %>>
-                 <%= link_to 'Servers', bourreaux_path %>
-               </li>               
-               <li <%= set_selected(params[:controller], :tools) %>>
-                <%= link_to 'Tools', tools_path %>
-               </li>
-               <li <%= set_selected(params[:controller], :users) %>>
-                <%= link_to 'Users', users_path %>
-               </li>
-             <% end %>
-             <% if current_user.has_role?(:admin_user) %>
-               <li <%= set_selected(params[:controller], :sites) %>>
-                 <%= link_to 'Sites', sites_path %>
-               </li> 
-               <li <%= set_selected(params[:controller], :exception_logs) %>>
-                 <%= link_to 'Exceptions', exception_logs_path %>
-               </li> 
-             <% end %>
-           </ul>
-      </div>  <!-- End id="main_menu_left" -->
-  <% end %>  
-</div>   <!-- End id="header" -->   
+
+  <% if current_user && current_user.has_role?(:admin_user) &&
+     ! (params[:controller] == 'portal' && params[:action] == 'search') %>
+    <div id="cbsearch">
+      <%= form_tag search_path, :method => :get do %>
+        <%= text_field_tag :search, nil, :placeholder => 'Search for anything' %>
+      <% end %>
+    </div>
+  <% end %>
+
+  <% if current_user %>
+    <div id="main-menu" class="main_menu_left">
+       <ul>
+         <% if !current_user.has_role?(:normal_user) || (current_session[:active_group_id] && !(params[:controller] == "groups" && params[:action] == "index")) %>
+           <li <%= set_selected(params[:controller], :userfiles) %>>
+             <%= link_to 'Files', userfiles_path %>
+           </li>
+           <li <%= set_selected(params[:controller], :tasks) %>>
+             <%= link_to 'Tasks', :controller => :tasks, :action => :index %>
+           </li>
+         <% end %>
+         <% unless current_user.has_role?(:normal_user) %>
+           <li <%= set_selected(params[:controller], :data_providers) %>>
+             <%= link_to 'Data Providers', data_providers_path %>
+           </li>
+           <li <%= set_selected(params[:controller], :bourreaux) %>>
+             <%= link_to 'Servers', bourreaux_path %>
+           </li>
+           <li <%= set_selected(params[:controller], :tools) %>>
+            <%= link_to 'Tools', tools_path %>
+           </li>
+           <li <%= set_selected(params[:controller], :users) %>>
+            <%= link_to 'Users', users_path %>
+           </li>
+         <% end %>
+         <% if current_user.has_role?(:admin_user) %>
+           <li <%= set_selected(params[:controller], :sites) %>>
+             <%= link_to 'Sites', sites_path %>
+           </li>
+           <li <%= set_selected(params[:controller], :exception_logs) %>>
+             <%= link_to 'Exceptions', exception_logs_path %>
+           </li>
+         <% end %>
+       </ul>
+    </div>  <!-- End id="main_menu" -->
+
+  <% end %>
+
+</div>   <!-- End id="header" -->
 
diff --git a/BrainPortal/app/views/portal/search.html.erb b/BrainPortal/app/views/portal/search.html.erb
new file mode 100644
index 000000000..cd91b67fc
--- /dev/null
+++ b/BrainPortal/app/views/portal/search.html.erb
@@ -0,0 +1,120 @@
+
+<% title 'Search' %>
+
+<%= form_tag(search_path, :method => :get) do %>
+   <%= text_field_tag :search, @search.presence, :placeholder => "Search for anything" %>
+   <span class="field_explanation">This will search files, tasks, users, tools, projects, etc by name or description. <%= @limit %> results shown maximum.</span>
+<% end %>
+
+<% if [ @users, @tasks, @groups, @files, @rrs, @dps, @sites, @tools, @tcs ].any? { |var| var.present? } %>
+  <%# <h2>Results</h2> %>
+  <p>
+<% end %>
+
+<% [ :files, :tasks, :users, :groups, :rrs, :dps, :sites, :tools, :tcs ].each do |var| %>
+  <%
+     # Compute a @x_size variable for each result set, and truncate results to 20 entries max.
+     # Should be using reflexive interface instead of an eval, but oh well.
+     eval "
+       array        = @#{var}
+       @#{var}_size = array.size
+       @#{var}      = @#{var}[0,#{@limit}] if array.size > #{@limit}
+     "
+  %>
+<% end %>
+
+<% # this is used by array_to_table() below
+   tables_options = {
+     :rows            => 5,
+     :fill_by_columns => true,
+     :table_class     => "simple",
+     :td_class        => "left_align",
+   }
+%>
+
+<% if @files.present? %>
+  <h3>Files (found: <%= @files_size %>)</h3>
+  <%= array_to_table(@files, tables_options) do |file,r,c| %>
+     <%= link_to_userfile_if_accessible(file) %> (<%= file.user.login %>)
+  <% end %>
+<% end %>
+
+<% if @tasks.present? %>
+  <h3>Tasks (found: <%= @tasks_size %>)</h3>
+  <%= array_to_table(@tasks, tables_options) do |task,r,c| %>
+     <%= link_to_model_if_accessible(CbrainTask,task,:name_and_bourreau) %> (<%= task.user.login %>)
+     <%= link_to "(edit)", edit_task_path(task), :class => 'action_link' %><br>
+     <%= overlay_description(task.description, :header_width => 35) %>
+  <% end %>
+<% end %>
+
+<% if @users.present? %>
+  <h3>Users (found: <%= @users_size %>)</h3>
+  <%= array_to_table(@users, tables_options) do |user,r,c| %>
+     <%= user.full_name %> (<%= link_to_user_if_accessible(user) %>)
+     <%= link_to '(switch)', switch_user_path(user), :method  => :post, :class => 'action_link' if current_user.has_role?(:admin_user) %>
+  <% end %>
+<% end %>
+
+<% if @groups.present? %>
+  <h3>Projects (found: <%= @groups_size %>)</h3>
+  <%= array_to_table(@groups, tables_options) do |group,r,c| %>
+     <%= link_to_group_if_accessible(group) %> (<%= group.creator.try(:login) %>)
+     <%= link_to '(switch)', { :controller => :groups, :action => :switch, :id => group.id } , :method  => :post, :class => 'action_link' %>
+  <% end %>
+<% end %>
+
+<% if @rrs.present? %>
+  <h3>Execution Servers (found: <%= @rrs_size %>)</h3>
+  <%= array_to_table(@rrs, tables_options) do |rr,r,c| %>
+     <%= link_to_bourreau_if_accessible(rr) %>
+     <% task_count = current_user.cbrain_tasks.real_tasks.where(:bourreau_id => rr.id).count %>
+     <% if task_count > 0 %>
+       (<%= index_count_filter(task_count, :tasks,
+            { :user_id => current_user.id, :bourreau_id => rr.id}) %> tasks)
+     <% end %>
+  <% end %>
+<% end %>
+
+<% if @dps.present? %>
+  <h3>Data Providers (found: <%= @dps_size %>)</h3>
+  <%= array_to_table(@dps, tables_options) do |dp,r,c| %>
+     <%= link_to_data_provider_if_accessible(dp) %>
+     <%= link_to '(browse)', browse_data_provider_path(dp), :class => 'action_link' if dp.is_browsable? %>
+     <% file_count = current_user.userfiles.where(:data_provider_id => dp.id).count %>
+     <% if file_count > 0 %>
+       (<%= index_count_filter(file_count, :userfiles,
+            { :user_id => current_user.id, :data_provider_id => dp.id}) %> registered files)
+     <% end %>
+  <% end %>
+<% end %>
+
+<% if @sites.present? %>
+  <h3>Sites (found: <%= @sites_size %>)</h3>
+  <%= array_to_table(@sites, tables_options) do |site,r,c| %>
+     <%= link_to_site_if_accessible(site) %>
+  <% end %>
+<% end %>
+
+<% if @tools.present? %>
+  <h3>Tools (found: <%= @tools_size %>)</h3>
+  <%= array_to_table(@tools, tables_options) do |tool,r,c| %>
+    <% if current_user.has_role?(:admin_user) %>
+      <%= link_to tool.name, edit_tool_path(tool) %>
+    <%  else %>
+      <%= tool.name %>
+    <% end %>
+  <% end %>
+<% end %>
+
+<% if @tcs.present? %>
+  <h3>Tool Versions (found: <%= @tcs_size %>)</h3>
+  <%= array_to_table(@tcs, tables_options) do |tc,r,c| %>
+    <% if current_user.has_role?(:admin_user) %>
+      <%= tc.tool.name %>@<%= tc.bourreau.name%> : <%= link_to tc.version_name, edit_tool_config_path(tc) %>
+    <%  else %>
+      <%= tc.tool.name %>@<%= tc.bourreau.name%> : <%= tc.version_name %>
+    <% end %>
+  <% end %>
+<% end %>
+
diff --git a/BrainPortal/config/initializers/validation_portal.rb b/BrainPortal/config/initializers/validation_portal.rb
index 42469593c..2a358a893 100644
--- a/BrainPortal/config/initializers/validation_portal.rb
+++ b/BrainPortal/config/initializers/validation_portal.rb
@@ -72,7 +72,7 @@
   #
   # Rake Exceptions By First Argument
   #
-  skip_validations_for = [ /^db:/, /^cbrain:plugins/ ]
+  skip_validations_for = [ /^db:/, /^cbrain:plugins/, /^route/ ]
   if skip_validations_for.any? { |p| first_arg =~ p }
     #------------------------------------------------------------------------------
     puts "C> \t- No validations needed. Skipping."
diff --git a/BrainPortal/config/routes.rb b/BrainPortal/config/routes.rb
index d782dbef4..c0122e30d 100644
--- a/BrainPortal/config/routes.rb
+++ b/BrainPortal/config/routes.rb
@@ -156,6 +156,7 @@
   post  '/home'                   => 'portal#welcome' # lock/unlock service
   get   '/credits'                => 'portal#credits'
   get   '/about_us'               => 'portal#about_us'
+  get   '/search'                 => 'portal#search'
   get   '/login'                  => 'sessions#new'
   get   '/logout'                 => 'sessions#destroy'
   get   '/session_status'         => 'sessions#show'
diff --git a/BrainPortal/lib/models_report.rb b/BrainPortal/lib/models_report.rb
index 96ab104f0..84187896f 100644
--- a/BrainPortal/lib/models_report.rb
+++ b/BrainPortal/lib/models_report.rb
@@ -131,5 +131,73 @@ def self.rr_usage_statistics(options)
     stats
   end
 
+  # This method implements the 'search for anything' for the controller portal action +search+
+  # It's also used in the rails console's shortcuts.
+  #
+  # If +token+ looks like an ID, the models are searched by ID only.
+  # Otherwise, models are searched by name, version_name, description, etc.
+  #
+  # It returns a hash table with these keys:
+  #
+  #   {
+  #     :users  => [],  # array of User objects
+  #     :tasks  => [],  # CbrainTask objects
+  #     :groups => [],  # Group objects
+  #     :files  => [],  # Userfile objects
+  #     :rrs    => [],  # RemoteResource objects
+  #     :dps    => [],  # DataProvider objects
+  #     :sites  => [],  # Site objects
+  #     :tools  => [],  # Tool objects
+  #     :tcs    => [],  # ToolConfig objects
+  #   }
+  def self.search_for_token(token, user=current_user) #:nodoc:
+
+    token       = token.to_s.presence || "-999"
+    is_numeric  = token =~ /^\d+$/    || token == "-999"
+
+
+    file_scope  = Userfile      .find_all_accessible_by_user(user) .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)
+    tool_scope  = Tool          .find_all_accessible_by_user(user) .order(:name)
+    tc_scope    = ToolConfig    .find_all_accessible_by_user(user) .order(:tool_id)
+
+    # For the next three, wow: 'available' and 'accessible' have reverse meaning!
+    # 'available' means user can modify them, 'accessible' means they can only view.
+    user_scope  = user.available_users  .order(:login)
+    group_scope = user.available_groups .order(:name)
+    site_scope  = user.accessible_sites .order(:name)
+
+    results = if (is_numeric)
+      {
+        :users  => Array(user_scope  .find_by_id(token)) ,
+        :tasks  => Array(task_scope  .find_by_id(token)) ,
+        :groups => Array(group_scope .find_by_id(token)) ,
+        :files  => Array(file_scope  .find_by_id(token)) ,
+        :rrs    => Array(rr_scope    .find_by_id(token)) ,
+        :dps    => Array(dp_scope    .find_by_id(token)) ,
+        :sites  => Array(site_scope  .find_by_id(token)) ,
+        :tools  => Array(tool_scope  .find_by_id(token)) ,
+        :tcs    => Array(tc_scope    .find_by_id(token)) ,
+      }
+    else
+      ptoken = "%#{token}%"
+      {
+        :users  => user_scope  .where( [ "login like ? OR full_name like ? OR email like ?", ptoken, ptoken, ptoken ] ).all ,
+        :tasks  => task_scope  .where( [ "description like ?"                              , ptoken                 ] ).all ,
+        :groups => group_scope .where( [ "name like ?"                                     , ptoken                 ] ).all ,
+        :files  => file_scope  .where( [ "name like ? OR description like ?"               , ptoken, ptoken         ] ).all ,
+        :rrs    => rr_scope    .where( [ "name like ? OR description like ?"               , ptoken, ptoken         ] ).all ,
+        :dps    => dp_scope    .where( [ "name like ? OR description like ?"               , ptoken, ptoken         ] ).all ,
+        :sites  => site_scope  .where( [ "name like ? OR description like ?"               , ptoken, ptoken         ] ).all ,
+        :tools  => tool_scope  .where( [ "name like ? OR description like ?"               , ptoken, ptoken         ] ).all ,
+        :tcs    => tc_scope    .where( [ "version_name like ? OR description like ?"       , ptoken, ptoken         ] ).all ,
+      }
+    end
+
+    results
+  end
+
 end
 
diff --git a/BrainPortal/public/stylesheets/cbrain.css b/BrainPortal/public/stylesheets/cbrain.css
index 2dd8502b7..4f05c651e 100644
--- a/BrainPortal/public/stylesheets/cbrain.css
+++ b/BrainPortal/public/stylesheets/cbrain.css
@@ -971,6 +971,13 @@ pre {
   padding: 0;
 }
 
+#cbsearch {
+      padding: 1em 1em 0 0;
+      text-align: right;
+      float: right;
+      vertical-align: top;
+}
+
 #main-menu {
   position: absolute;
   bottom: 0px;

From b9f4d08ea1085f779f1860b0831f886a531b2c7f Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Mon, 28 Sep 2015 16:09:15 -0400
Subject: [PATCH 55/85] Fix for custom filters + scopes available filters bug

The available filters now recognize (somewhat) the presence of custom
filters and the filter menus are populated as expected. Note that this
fix relies on undo_where, and will probably bring back issue #125, which
would've been fixed by relying purely on Scope objects.

This changeset can be reverted once custom filters are ported to the
Scope API, which will let filter_values_for remove the corresponding
filter without having to rely on undo_where (provided it is enhanced to
allow using multiple Scope objects).
---
 BrainPortal/app/helpers/scope_helper.rb                  | 9 ++++++++-
 .../relation_extensions/undo_where.rb                    | 3 ++-
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/BrainPortal/app/helpers/scope_helper.rb b/BrainPortal/app/helpers/scope_helper.rb
index 5da5eb26a..6b25b7703 100644
--- a/BrainPortal/app/helpers/scope_helper.rb
+++ b/BrainPortal/app/helpers/scope_helper.rb
@@ -572,9 +572,16 @@ def model_filter_values(model, attribute, label, association: nil, scope: nil)
     # as +attribute+.
     label_alias = model.connection.quote_column_name('label')
 
+    # FIXME: undo_where is somewhat hacky and not exactly correct sometimes, but
+    # it is still required as some filters (custom filters) are still applied
+    # directly (without a Scope) and cannot be easily removed. Ideally, those
+    # filters should be ported to the Scope API and filter_values_for should
+    # accept a collection of scope objects to generate the separate counts with.
+    bare_model = model.undo_where(attribute)
+
     # Fetch the main filter values as an array of arrays:
     # [[value, label, count], [...]]
-    filters = model
+    filters = bare_model
       .where("#{attribute} IS NOT NULL")
       .order(label, attribute)
       .group(attribute, label)
diff --git a/BrainPortal/lib/cbrain_extensions/active_record_extensions/relation_extensions/undo_where.rb b/BrainPortal/lib/cbrain_extensions/active_record_extensions/relation_extensions/undo_where.rb
index c1f22a718..859e5c4e7 100644
--- a/BrainPortal/lib/cbrain_extensions/active_record_extensions/relation_extensions/undo_where.rb
+++ b/BrainPortal/lib/cbrain_extensions/active_record_extensions/relation_extensions/undo_where.rb
@@ -54,7 +54,8 @@ def undo_where(*args)
 
           to_reject = {} #  "tab1.col1" => true, "tab1.col2" => true etc...
           args.map do |colspec|  #  "col" or "table.col"
-            raise "Invalid column specification \"#{colspec}\"." unless colspec.to_s =~ /^((\w+)\.)?(\w+)$/
+            raise "Invalid column specification \"#{colspec}\"." unless
+              colspec.to_s =~ /^(\`?(\w+)\`?\.)?\`?(\w+)\`?$/
             tab = Regexp.last_match[2].presence || mytable
             col = Regexp.last_match[3]
             to_reject["#{tab}.#{col}"] = true

From e2b1c2208d0609b38a2d2dc51fcbeb650d9ef893 Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Fri, 2 Oct 2015 14:51:23 -0400
Subject: [PATCH 56/85] Dual-count (AR relation/Scope) filters

Final (hopefully) implementation of scoped/dual-count filters, to
restore the missing functionality from the old filtering system. This
new implementation also fixes two bugs related to filtering and
undo_where (as it is no longer used for filters and will be refactored
out in a later commit), and allows for future expansion by supporting
both Scope-based filtering (on one or more Scopes) and classical AR
filtering.

This changeset also fixes a minor bug where custom filters could not be
removed by the 'clear' link.
---
 .../app/controllers/tasks_controller.rb       |   8 +-
 .../app/controllers/userfiles_controller.rb   |   7 +-
 BrainPortal/app/helpers/scope_helper.rb       | 353 +++++++++++-------
 .../messages/_message_index_display.html.erb  |  30 +-
 .../app/views/shared/_active_filters.html.erb |   9 +-
 .../app/views/tasks/_tasks_display.html.erb   |  12 +-
 .../userfiles/_userfiles_display.html.erb     |   8 +-
 7 files changed, 261 insertions(+), 166 deletions(-)

diff --git a/BrainPortal/app/controllers/tasks_controller.rb b/BrainPortal/app/controllers/tasks_controller.rb
index 745cdc3bf..18d5f4334 100644
--- a/BrainPortal/app/controllers/tasks_controller.rb
+++ b/BrainPortal/app/controllers/tasks_controller.rb
@@ -42,10 +42,10 @@ def index #:nodoc:
     end
 
     @scope.pagination ||= Scope::Pagination.from_hash({ :per_page => 25 })
-    @base_scope = custom_scope(user_scope(
-      current_user.available_tasks.includes([:bourreau, :user, :group])
-    ))
-    @view_scope = @scope.apply(@base_scope)
+    @base_scope   = user_scope(current_user.available_tasks)
+      .includes([:bourreau, :user, :group])
+    @custom_scope = custom_scope(@base_scope)
+    @view_scope   = @scope.apply(@custom_scope)
 
     # Display totals
     @total_tasks       = @view_scope.count
diff --git a/BrainPortal/app/controllers/userfiles_controller.rb b/BrainPortal/app/controllers/userfiles_controller.rb
index 38b012ced..cdfb64947 100644
--- a/BrainPortal/app/controllers/userfiles_controller.rb
+++ b/BrainPortal/app/controllers/userfiles_controller.rb
@@ -53,10 +53,9 @@ def index #:nodoc:
 
     # Apply basic and @scope-based scoping
     scope_default_order(@scope, 'name')
-    @base_scope = custom_scope(
-      base_scope.includes([:user, :data_provider, :sync_status, :tags, :group])
-    )
-    @view_scope = @scope.apply(@base_scope)
+    @base_scope   = base_scope.includes([:user, :data_provider, :sync_status, :tags, :group])
+    @custom_scope = custom_scope(@base_scope)
+    @view_scope   = @scope.apply(@custom_scope)
 
     # Generate tag filters
     tag_counts   = @view_scope.joins(:tags).group('tags.name').count
diff --git a/BrainPortal/app/helpers/scope_helper.rb b/BrainPortal/app/helpers/scope_helper.rb
index 6b25b7703..0c89a0a31 100644
--- a/BrainPortal/app/helpers/scope_helper.rb
+++ b/BrainPortal/app/helpers/scope_helper.rb
@@ -339,21 +339,6 @@ def pretty_scope_filter(filter, model: nil)
   #  filter values but without having to unpack the +DynamicTable+'s filter
   #  format hash.
   #
-  # [scope]
-  #  Generate a separate set of filter value counts (how many times a given
-  #  filter value is found) for +collection+ when scoped under +scope+. For
-  #  example, if a given userfile collection has 30 TextFiles out of 40 and
-  #  10 of those 30 belong to a given user, the unscoped TextFile filter count
-  #  would be 30 and the user-scoped count 10. When this option is specified,
-  #  +format+ takes a fourth argument; the corresponding scoped count, and,
-  #  if +format+ is unspecified, the two counts (normal and scoped) are appended
-  #  to the default label value. For example, in the above TextFile example,
-  #  the label would look like 'TextFile (10/30)'.
-  #
-  #  Note that any Filter filtering on +attribute+ in +scope+ will be skipped to
-  #  avoid generating empty filter values (while this behavior is
-  #  counter-intuitive and clunky, it is required for table filtering).
-  #
   #  NOTE: The filters generated by this method are commonly used with the Scope
   #  and DynamicTable APIs, which impose an hidden restriction on the values
   #  that can be taken for +attribute+'s values; they must be safely
@@ -361,28 +346,18 @@ def pretty_scope_filter(filter, model: nil)
   #  types with the notable exception of Symbols. If +attribute+'s values are
   #  symbols, consider converting them the resulting filter values to strings
   #  before using them to construct filtering URLs.
-  def filter_values_for(collection, attribute, label: nil, association: nil, format: nil, scope: nil)
+  def filter_values_for(collection, attribute, label: nil, association: nil, format: nil)
     return [] if collection.blank?
 
-    # Remove any +attribute+ filter on +scope+
-    if scope
-      scope = scope.dup
-      scope.filters.reject! do |f|
-        f.attribute.to_s.downcase == attribute.to_s.downcase
-      end
-    end
-
     # Invoke the model/collection specific method
     if (collection <= ActiveRecord::Base rescue nil)
-      filters = model_filter_values(
+      filters = ScopeHelper.model_filter_values(
         collection, attribute, label,
-        association: association,
-        scope: scope
+        association: association
       )
     else
-      filters = collection_filter_values(
-        collection, attribute, label,
-        scope: scope
+      filters = ScopeHelper.collection_filter_values(
+        collection, attribute, label
       )
     end
 
@@ -390,66 +365,204 @@ def filter_values_for(collection, attribute, label: nil, association: nil, forma
     return filters.map(&format) if format
 
     # Format the generated filter arrays as DynamicTable's filter hashes
-    filters.map do |value, label, count, *rest|
-      scoped = rest.first
-      label  = "#{label} (of #{count})" if scoped
+    filters.map do |value, label, count|
       {
         :value     => value,
         :label     => label,
-        :indicator => scoped || count,
-        :empty     => (scoped || count) == 0
+        :indicator => count,
+        :empty     => count == 0
       }
     end
   end
 
-  # Fetch the possible values for +attribute+ within +collection+.
-  # A simple wrapper around +filter_values_for+, this method offers a set
-  # of commonly used defaults to +filter_values_for+ when generating simple
+  # Fetch the possible filtering values for +attribute+ (symbol or string)
+  # within +base+, viewed through +view+. +base+ is expected to be either an
+  # ActiveRecord model (or scope) or Ruby Enumerable, while +view+ is expected
+  # to be either the same type as +base+ or one or more Scope objects. This
+  # method generates filtering values (similarly to +filter_values_for+),
+  # considering +view+ as a filtered version of +base+ and counting possible
+  # values in both.
+  #
+  # For example, if +base+ is the Userfiles model containing TextFiles, CSVFiles
+  # and MincFiles and +view+ is a scope of base with just a few CSVFiles and
+  # MincFiles, +scoped_filters_for+ one could have:
+  #   scoped_filters_for(base, view, :type) # =>
+  #   [
+  #     { :value => 'TextFile', :indicator => 0, :label => '... (of 30)', ... },
+  #     { :value => 'CSVFile',  :indicator => 9, :label => '... (of 10)', ... },
+  #     { :value => 'MincFile', :indicator => 3, :label => '... (of 53)', ... },
+  #   ]
+  #
+  # This method accepts the following optional (named) arguments:
+  # [scope]
+  #  One or more Scope objects to add on top of +view+, when +view+ isn't a
+  #  collection of Scopes already.
+  #
+  # [label]
+  #  Handled the same way as +filter_values_for+'s own +label+ parameter. Note
+  #  that this includes the 'name' default if +attribute+ is nil and
+  #  +association+ is specified.
+  #
+  # [association]
+  #  Handled the same way as +filter_values_for+'s own +association+ parameter.
+  #
+  # [format]
+  #  Lambda (or proc) to format the filter list with. Similar in behavior and
+  #  handled the same way as +filter_values_for+'s own +format+ argument. The
+  #  only difference between this method's +format+ and +filter_values_for+'s
+  #  is a fourth argument, the possible value count under +view+.
+  #  The arguments given to +format+ are thus: value, label, base count and
+  #  view count.
+  #
+  # [strip_filters]
+  #  Remove any Filter filtering on +attribute+ in all given Scope instances
+  #  before applying them to +view+ (and generating filter counts). This avoids
+  #  generating almost-empty filters (only a single value would have a count
+  #  higher than 0). Defaults to active (true).
+  #
+  # Note that if Scope objects are supplied, any of their Filters filtering on
+  # +attribute+ will be removed to avoid generating empty filters values unless
+  # the +strip_filters+ argument is specified as false.
+  #
+  # Also note that this method shares +filter_values_for+'s special
+  # interaction between +association+ and +attribute+; if +association+ is
+  # specified and +attribute+ is nil, +attribute+ is taken as +base+'s
+  # foreign key on +association+ (see +filter_values_for+'s +association+
+  # parameter for more information).
+  def scoped_filters_for(base, view, attribute, scope: nil, label: nil, association: nil, format: nil, strip_filters: true)
+    # Handle +filter_values_for+'s special case where +attribute+ is nil and
+    # corresponds to +base+'s foreign key for +association+
+    attribute, label, association = ScopeHelper.find_assoc_key(base, association, label) if
+      ! attribute && association
+
+    # Normalize +attribute+ to a lower-case string, as per Scope API conventions
+    attribute = attribute.to_s.downcase
+
+    # Normalize the scopes in +view+ and +scope+ into just scopes
+    scopes = scope || []
+    scopes = [scopes] unless scopes.is_a?(Enumerable)
+
+    if view.is_a?(Scope) || (view.is_a?(Enumerable) && view.all? { |v| v.is_a?(Scope) })
+      scopes += Array(view)
+      view = base
+    end
+
+    # Filter out +attribute+ filters, if theres any (and strip_filters
+    # is enabled)
+    scopes.map! do |scope|
+      next scope unless scope.filters.map(&:attribute).include?(attribute)
+
+      scope = scope.dup
+      scope.filters.reject! { |f| f.attribute == attribute }
+
+      scope
+    end if strip_filters
+
+    # Generate the base filter set, with all possible values for +attribute+ in
+    # +base+
+    filters = filter_values_for(
+      base, attribute, label: label,
+      association: association,
+      format: lambda { |x| x }
+    )
+
+    # Generate another filter set under +view+ (and all given scopes), as a
+    # hash (<value> => [<filter>]) and append the generated counts to each
+    # value in the base filter set
+    view_filters = filter_values_for(
+      scopes.inject(view) { |v, s| s.apply(v) },
+      attribute,
+      association: association,
+      format: lambda { |x| x }
+    ).index_by { |f| f.first }
+
+    filters.each { |f| f << (view_filters[f.first].last rescue 0) }
+
+    # Use the specified +format+ if there is one
+    return filters.map(&format) if format
+
+    # Otherwise format the generated filter arrays as DynamicTable's filter
+    # hashes, just like +filter_values_for+'s default format.
+    filters.map do |value, label, base, view|
+      {
+        :value     => value,
+        :label     => "#{label} (of #{base})",
+        :indicator => view,
+        :empty     => view == 0
+      }
+    end
+  end
+
+  # Fetch the possible values for an +attribute+ within a given +collection+,
+  # optionally filtered under +view+. There are two ways to invoke
+  # +default_filters_for+:
+  #   default_filters_for(collection, attribute)
+  # and:
+  #   default_filters_for(collection, view, attribute)
+  # depending on whether or not +view+ is set.
+  # A simple wrapper around +filter_values_for+ and +scoped_filters_for+, this
+  # method offers a set of commonly used defaults when generating simple
   # attribute filters.
   #
-  # +collection+ and +attribute+ are passed directly to +filter_values_for+,
-  # with one exception; if both +collection+ and +attribute+ are AR models
-  # (or scopes), +default_filters_for+ will pass +attribute+ as an association
-  # on +collection+ instead:
+  # +collection+ and +attribute+ are passed directly to +filter_values_for+ or
+  # +scoped_filters_for+, with one exception; if both +collection+ and
+  # +attribute+ are AR models (or scopes), +default_filters_for+ will pass
+  # +attribute+ as an association on +collection+ instead:
   #   default_filters_for(some_scope, SomeModel)
   # corresponds to:
   #   filter_values_for(scope_scope, nil, association: SomeModel)
   #
   # For more information on how filter values are generated,
-  # see +filter_values_for+.
-  def default_filters_for(collection, attribute)
+  # see +filter_values_for+ and +scoped_filters_for+.
+  def default_filters_for(*args)
     # Generate a formatting lambda which will call +block+ to format a filter
     # value's label.
     formatter = lambda do |block|
       return unless block
 
       lambda do |args|
-        value, label, count, scoped = args
+        value, label, base, view = args
         label = block.(label) rescue label
-        label = "#{label} (of #{count})" if scoped
+        label = "#{label} (of #{base})" if view
         {
           :value     => value,
           :label     => label,
-          :indicator => scoped || count,
-          :empty     => (scoped || count) == 0
+          :indicator => view || base,
+          :empty     => (view || base) == 0
         }
       end
     end
 
+    # Unpack args, respecting the possible ways to call +default_filters_for+
+    collection = args.shift
+    attribute  = args.pop
+    view       = args.first
+
+    # Pre-set some defaults
+    is_assoc = attribute <= ActiveRecord::Base rescue nil
+    label  = 'login' if is_assoc && attribute <= User
+    format = formatter.((
+      proc { |l| l.constantize.pretty_type } if
+        attribute.to_s.downcase == 'type'
+    )) unless is_assoc
+
+    # Invoke +filter_values_for+ or +scoped_filters_for+ to generate the actual
+    # filters, depending or whether or not a scope/view has been specified.
     filters = (
-      # Is +attribute+ an association?
-      if (attribute <= ActiveRecord::Base rescue nil)
-        filter_values_for(collection, nil, association: attribute,
-          scope: @scope,
-          label: ('login' if attribute <= User)
+      if view || @scope
+        scoped_filters_for(
+          collection, (view || collection), (attribute unless is_assoc),
+          association: (attribute if is_assoc),
+          scope:  @scope,
+          label:  label,
+          format: format
         )
       else
-        filter_values_for(collection, attribute,
-          scope:  @scope,
-          format: formatter.((
-            proc { |l| l.constantize.pretty_type } if
-              attribute.to_s.downcase == 'type'
-          ))
+        filter_values_for(
+          collection, (attribute unless is_assoc),
+          association: (attribute if is_assoc),
+          label:  label,
+          format: format
         )
       end
     )
@@ -529,33 +642,16 @@ def generic_scope_link(label, url, options)
   # Fetch the possible values (and their count) for +attribute+ within +model+,
   # an ActiveRecord model. Internal model-specific implementation of
   # +filter_values_for+ for AR models; see +filter_values_for+ for more
-  # information on this method's arguments (which are handled just like
-  # +filter_values_for+'s, save for +scope+).
+  # information on this method's arguments.
   #
   # Note that the filter values returned by this method are in array format,
-  # ([value, label, count, (scoped_count)]) as this method is intended for
-  # internal use by +filter_values_for+ which will perform final formatting.
-  def model_filter_values(model, attribute, label, association: nil, scope: nil)
+  # ([value, label, count]) as this method is intended for internal use by
+  # +filter_values_for+ which will perform final formatting.
+  def self.model_filter_values(model, attribute, label, association: nil)
     # Handle the special case where +attribute+ is nil and corresponds to
     # +model+'s foreign key for +association+
-    if ! attribute && association
-      # Find the matching +association+ reflection on +model+
-      assoc = association.respond_to?(:klass) ? association.klass : association
-      reflection = model
-        .reflect_on_all_associations
-        .find { |r| r.klass == assoc }
-      raise "no associations on '#{model.table_name}' matching '#{assoc.table_name}'" unless
-        reflection
-
-      # Use +association+'s reflection to set missing argument values
-      attribute   = reflection.foreign_key
-      label       = "#{reflection.table_name}.#{label || 'name'}"
-      association = [
-        assoc,
-        reflection.association_primary_key,
-        reflection.association_foreign_key
-      ]
-    end
+    attribute, label, association = ScopeHelper.find_assoc_key(base, association, label) if
+      ! attribute && association
 
     # Resolve and validate the main +attribute+ to fetch the values of
     attribute, model = ViewScopes.resolve_model_attribute(attribute, model, association)
@@ -572,16 +668,9 @@ def model_filter_values(model, attribute, label, association: nil, scope: nil)
     # as +attribute+.
     label_alias = model.connection.quote_column_name('label')
 
-    # FIXME: undo_where is somewhat hacky and not exactly correct sometimes, but
-    # it is still required as some filters (custom filters) are still applied
-    # directly (without a Scope) and cannot be easily removed. Ideally, those
-    # filters should be ported to the Scope API and filter_values_for should
-    # accept a collection of scope objects to generate the separate counts with.
-    bare_model = model.undo_where(attribute)
-
     # Fetch the main filter values as an array of arrays:
     # [[value, label, count], [...]]
-    filters = bare_model
+    model
       .where("#{attribute} IS NOT NULL")
       .order(label, attribute)
       .group(attribute, label)
@@ -589,61 +678,67 @@ def model_filter_values(model, attribute, label, association: nil, scope: nil)
       .reject { |r| r.first.blank? }
       .map(&:to_a)
       .to_a
-
-    # No +scope+? Then +filters+ is ready
-    return filters unless scope
-
-    # Add in the scoped counts
-    scoped = scope.apply(model)
-      .where("#{attribute} IS NOT NULL")
-      .group(attribute)
-      .raw_rows(attribute, "COUNT(#{attribute})")
-      .to_h
-
-    filters.map { |f| f << (scoped[f.first] || 0) }
   end
 
   # Fetch the possible values (and their count) for +attribute+ within
   # +collection+, a generic Ruby collection. Internal collection-specific
   # implementation of +filter_values_for+ for Ruby collections; see
-  # +filter_values_for+ for more information on this method's arguments
-  # (which are handled just like +filter_values_for+'s, save for +scope+).
+  # +filter_values_for+ for more information on this method's arguments.
   #
   # Note that the filter values returned by this method are in array format,
-  # ([value, label, count, (scoped_count)]) as this method is intended for
-  # internal use by +filter_values_for+ which will perform final formatting.
-  def collection_filter_values(collection, attribute, label, scope: nil)
+  # ([value, label, count]) as this method is intended for internal use by
+  # +filter_values_for+ which will perform final formatting.
+  def self.collection_filter_values(collection, attribute, label)
     # Make sure +attribute+ and +label+ can be accessed in
     # +collection+'s items.
     attr_get = ViewScopes.generate_getter(collection.first, attribute)
     raise "no way to get '#{attribute}' out of collection items" unless attr_get
 
-    if label == attribute
-      lbl_get = attr_get
-    else
-      lbl_get = ViewScopes.generate_getter(collection.first, label || attribute)
+    if label && label != attribute
+      lbl_get = ViewScopes.generate_getter(collection.first, label)
       raise "no way to get '#{label}' out of collection items" unless lbl_get
+    else
+      lbl_get = attr_get
     end
 
-    # Generate the main filter values as a hash; [value, label] => count
-    count_values = lambda do |collection|
-      collection
-        .map     { |i| [attr_get.(i), lbl_get.(i)].freeze }
-        .reject  { |v, l| v.blank? }
-        .sort_by { |v, l| l }
-        .inject(Hash.new(0)) { |h, i| h[i] += 1; h }
-    end
-
-    filters = count_values.(collection)
+    # Generate the main filter values as an array of arrays:
+    # [[value, label, count], [...]]
+    collection
+      .map     { |i| [attr_get.(i), lbl_get.(i)].freeze }
+      .reject  { |v, l| v.blank? }
+      .sort_by { |v, l| l }
+      .inject(Hash.new(0)) { |h, i| h[i] += 1; h }
+      .map     { |(v, l), c| [v, l, c] }
+  end
 
-    # Add in the scoped counts, if required, then flatten the hash into
-    # array format
-    if scope
-      scoped = count_values.(scope.apply(collection))
-      filters.map { |i, c| [*i, c, scoped[i] || 0] }
-    else
-      filters.map { |(v, l), c| [v, l, c] }
-    end
+  # Find the first association/relation on +model+ matching +association+,
+  # if it exists, and return, as an array;
+  # - The foreign key between +model+ and +association+,
+  # - A qualified +label+ column name for the association (defaults to 'name'),
+  # - A fully qualified association specification (assoc and join columns)
+  # This array format directly corresponds to +scoped_filters_for+ and
+  # +filter_values_for+'s attribute, label and association parameters.
+  #
+  # Internal method to implement +scoped_filters_for+ and +filter_values_for+'s
+  # special +attribute+-is-nil handling.
+  def self.find_assoc_key(model, association, label = nil)
+    # Find the matching +association+ reflection on +model+
+    association = association.klass if association.respond_to?(:klass)
+    reflection  = model
+      .reflect_on_all_associations
+      .find { |r| r.klass == association }
+    raise "no associations on '#{model.table_name}' matching '#{association.table_name}'" unless
+      reflection
+
+    [
+      reflection.foreign_key,
+      "#{reflection.table_name}.#{label || 'name'}",
+      [
+        association,
+        reflection.association_primary_key,
+        reflection.association_foreign_key
+      ]
+    ]
   end
 
   # Deprecated/old methods
diff --git a/BrainPortal/app/views/messages/_message_index_display.html.erb b/BrainPortal/app/views/messages/_message_index_display.html.erb
index 84d5f443a..88c11e68c 100644
--- a/BrainPortal/app/views/messages/_message_index_display.html.erb
+++ b/BrainPortal/app/views/messages/_message_index_display.html.erb
@@ -100,16 +100,15 @@
       t.column("&#9888;".html_safe, :critical,
         :pretty_name => 'Critical',
         :hidden      => true,
-        :filters     => filter_values_for(
-          @base_scope, :critical,
-          scope:  @scope,
-          format: lambda do |value, label, count, scoped|
+        :filters     => scoped_filters_for(
+          @base_scope, @scope, :critical,
+          format: lambda do |value, label, base, view|
             label = (! value || value == 0) ? 'Not critical' : 'Critical'
             {
               :value     => value,
-              :label     => "#{label} (of #{count})",
-              :indicator => scoped,
-              :empty     => scoped == 0
+              :label     => "#{label} (of #{base})",
+              :indicator => view,
+              :empty     => view == 0
             }
           end
         )
@@ -118,15 +117,14 @@
       t.column("Type", :message_type,
         :hidden   => true,
         :sortable => true,
-        :filters  => filter_values_for(
-          @base_scope, :message_type,
-          scope:  @scope,
-          format: lambda do |value, label, count, scoped|
+        :filters  => scoped_filters_for(
+          @base_scope, @scope, :message_type,
+          format: lambda do |value, label, base, view|
             {
               :value     => value,
-              :label     => "#{label.humanize} (of #{count})",
-              :indicator => scoped,
-              :empty     => scoped == 0
+              :label     => "#{label.humanize} (of #{base})",
+              :indicator => view,
+              :empty     => view == 0
             }
           end
         )
@@ -145,9 +143,8 @@
         :sortable => true,
         :filters  => filter_values_for(
           @base_scope, :sender_id,
-          scope: @scope,
           label: 'users.login',
-          association: [User, 'id', 'sender_id'],
+          association: [User, 'id', 'sender_id']
         ) + [{
           :value     => nil,
           :label     => 'System',
@@ -161,7 +158,6 @@
         :sortable => true,
         :filters  => filter_values_for(
           @base_scope, :user_id,
-          scope: @scope,
           label: 'users.login',
           association: [User, 'id', 'user_id']
         )
diff --git a/BrainPortal/app/views/shared/_active_filters.html.erb b/BrainPortal/app/views/shared/_active_filters.html.erb
index 922e353fb..8335ab4c1 100644
--- a/BrainPortal/app/views/shared/_active_filters.html.erb
+++ b/BrainPortal/app/views/shared/_active_filters.html.erb
@@ -32,8 +32,13 @@
   <span class="active_status_left_side">
     <span class="active_label">Active Filters</span>
     (<%=
-      scope_filter_link('clear',
-        scope, :clear, nil,
+      empty = scope.dup
+      empty.filters.clear
+      empty.custom[:custom_filters] = [] if
+        empty.custom.has_key?(:custom_filters)
+
+      scope_link('clear',
+        scope.name, empty.to_hash,
         link: { :ajax => true }
       )
     %>)
diff --git a/BrainPortal/app/views/tasks/_tasks_display.html.erb b/BrainPortal/app/views/tasks/_tasks_display.html.erb
index ff03c9897..d80b14754 100644
--- a/BrainPortal/app/views/tasks/_tasks_display.html.erb
+++ b/BrainPortal/app/views/tasks/_tasks_display.html.erb
@@ -125,7 +125,7 @@
   <%
     t.column("Task Type", :type,
       :sortable => true,
-      :filters  => default_filters_for(@base_scope, :type)
+      :filters  => default_filters_for(@base_scope, @custom_scope, :type)
     ) do |type,id,count,task|
   %>
     <% case type %>
@@ -146,22 +146,22 @@
 
     t.column("Owner", :owner,
       :sortable => true,
-      :filters  => default_filters_for(@base_scope, User)
+      :filters  => default_filters_for(@base_scope, @custom_scope, User)
     ) do |type,id,count,task|
       link_to_user_if_accessible(task.user) unless type == :loaded_batch
     end
 
     t.column("Project", :project,
       :sortable => true,
-      :filters  => default_filters_for(@base_scope, Group)
+      :filters  => default_filters_for(@base_scope, @custom_scope, Group)
     ) do |type,id,count,task|
       link_to_group_if_accessible(task.group) unless type == :loaded_batch
     end unless current_project
 
     t.column("Execution Server", :server,
       :sortable => true,
-      :filters  => filter_values_for(
-        @base_scope, :bourreau_id,
+      :filters  => scoped_filters_for(
+        @base_scope, @custom_scope, :bourreau_id,
         scope: @scope,
         label: 'remote_resources.name',
         association: [Bourreau, 'id', 'bourreau_id']
@@ -174,7 +174,7 @@
   <%
     t.column("Current Status", :status,
       :sortable => true,
-      :filters  => default_filters_for(@base_scope, :status)
+      :filters  => default_filters_for(@base_scope, @custom_scope, :status)
     ) do |type,id,count,task|
   %>
     <%
diff --git a/BrainPortal/app/views/userfiles/_userfiles_display.html.erb b/BrainPortal/app/views/userfiles/_userfiles_display.html.erb
index ddc565f80..38e353900 100644
--- a/BrainPortal/app/views/userfiles/_userfiles_display.html.erb
+++ b/BrainPortal/app/views/userfiles/_userfiles_display.html.erb
@@ -115,12 +115,12 @@
     t.column("File Type", :type,
       :field_name => :pretty_type,
       :sortable   => true,
-      :filters    => default_filters_for(@base_scope, :type)
+      :filters    => default_filters_for(@base_scope, @custom_scope, :type)
     )
 
     t.column("Owner", :login,
       :sortable => true,
-      :filters  => default_filters_for(@base_scope, User)
+      :filters  => default_filters_for(@base_scope, @custom_scope, User)
     ) { |u| link_to_user_if_accessible(u.user) }
 
     t.column("Creation Date", :creation_date,
@@ -185,7 +185,7 @@
     unless current_project
       t.column("Project", :group,
         :sortable => true,
-        :filters  => default_filters_for(@base_scope, Group)
+        :filters  => default_filters_for(@base_scope, @custom_scope, Group)
       ) do |u|
         link_to_group_if_accessible(u.group) if u.group
       end
@@ -199,7 +199,7 @@
 
     t.column("Provider", :data_provider,
       :sortable => true,
-      :filters  => default_filters_for(@base_scope, DataProvider)
+      :filters  => default_filters_for(@base_scope, @custom_scope, DataProvider)
     ) do |u|
       link_to_data_provider_if_accessible(u.data_provider)
     end

From 4e4c71f6a5228a379a06bd5cd665bc5d97211a6b Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Fri, 2 Oct 2015 15:13:59 -0400
Subject: [PATCH 57/85] Removal of undo_where.rb

undo_where was mainly used for computing filter counts, and was causing
subtle bugs. As this functionality has been completely replaced as of
the last commit, this changeset removes undo_where and refactors the
only other place it was in use (userfiles controller, for view_hidden).
---
 .../app/controllers/userfiles_controller.rb   |  11 +-
 .../relation_extensions/undo_where.rb         | 101 ------------------
 2 files changed, 7 insertions(+), 105 deletions(-)
 delete mode 100644 BrainPortal/lib/cbrain_extensions/active_record_extensions/relation_extensions/undo_where.rb

diff --git a/BrainPortal/app/controllers/userfiles_controller.rb b/BrainPortal/app/controllers/userfiles_controller.rb
index cdfb64947..d73c7665b 100644
--- a/BrainPortal/app/controllers/userfiles_controller.rb
+++ b/BrainPortal/app/controllers/userfiles_controller.rb
@@ -57,6 +57,12 @@ def index #:nodoc:
     @custom_scope = custom_scope(@base_scope)
     @view_scope   = @scope.apply(@custom_scope)
 
+    # Are hidden files displayed?
+    unless @scope.custom[:view_hidden]
+      @hidden_total = @view_scope.where(:hidden => true).count
+      @view_scope = @view_scope.where(:hidden => false)
+    end
+
     # Generate tag filters
     tag_counts   = @view_scope.joins(:tags).group('tags.name').count
     @tag_filters = @base_scope
@@ -74,10 +80,8 @@ def index #:nodoc:
 
     # Generate display totals
     @userfiles_total = @view_scope.count('distinct userfiles.id')
-    @archived_total  = @view_scope.where(:archived => true).count
+    @archived_total  = @view_scope.where(:archived  => true).count
     @immutable_total = @view_scope.where(:immutable => true).count
-    @hidden_total    = @view_scope.undo_where(:hidden).where(:hidden => true).count unless
-      @scope.custom[:view_hidden]
     @userfiles_total_size = @view_scope.sum(:size)
 
     # Prepare the Pagination object
@@ -1606,7 +1610,6 @@ def base_scope
     end
 
     base = base.where(:group_id => current_project.id) if current_project
-    base = base.where(:hidden => false) unless @scope.custom[:view_hidden]
     base
   end
 
diff --git a/BrainPortal/lib/cbrain_extensions/active_record_extensions/relation_extensions/undo_where.rb b/BrainPortal/lib/cbrain_extensions/active_record_extensions/relation_extensions/undo_where.rb
deleted file mode 100644
index 859e5c4e7..000000000
--- a/BrainPortal/lib/cbrain_extensions/active_record_extensions/relation_extensions/undo_where.rb
+++ /dev/null
@@ -1,101 +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 <http://www.gnu.org/licenses/>.  
-#
-
-module CBRAINExtensions #:nodoc:
-  module ActiveRecordExtensions #:nodoc:
-    module RelationExtensions
-      # ActiveRecord::Relation Added Behavior; remove a where() condition from an existing relation.
-      module UndoWhere
-      
-        Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
-      
-        # Returns a new Relation where some clauses have been
-        # removed; the arguments can be one or several attribute
-        # names (which can be qualified with table names).
-        # Any previous 'where' clauses that match one of these
-        # attributes will be removed.
-        #
-        #   r = Author.joins(:book).where(:last => 'Austen').where('first like "J%"').where('books.title' like "Pride%")
-        #   r.undo_where(:first, 'books.title') # => same as just:   last = 'Austen'
-        #   r.undo_where('title')               # => does nothing (unless Author has also a :title !)
-        #   r.undo_where('authors.last')        # => same as undo_where(:last)
-        #
-        # Note that if a previous where() restriction was a long string
-        # with several subclauses, the entire string will be rejected
-        # as soon as somewhere inside we can detect that at least one
-        # subclause contained one of the attributes given in argument.
-        #
-        #   r = Author.where([ "(id not in (?) or type = ?)", [2,3,4], 'AdminUser' ])
-        #   r.undo_where(:type)   # => also rejects the restriction on :id !
-        def undo_where(*args)
-          mymodel    = self.model_name.classify.constantize
-          mytable    = mymodel.table_name
-          without    = clone # will create a new array for its where_values, but having the SAME elems!
-          where_vals = without.where_values.clone # this is what we need to prune
-
-          to_reject = {} #  "tab1.col1" => true, "tab1.col2" => true etc...
-          args.map do |colspec|  #  "col" or "table.col"
-            raise "Invalid column specification \"#{colspec}\"." unless
-              colspec.to_s =~ /^(\`?(\w+)\`?\.)?\`?(\w+)\`?$/
-            tab = Regexp.last_match[2].presence || mytable
-            col = Regexp.last_match[3]
-            to_reject["#{tab}.#{col}"] = true
-          end
-          #puts_yellow "TO REJ=#{to_reject.inspect}"
-
-          return without if to_reject.empty? && ! block_given?
-
-          where_vals.reject! do |node|
-            if block_given? && yield(node) # custom rejection code ?
-              #puts_red "Rejected by block"
-              true
-            elsif to_reject.empty? # optimize case of no args with block_given
-              #puts_red "No args yet block"
-              false
-            elsif node.is_a?(Arel::Nodes::Equality)
-              tab = node.left.relation.name rescue '???'
-              col = node.left.name          rescue '???'
-              #puts_red "EQ #{tab} #{col}"
-              to_reject["#{tab}.#{col}"]
-            elsif node.is_a?(String)   #     ((`table`.`col`) = 3) and col = 5
-              #puts_red "STR #{node}"
-              node.scan(/([\`\'\"]*(\w+)[\`\'\"]*\.)?[\`\'\"]*(\w+)[\`\'\"]*\s*(=|<|>|\sis\s|\snot\s|\sin\s|\slike\s)/i).any? do |submatch|
-                tab = submatch[1] || mytable   # note: numbering in submatch array is not like in Regexp.last_match !
-                col = submatch[2]
-                #puts_red "--> MATCH #{tab}.#{col}"
-                to_reject["#{tab}.#{col}"]
-              end
-            else # unknown node type in Relation; TODO!
-              #puts_red "UNKNOWN: #{node.class}"
-              false
-            end
-          end
-
-          without.where_values = where_vals
-          without
-        end
-        
-        
-      end
-    end
-  end
-end

From 1bb94e5967bfff6da2245cb38819fef3a52b322c Mon Sep 17 00:00:00 2001
From: Natacha Beck <natacha.beck@mcgill.ca>
Date: Mon, 5 Oct 2015 15:28:44 -0400
Subject: [PATCH 58/85] Added tool config extra qsub option

---
 BrainPortal/app/controllers/tool_configs_controller.rb     | 2 +-
 BrainPortal/app/models/cluster_task.rb                     | 7 +++++++
 BrainPortal/app/models/tool_config.rb                      | 2 +-
 BrainPortal/app/views/tool_configs/_form_fields.html.erb   | 7 +++++++
 .../20150929193957_add_extra_qsub_args_to_tool_config.rb   | 5 +++++
 BrainPortal/lib/scir.rb                                    | 2 +-
 BrainPortal/lib/scir_moab.rb                               | 7 ++++---
 BrainPortal/lib/scir_pbs.rb                                | 7 ++++---
 BrainPortal/lib/scir_sge.rb                                | 7 ++++---
 BrainPortal/lib/scir_sharcnet.rb                           | 5 +++--
 10 files changed, 37 insertions(+), 14 deletions(-)
 create mode 100644 BrainPortal/db/migrate/20150929193957_add_extra_qsub_args_to_tool_config.rb

diff --git a/BrainPortal/app/controllers/tool_configs_controller.rb b/BrainPortal/app/controllers/tool_configs_controller.rb
index 0a68b6b62..b538e328d 100644
--- a/BrainPortal/app/controllers/tool_configs_controller.rb
+++ b/BrainPortal/app/controllers/tool_configs_controller.rb
@@ -142,7 +142,7 @@ def update #:nodoc:
     form_tool_config.bourreau_id = @tool_config.bourreau_id
 
     # Update everything else
-    [ :version_name, :description, :script_prologue, :group_id, :ncpus, :docker_image ].each do |att|
+    [ :version_name, :description, :script_prologue, :group_id, :ncpus, :docker_image, :extra_qsub_args ].each do |att|
        @tool_config[att] = form_tool_config[att]
     end
 
diff --git a/BrainPortal/app/models/cluster_task.rb b/BrainPortal/app/models/cluster_task.rb
index 13ebc1591..2353bbe3a 100644
--- a/BrainPortal/app/models/cluster_task.rb
+++ b/BrainPortal/app/models/cluster_task.rb
@@ -1493,6 +1493,13 @@ def submit_cluster_job
     job.name     = self.tname_tid  # "#{self.name}-#{self.id}" # some clusters want all names to be different!
     job.walltime = self.job_walltime_estimate
 
+    # Note: all extra_qsub_args defined in the tool_configs (bourreau, tool and bourreau/tool)
+    # are appended by level of priority. 'less' specific first, 'more' specific later.
+    # In this way if the same option is defined twice the more specific one will be the used.
+    job.tc_extra_qsub_args += "#{bourreau_glob_config.extra_qsub_args} "
+    job.tc_extra_qsub_args += "#{tool_glob_config.extra_qsub_args} "
+    job.tc_extra_qsub_args += "#{tool_config.extra_qsub_args} "
+
     # Log version of Scir lib
     drm     = scir_class.drm_system
     version = scir_class.version
diff --git a/BrainPortal/app/models/tool_config.rb b/BrainPortal/app/models/tool_config.rb
index 0c2ea1b68..8e18d9e39 100644
--- a/BrainPortal/app/models/tool_config.rb
+++ b/BrainPortal/app/models/tool_config.rb
@@ -56,7 +56,7 @@ class ToolConfig < ActiveRecord::Base
   cb_scope        :global_for_bourreaux , where( { :tool_id => nil } )
   cb_scope        :specific_versions    , where( "bourreau_id is not null and tool_id is not null" )
 
-  attr_accessible :version_name, :description, :tool_id, :bourreau_id, :env_array, :script_prologue, :group_id, :ncpus, :docker_image
+  attr_accessible :version_name, :description, :tool_id, :bourreau_id, :env_array, :script_prologue, :group_id, :ncpus, :docker_image, :extra_qsub_args
 
   # CBRAIN extension
   force_text_attribute_encoding 'UTF-8', :description, :version_name
diff --git a/BrainPortal/app/views/tool_configs/_form_fields.html.erb b/BrainPortal/app/views/tool_configs/_form_fields.html.erb
index 692229cdd..30fa9444b 100644
--- a/BrainPortal/app/views/tool_configs/_form_fields.html.erb
+++ b/BrainPortal/app/views/tool_configs/_form_fields.html.erb
@@ -102,5 +102,12 @@
     </p>
   </span>
 
+  <span title="Extra 'qsub' options:">
+    <p><%= f.label :extra_qsub_args, "Extra 'qsub' options:" %><br/>
+      <%= f.text_field :extra_qsub_args %><br/>
+      <div class="field_explanation"><b>Note:</b> This option will be appended to the extra 'qsub' option defined at the bourreau level.</div>
+    </p>
+  </span>
+
 </div>
 
diff --git a/BrainPortal/db/migrate/20150929193957_add_extra_qsub_args_to_tool_config.rb b/BrainPortal/db/migrate/20150929193957_add_extra_qsub_args_to_tool_config.rb
new file mode 100644
index 000000000..52d6cbd42
--- /dev/null
+++ b/BrainPortal/db/migrate/20150929193957_add_extra_qsub_args_to_tool_config.rb
@@ -0,0 +1,5 @@
+class AddExtraQsubArgsToToolConfig < ActiveRecord::Migration
+  def change
+    add_column :tool_configs, :extra_qsub_args, :string
+  end
+end
diff --git a/BrainPortal/lib/scir.rb b/BrainPortal/lib/scir.rb
index 544ec463a..c7f2b30c9 100644
--- a/BrainPortal/lib/scir.rb
+++ b/BrainPortal/lib/scir.rb
@@ -202,7 +202,7 @@ def bash_this_and_capture_out_err(command) #:nodoc:
   class JobTemplate #:nodoc:
 
     # We only support a subset of DRMAA's job template
-    attr_accessor :name, :command, :arg, :wd, :stdin, :stdout, :stderr, :join, :queue, :walltime
+    attr_accessor :name, :command, :arg, :wd, :stdin, :stdout, :stderr, :join, :queue, :walltime, :extra_qsub_args
 
     def revision_info #:nodoc:
       Class.const_get(self.class.to_s.sub(/::JobTemplate/,"")).revision_info
diff --git a/BrainPortal/lib/scir_moab.rb b/BrainPortal/lib/scir_moab.rb
index e131efc24..33a016079 100644
--- a/BrainPortal/lib/scir_moab.rb
+++ b/BrainPortal/lib/scir_moab.rb
@@ -17,7 +17,7 @@
 # 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 <http://www.gnu.org/licenses/>.  
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 
 # This is a replacement for the drmaa.rb library; this particular subclass
@@ -152,8 +152,9 @@ def qsub_command
       command += "-o #{shell_escape(self.stdout)} " if self.stdout
       command += "-e #{shell_escape(self.stderr)} " if self.stderr
       command += "-j oe "                           if self.join
-      command += " #{Scir.cbrain_config[:extra_qsub_args]} "     unless Scir.cbrain_config[:extra_qsub_args].blank?
-      command += "-l walltime=#{self.walltime.to_i} " unless self.walltime.blank?
+      command += "#{Scir.cbrain_config[:extra_qsub_args]} " unless Scir.cbrain_config[:extra_qsub_args].blank?
+      command += "#{self.tc_extra_qsub_args} "              unless self.tc_extra_qsub_args.blank?
+      command += "-l walltime=#{self.walltime.to_i} "       unless self.walltime.blank?
       command += "#{shell_escape(self.arg[0])}"
       command += " 2>&1"
 
diff --git a/BrainPortal/lib/scir_pbs.rb b/BrainPortal/lib/scir_pbs.rb
index a1117acea..1e9bf90b3 100644
--- a/BrainPortal/lib/scir_pbs.rb
+++ b/BrainPortal/lib/scir_pbs.rb
@@ -17,7 +17,7 @@
 # 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 <http://www.gnu.org/licenses/>.  
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 
 # This is a replacement for the drmaa.rb library; this particular subclass
@@ -131,8 +131,9 @@ def qsub_command
       command += "-e #{shell_escape(self.stderr)} " if self.stderr
       command += "-j oe "                           if self.join
       command += "-q #{shell_escape(self.queue)} "  unless self.queue.blank?
-      command += " #{Scir.cbrain_config[:extra_qsub_args]} "     unless Scir.cbrain_config[:extra_qsub_args].blank?
-      command += "-l walltime=#{self.walltime.to_i} " unless self.walltime.blank?
+      command += "#{Scir.cbrain_config[:extra_qsub_args]} " unless Scir.cbrain_config[:extra_qsub_args].blank?
+      command += "#{self.tc_extra_qsub_args} "              unless self.tc_extra_qsub_args.blank?
+      command += "-l walltime=#{self.walltime.to_i} "       unless self.walltime.blank?
       command += "#{shell_escape(self.arg[0])}"
       command += " 2>&1"
 
diff --git a/BrainPortal/lib/scir_sge.rb b/BrainPortal/lib/scir_sge.rb
index c5f60078d..c4595a16b 100644
--- a/BrainPortal/lib/scir_sge.rb
+++ b/BrainPortal/lib/scir_sge.rb
@@ -17,7 +17,7 @@
 # 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 <http://www.gnu.org/licenses/>.  
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 
 # This is a replacement for the drmaa.rb library; this particular subclass
@@ -142,8 +142,9 @@ def qsub_command
       command += "-e #{shell_escape(self.stderr)} " if self.stderr
       command += "-j y "                            if self.join
       command += "-q #{shell_escape(self.queue)} "  unless self.queue.blank?
-      command += " #{Scir.cbrain_config[:extra_qsub_args]} "     unless Scir.cbrain_config[:extra_qsub_args].blank?
-      command += "-l h_rt=#{self.walltime.to_i} "   unless self.walltime.blank?
+      command += "#{Scir.cbrain_config[:extra_qsub_args]} " unless Scir.cbrain_config[:extra_qsub_args].blank?
+      command += "#{self.tc_extra_qsub_args} "              unless self.tc_extra_qsub_args.blank?
+      command += "-l h_rt=#{self.walltime.to_i} "           unless self.walltime.blank?
       command += "#{shell_escape(self.arg[0])}"
       command += " 2>&1"
 
diff --git a/BrainPortal/lib/scir_sharcnet.rb b/BrainPortal/lib/scir_sharcnet.rb
index 09e351dcb..2fef15ae9 100644
--- a/BrainPortal/lib/scir_sharcnet.rb
+++ b/BrainPortal/lib/scir_sharcnet.rb
@@ -17,7 +17,7 @@
 # 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 <http://www.gnu.org/licenses/>.  
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 
 # This is a replacement for the drmaa.rb library; this particular subclass
@@ -144,7 +144,8 @@ def qsub_command
       command += "-e #{shell_escape(stderrfile)} "  if stderrfile && ! self.join && stderrfile != stdoutfile
       command += "-q #{shell_escape(self.queue)} "  unless self.queue.blank?
       command += "-r #{(self.walltime.to_i/60)+1} " unless self.walltime.blank?  # sqsub uses minutes
-      command += " #{Scir.cbrain_config[:extra_qsub_args]} "     unless Scir.cbrain_config[:extra_qsub_args].blank?
+      command += "#{Scir.cbrain_config[:extra_qsub_args]} " unless Scir.cbrain_config[:extra_qsub_args].blank?
+      command += "#{self.tc_extra_qsub_args} "              unless self.tc_extra_qsub_args.blank?
       command += "/bin/bash #{shell_escape(self.arg[0])}"
       command += " 2>&1" # they mix stdout and stderr !!! grrrrrr
 

From 6974a62cc29e976e9c76c6cb170aaba248587266 Mon Sep 17 00:00:00 2001
From: Natacha Beck <natacha.beck@mcgill.ca>
Date: Mon, 5 Oct 2015 16:31:51 -0400
Subject: [PATCH 59/85] Fixed some bugs

---
 BrainPortal/app/models/cluster_task.rb | 7 ++++---
 BrainPortal/lib/scir.rb                | 2 +-
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/BrainPortal/app/models/cluster_task.rb b/BrainPortal/app/models/cluster_task.rb
index 2353bbe3a..3fd34e2a2 100644
--- a/BrainPortal/app/models/cluster_task.rb
+++ b/BrainPortal/app/models/cluster_task.rb
@@ -1496,9 +1496,10 @@ def submit_cluster_job
     # Note: all extra_qsub_args defined in the tool_configs (bourreau, tool and bourreau/tool)
     # are appended by level of priority. 'less' specific first, 'more' specific later.
     # In this way if the same option is defined twice the more specific one will be the used.
-    job.tc_extra_qsub_args += "#{bourreau_glob_config.extra_qsub_args} "
-    job.tc_extra_qsub_args += "#{tool_glob_config.extra_qsub_args} "
-    job.tc_extra_qsub_args += "#{tool_config.extra_qsub_args} "
+    job.tc_extra_qsub_args  = ""
+    job.tc_extra_qsub_args += "#{bourreau_glob_config.extra_qsub_args} " if bourreau_glob_config
+    job.tc_extra_qsub_args += "#{tool_glob_config.extra_qsub_args} "     if tool_glob_config
+    job.tc_extra_qsub_args += "#{tool_config.extra_qsub_args} "          if tool_config
 
     # Log version of Scir lib
     drm     = scir_class.drm_system
diff --git a/BrainPortal/lib/scir.rb b/BrainPortal/lib/scir.rb
index c7f2b30c9..b3768c52d 100644
--- a/BrainPortal/lib/scir.rb
+++ b/BrainPortal/lib/scir.rb
@@ -202,7 +202,7 @@ def bash_this_and_capture_out_err(command) #:nodoc:
   class JobTemplate #:nodoc:
 
     # We only support a subset of DRMAA's job template
-    attr_accessor :name, :command, :arg, :wd, :stdin, :stdout, :stderr, :join, :queue, :walltime, :extra_qsub_args
+    attr_accessor :name, :command, :arg, :wd, :stdin, :stdout, :stderr, :join, :queue, :walltime, :tc_extra_qsub_args
 
     def revision_info #:nodoc:
       Class.const_get(self.class.to_s.sub(/::JobTemplate/,"")).revision_info

From 37c72dafcaf110e02195c848b9017bec55fbc943 Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Mon, 5 Oct 2015 17:32:06 -0400
Subject: [PATCH 60/85] Removal of leftover UndoWhere include, minor users
 table fix

This changeset removes the previously removed UndoWhere module from
the AR extensions initializer and fixes an incorrect call in the users
table following a recent refactor of filter_values_for. (In other words,
two simple bugfixes)
---
 BrainPortal/app/views/users/_users_table.html.erb    | 12 ++++++------
 .../initializers/core_extensions/active_record.rb    |  8 +-------
 2 files changed, 7 insertions(+), 13 deletions(-)

diff --git a/BrainPortal/app/views/users/_users_table.html.erb b/BrainPortal/app/views/users/_users_table.html.erb
index 4c054bcfa..1d6bee79e 100644
--- a/BrainPortal/app/views/users/_users_table.html.erb
+++ b/BrainPortal/app/views/users/_users_table.html.erb
@@ -80,15 +80,15 @@
 
     t.column("Login", :login,
       :sortable => true,
-      :filters  => filter_values_for(@base_scope, :account_locked,
-        scope:  @scope,
-        format: lambda do |value, label, count, scoped|
+      :filters  => scoped_filters_for(
+        @base_scope, @scope, :account_locked,
+        format: lambda do |value, label, base, view|
           label = (!value || value == 0 ? 'Unlocked' : 'Locked')
           {
             :value     => value,
-            :label     => "#{label} (of #{count})",
-            :indicator => scoped,
-            :empty     => scoped == 0
+            :label     => "#{label} (of #{base})",
+            :indicator => view,
+            :empty     => view == 0
           }
         end
       )
diff --git a/BrainPortal/config/initializers/core_extensions/active_record.rb b/BrainPortal/config/initializers/core_extensions/active_record.rb
index 0af94f3f8..0e167a898 100644
--- a/BrainPortal/config/initializers/core_extensions/active_record.rb
+++ b/BrainPortal/config/initializers/core_extensions/active_record.rb
@@ -108,19 +108,13 @@ class Relation
 
     include CBRAINExtensions::ActiveRecordExtensions::RelationExtensions::RawData
 
-    #####################################################################
-    # ActiveRecord::Relation Added Behavior For To Undo Conditions
-    #####################################################################
-
-    include CBRAINExtensions::ActiveRecordExtensions::RelationExtensions::UndoWhere
-
   end
 
   # CBRAIN ActiveRecord::Associations::CollectionProxy extensions
   # delegating extended Relation methods.
   module Associations #:nodoc:
     class CollectionProxy #:nodoc:
-      delegate :raw_first_column, :raw_rows, :undo_where, :to => :scoped
+      delegate :raw_first_column, :raw_rows, :to => :scoped
     end
   end
 

From c62f039c53cac1add07fad18b28fa9a099a616d7 Mon Sep 17 00:00:00 2001
From: Pierre Rioux <pierre.rioux@mcgill.ca>
Date: Tue, 6 Oct 2015 15:28:21 -0400
Subject: [PATCH 61/85] Fixed inconsistent codebase bugs.

---
 BrainPortal/app/models/user.rb                         | 10 +++++-----
 .../initializers/core_extensions/active_record.rb      |  8 +-------
 2 files changed, 6 insertions(+), 12 deletions(-)

diff --git a/BrainPortal/app/models/user.rb b/BrainPortal/app/models/user.rb
index 69e29fbc3..33736cd7c 100644
--- a/BrainPortal/app/models/user.rb
+++ b/BrainPortal/app/models/user.rb
@@ -289,7 +289,7 @@ def has_role?(role)
 
   # Find the tools that this user has access to.
   def available_tools
-    cb_error "#available_tools called from User base class! Method must be implement in a subclass."
+    cb_error "#available_tools called from User base class! Method must be implemented in a subclass."
   end
 
   # Find the scientific tools that this user has access to.
@@ -304,7 +304,7 @@ def available_conversion_tools
 
   # Returns the list of groups available to this user based on role.
   def available_groups
-    cb_error "#available_groups called from User base class! Method must be implement in a subclass."
+    cb_error "#available_groups called from User base class! Method must be implemented in a subclass."
   end
 
   # Returns the list of tags available to this user.
@@ -314,17 +314,17 @@ def available_tags
 
   # Returns the list of tasks available to this user.
   def available_tasks
-    cb_error "#available_tasks called from User base class! Method must be implement in a subclass."
+    cb_error "#available_tasks called from User base class! Method must be implemented in a subclass."
   end
 
   # Return the list of users under this user's control based on role.
   def available_users
-    cb_error "#available_users called from User base class! Method must be implement in a subclass."
+    cb_error "#available_users called from User base class! Method must be implemented in a subclass."
   end
 
   # Return the list of sites accessible to the user
   def accessible_sites
-    cb_error "#accessible_sites called from User base class! Method must be implement in a subclass."
+    cb_error "#accessible_sites called from User base class! Method must be implemented in a subclass."
   end
 
   # Can this user be accessed by +user+?
diff --git a/BrainPortal/config/initializers/core_extensions/active_record.rb b/BrainPortal/config/initializers/core_extensions/active_record.rb
index 0af94f3f8..0e167a898 100644
--- a/BrainPortal/config/initializers/core_extensions/active_record.rb
+++ b/BrainPortal/config/initializers/core_extensions/active_record.rb
@@ -108,19 +108,13 @@ class Relation
 
     include CBRAINExtensions::ActiveRecordExtensions::RelationExtensions::RawData
 
-    #####################################################################
-    # ActiveRecord::Relation Added Behavior For To Undo Conditions
-    #####################################################################
-
-    include CBRAINExtensions::ActiveRecordExtensions::RelationExtensions::UndoWhere
-
   end
 
   # CBRAIN ActiveRecord::Associations::CollectionProxy extensions
   # delegating extended Relation methods.
   module Associations #:nodoc:
     class CollectionProxy #:nodoc:
-      delegate :raw_first_column, :raw_rows, :undo_where, :to => :scoped
+      delegate :raw_first_column, :raw_rows, :to => :scoped
     end
   end
 

From 1ddadd6b8b0098ada75f973f681cdec40fb73054 Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Wed, 7 Oct 2015 12:10:45 -0400
Subject: [PATCH 62/85] Issue #228 - Improve 'search for anything' code

Refactored duplicated & eval blocks by a lambda function, made the
controller pass the result set hash instead of a bunch of instance
variables. This changeset also adds the missing copyright block.
---
 .../app/controllers/portal_controller.rb      |  18 +-
 BrainPortal/app/views/portal/search.html.erb  | 167 +++++++++---------
 2 files changed, 82 insertions(+), 103 deletions(-)

diff --git a/BrainPortal/app/controllers/portal_controller.rb b/BrainPortal/app/controllers/portal_controller.rb
index 25d9d1e95..630b0120a 100644
--- a/BrainPortal/app/controllers/portal_controller.rb
+++ b/BrainPortal/app/controllers/portal_controller.rb
@@ -359,22 +359,10 @@ def report #:nodoc:
   # This action searches among all sorts of models for IDs or strings,
   # and reports links to the matches found.
   def search
+    @search  = params[:search]
+    @limit   = 20 # used by interface only
 
-    @search = params[:search]
-    @limit  = 20 # used by interface only
-
-    results = @search.present? ? ModelsReport.search_for_token(@search, current_user) : {}
-
-    @users  = results[:users]  || []
-    @tasks  = results[:tasks]  || []
-    @groups = results[:groups] || []
-    @files  = results[:files]  || []
-    @rrs    = results[:rrs]    || []
-    @dps    = results[:dps]    || []
-    @sites  = results[:sites]  || []
-    @tools  = results[:tools]  || []
-    @tcs    = results[:tcs]    || []
-
+    @results = @search.present? ? ModelsReport.search_for_token(@search, current_user) : {}
   end
 
   private
diff --git a/BrainPortal/app/views/portal/search.html.erb b/BrainPortal/app/views/portal/search.html.erb
index cd91b67fc..a8bffbc0b 100644
--- a/BrainPortal/app/views/portal/search.html.erb
+++ b/BrainPortal/app/views/portal/search.html.erb
@@ -1,4 +1,27 @@
 
+<%-
+#
+# 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 <http://www.gnu.org/licenses/>.
+#
+-%>
+
 <% title 'Search' %>
 
 <%= form_tag(search_path, :method => :get) do %>
@@ -6,115 +29,83 @@
    <span class="field_explanation">This will search files, tasks, users, tools, projects, etc by name or description. <%= @limit %> results shown maximum.</span>
 <% end %>
 
-<% if [ @users, @tasks, @groups, @files, @rrs, @dps, @sites, @tools, @tcs ].any? { |var| var.present? } %>
-  <%# <h2>Results</h2> %>
-  <p>
-<% end %>
-
-<% [ :files, :tasks, :users, :groups, :rrs, :dps, :sites, :tools, :tcs ].each do |var| %>
-  <%
-     # Compute a @x_size variable for each result set, and truncate results to 20 entries max.
-     # Should be using reflexive interface instead of an eval, but oh well.
-     eval "
-       array        = @#{var}
-       @#{var}_size = array.size
-       @#{var}      = @#{var}[0,#{@limit}] if array.size > #{@limit}
-     "
+<%#
+  Display a nice short table for the result set named +name+ with title +title+.
+  Each table cell is formatted by the given block (which is passed directly to
+  array_to_table).
+%>
+<% result_table = lambda do |name, title = nil, &block| %>
+  <% return if (result = @results[name]).blank? %>
+  <h3><%= title || name.to_s.humanize %> (found: <%= result.size %>)</h3>
+  <%=
+    array_to_table(result[0, @limit], {
+      :rows            => 5,
+      :fill_by_columns => true,
+      :table_class     => "simple",
+      :td_class        => "left_align",
+    }, &block)
   %>
 <% end %>
 
-<% # this is used by array_to_table() below
-   tables_options = {
-     :rows            => 5,
-     :fill_by_columns => true,
-     :table_class     => "simple",
-     :td_class        => "left_align",
-   }
-%>
-
-<% if @files.present? %>
-  <h3>Files (found: <%= @files_size %>)</h3>
-  <%= array_to_table(@files, tables_options) do |file,r,c| %>
-     <%= link_to_userfile_if_accessible(file) %> (<%= file.user.login %>)
-  <% end %>
+<% result_table.(:files) do |file, r, c| %>
+  <%= link_to_userfile_if_accessible(file) %> (<%= file.user.login %>)
 <% end %>
 
-<% if @tasks.present? %>
-  <h3>Tasks (found: <%= @tasks_size %>)</h3>
-  <%= array_to_table(@tasks, tables_options) do |task,r,c| %>
-     <%= link_to_model_if_accessible(CbrainTask,task,:name_and_bourreau) %> (<%= task.user.login %>)
-     <%= link_to "(edit)", edit_task_path(task), :class => 'action_link' %><br>
-     <%= overlay_description(task.description, :header_width => 35) %>
-  <% end %>
+<% result_table.(:tasks) do |task, r, c| %>
+  <%= link_to_model_if_accessible(CbrainTask,task,:name_and_bourreau) %> (<%= task.user.login %>)
+  <%= link_to "(edit)", edit_task_path(task), :class => 'action_link' %><br>
+  <%= overlay_description(task.description, :header_width => 35) %>
 <% end %>
 
-<% if @users.present? %>
-  <h3>Users (found: <%= @users_size %>)</h3>
-  <%= array_to_table(@users, tables_options) do |user,r,c| %>
-     <%= user.full_name %> (<%= link_to_user_if_accessible(user) %>)
-     <%= link_to '(switch)', switch_user_path(user), :method  => :post, :class => 'action_link' if current_user.has_role?(:admin_user) %>
-  <% end %>
+<% result_table.(:users) do |user, r, c| %>
+  <%= user.full_name %> (<%= link_to_user_if_accessible(user) %>)
+  <%= link_to '(switch)', switch_user_path(user), :method  => :post, :class => 'action_link' if current_user.has_role?(:admin_user) %>
 <% end %>
 
-<% if @groups.present? %>
-  <h3>Projects (found: <%= @groups_size %>)</h3>
-  <%= array_to_table(@groups, tables_options) do |group,r,c| %>
-     <%= link_to_group_if_accessible(group) %> (<%= group.creator.try(:login) %>)
-     <%= link_to '(switch)', { :controller => :groups, :action => :switch, :id => group.id } , :method  => :post, :class => 'action_link' %>
-  <% end %>
+<% result_table.(:groups, 'Projects') do |group, r, c| %>
+  <%= link_to_group_if_accessible(group) %> (<%= group.creator.try(:login) %>)
+  <%= link_to '(switch)', { :controller => :groups, :action => :switch, :id => group.id } , :method  => :post, :class => 'action_link' %>
 <% end %>
 
-<% if @rrs.present? %>
-  <h3>Execution Servers (found: <%= @rrs_size %>)</h3>
-  <%= array_to_table(@rrs, tables_options) do |rr,r,c| %>
-     <%= link_to_bourreau_if_accessible(rr) %>
-     <% task_count = current_user.cbrain_tasks.real_tasks.where(:bourreau_id => rr.id).count %>
-     <% if task_count > 0 %>
-       (<%= index_count_filter(task_count, :tasks,
-            { :user_id => current_user.id, :bourreau_id => rr.id}) %> tasks)
-     <% end %>
+<% result_table.(:rrs, 'Execution Servers') do |rr, r, c| %>
+  <%= link_to_bourreau_if_accessible(rr) %>
+  <% task_count = current_user.cbrain_tasks.real_tasks.where(:bourreau_id => rr.id).count %>
+  <% if task_count > 0 %>
+    (<%= index_count_filter(
+      task_count, :tasks,
+      { :user_id => current_user.id, :bourreau_id => rr.id }
+    ) %> tasks)
   <% end %>
 <% end %>
 
-<% if @dps.present? %>
-  <h3>Data Providers (found: <%= @dps_size %>)</h3>
-  <%= array_to_table(@dps, tables_options) do |dp,r,c| %>
-     <%= link_to_data_provider_if_accessible(dp) %>
-     <%= link_to '(browse)', browse_data_provider_path(dp), :class => 'action_link' if dp.is_browsable? %>
-     <% file_count = current_user.userfiles.where(:data_provider_id => dp.id).count %>
-     <% if file_count > 0 %>
-       (<%= index_count_filter(file_count, :userfiles,
-            { :user_id => current_user.id, :data_provider_id => dp.id}) %> registered files)
-     <% end %>
+<% result_table.(:dps, 'Data Providers') do |dp, r, c| %>
+  <%= link_to_data_provider_if_accessible(dp) %>
+  <%= link_to '(browse)', browse_data_provider_path(dp), :class => 'action_link' if dp.is_browsable? %>
+  <% file_count = current_user.userfiles.where(:data_provider_id => dp.id).count %>
+  <% if file_count > 0 %>
+    (<%= index_count_filter(
+      file_count, :userfiles,
+      { :user_id => current_user.id, :data_provider_id => dp.id }
+    ) %> registered files)
   <% end %>
 <% end %>
 
-<% if @sites.present? %>
-  <h3>Sites (found: <%= @sites_size %>)</h3>
-  <%= array_to_table(@sites, tables_options) do |site,r,c| %>
-     <%= link_to_site_if_accessible(site) %>
-  <% end %>
+<% result_table.(:sites) do |site, r, c| %>
+  <%= link_to_site_if_accessible(site) %>
 <% end %>
 
-<% if @tools.present? %>
-  <h3>Tools (found: <%= @tools_size %>)</h3>
-  <%= array_to_table(@tools, tables_options) do |tool,r,c| %>
-    <% if current_user.has_role?(:admin_user) %>
-      <%= link_to tool.name, edit_tool_path(tool) %>
-    <%  else %>
-      <%= tool.name %>
-    <% end %>
+<% result_table.(:tools) do |tool, r, c| %>
+  <% if current_user.has_role?(:admin_user) %>
+    <%= link_to tool.name, edit_tool_path(tool) %>
+  <%  else %>
+    <%= tool.name %>
   <% end %>
 <% end %>
 
-<% if @tcs.present? %>
-  <h3>Tool Versions (found: <%= @tcs_size %>)</h3>
-  <%= array_to_table(@tcs, tables_options) do |tc,r,c| %>
-    <% if current_user.has_role?(:admin_user) %>
-      <%= tc.tool.name %>@<%= tc.bourreau.name%> : <%= link_to tc.version_name, edit_tool_config_path(tc) %>
-    <%  else %>
-      <%= tc.tool.name %>@<%= tc.bourreau.name%> : <%= tc.version_name %>
-    <% end %>
+<% result_table.(:tcs, 'Tool Versions') do |tc, r, c| %>
+  <% if current_user.has_role?(:admin_user) %>
+    <%= tc.tool.name %>@<%= tc.bourreau.name%> : <%= link_to tc.version_name, edit_tool_config_path(tc) %>
+  <%  else %>
+    <%= tc.tool.name %>@<%= tc.bourreau.name%> : <%= tc.version_name %>
   <% end %>
 <% end %>
-

From bbac3085b4f84fb52c2bccaa25e2409d84c52000 Mon Sep 17 00:00:00 2001
From: Remi Bernard <remi.bernard@mail.mcgill.ca>
Date: Wed, 7 Oct 2015 17:12:58 -0400
Subject: [PATCH 63/85] Missing userfiles scoping method (view_scope)

This short changeset fixes a small oversight; the view_scope method has
been refactored with the Scope API port, and was yet still called at
some places. This is fixed by matching (more-or-less) what is done in
the tasks controller with a filtered_scope method which applies all
known filters.
---
 BrainPortal/app/controllers/userfiles_controller.rb | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/BrainPortal/app/controllers/userfiles_controller.rb b/BrainPortal/app/controllers/userfiles_controller.rb
index d73c7665b..7a53ca416 100644
--- a/BrainPortal/app/controllers/userfiles_controller.rb
+++ b/BrainPortal/app/controllers/userfiles_controller.rb
@@ -286,7 +286,7 @@ def show #:nodoc:
 
       # Rebuild the sorted Userfile scope
       @scope       = scope_from_session('userfiles')
-      sorted_scope = view_scope
+      sorted_scope = filtered_scope
 
       # Fetch the neighbors of the shown userfile in the ordered scope's order
       neighbors = sorted_scope.where("userfiles.id != ?", @userfile.id).offset([0, @sort_index - 1].max).limit(2).all
@@ -927,7 +927,7 @@ def manage_persistent
     persistent = Set.new(current_session[:persistent_userfiles])
 
     if operation =~ /select/
-      files = view_scope
+      files = filtered_scope
         .select(&:available?)
         .map(&:id)
         .map(&:to_s)
@@ -1623,6 +1623,13 @@ def custom_scope(base = nil)
       .inject(base || base_scope) { |scope, filter| filter.filter_scope(scope) }
   end
 
+  # Combination of +base_scope+, +custom_scope+ and @scope object; returns a
+  # scoped list of userfiles fitlered/ordered by all three.
+  # Requires a valid @scope object.
+  def filtered_scope
+    @scope.apply(custom_scope(base_scope))
+  end
+
   # Userfiles-specific tag Scope filter; filter by a set of tags which must
   # all be on a given userfile for it to pass the filter. Note that this is
   # an all-or-nothing filter; to pass, an userfile needs *all* tags.

From 3ce689f1568cdabe5d2f6d74e62a321ef2b5dad9 Mon Sep 17 00:00:00 2001
From: Ehsan Afkhami <eafkhami@dhcp56-241.mni.mcgill.ca>
Date: Tue, 13 Oct 2015 14:36:58 -0400
Subject: [PATCH 64/85] fixes for issues 193 and 104

---
 .../app/controllers/userfiles_controller.rb   |  7 ++-
 .../app/views/layouts/application.html.erb    |  1 +
 .../javascripts/custom-confirm-dialog.js      | 54 +++++++++++++++++++
 BrainPortal/public/stylesheets/cbrain.css     |  6 +++
 4 files changed, 67 insertions(+), 1 deletion(-)
 create mode 100644 BrainPortal/public/javascripts/custom-confirm-dialog.js

diff --git a/BrainPortal/app/controllers/userfiles_controller.rb b/BrainPortal/app/controllers/userfiles_controller.rb
index d73c7665b..fd9f18baa 100644
--- a/BrainPortal/app/controllers/userfiles_controller.rb
+++ b/BrainPortal/app/controllers/userfiles_controller.rb
@@ -647,7 +647,12 @@ def update_multiple #:nodoc:
     failed_list   = {}
     CBRAIN.spawn_with_active_records_if(do_in_spawn,current_user,"Sending update to files") do
       access_requested = commit_name == :update_tags ? :read : :write
-      filelist         = Userfile.find_all_accessible_by_user(current_user, :access_requested => access_requested ).where(:id => file_ids).all
+      # if the current user is admin or site manager they're allowed to update attributes of any file even if they're not the owner. Otherwise, the current user must be the owner to modify the attributes.
+      if current_user.has_role?(:site_manager) || current_user.has_role?(:admin_user)
+        filelist       = Userfile.find_all_accessible_by_user(current_user, :access_requested => access_requested ).where(:id => file_ids).all
+      else
+        filelist       = Userfile.find_all_accessible_by_user(current_user, :access_requested => access_requested ).where(:id => file_ids, :user_id => current_user.id).all
+      end
       failure_ids      = file_ids - filelist.map {|u| u.id.to_s }
       failed_files     = Userfile.where(:id => failure_ids).select([:id, :name, :type]).all
       failed_list["you don't have write access"] = failed_files if failed_files.present?
diff --git a/BrainPortal/app/views/layouts/application.html.erb b/BrainPortal/app/views/layouts/application.html.erb
index 857fc4f05..9f8768c77 100644
--- a/BrainPortal/app/views/layouts/application.html.erb
+++ b/BrainPortal/app/views/layouts/application.html.erb
@@ -54,6 +54,7 @@
     <%= javascript_include_tag "cbrain" %>
     <%= javascript_include_tag "dynamic-table" %>
     <%= javascript_include_tag "rails" %>
+	<%= javascript_include_tag "custom-confirm-dialog" %>
     <%= yield :scripts %>
 
     <!-- Dynamically Appended Body Elements Below This -->
diff --git a/BrainPortal/public/javascripts/custom-confirm-dialog.js b/BrainPortal/public/javascripts/custom-confirm-dialog.js
new file mode 100644
index 000000000..59b26855c
--- /dev/null
+++ b/BrainPortal/public/javascripts/custom-confirm-dialog.js
@@ -0,0 +1,54 @@
+// This call will override the rails allowAction method to allow us to present a custom dialog for
+// a link with data-confirm attribute
+
+(function () {
+
+// The custom dialog box actually gets created in the function below
+function myCustomConfirmBox(message, callback) {
+
+	if ($('#dialog-confirm').length == 0){
+		$(document.body).append('<div id="dialog-confirm"></div>');
+	}
+
+	$("#dialog-confirm").html(message);
+
+	// Define the Dialog and its properties.
+	$("#dialog-confirm").dialog({
+		resizable: false,
+		modal: true,
+		title: "Confirmation",
+		height: 150,
+		width: 400,
+		buttons: {
+			"Yes": function () {
+				$(this).dialog('close');
+				callback();
+			},
+			"No": function () {
+				$(this).dialog('close');
+			}
+		}
+	});
+}
+
+// The function below overrides the allowAction to create a custom dialog box
+$.rails.allowAction = function(element) {
+	var message = element.data('confirm'), callback;
+	if (!message) { return true; } // if there is no message, proceed with action
+
+	if ($.rails.fire(element, 'confirm')) {
+		myCustomConfirmBox(message, function() {
+			callback = $.rails.fire(element,'confirm:complete', [false]);
+			if(callback) {
+				var oldAllowAction = $.rails.allowAction;
+				$.rails.allowAction = function() { return true; };
+				element.trigger('click');
+				$.rails.allowAction = oldAllowAction;
+			}
+		});
+	}
+	return false;
+}
+
+}());
+
diff --git a/BrainPortal/public/stylesheets/cbrain.css b/BrainPortal/public/stylesheets/cbrain.css
index 4fd1f116e..037c926f6 100644
--- a/BrainPortal/public/stylesheets/cbrain.css
+++ b/BrainPortal/public/stylesheets/cbrain.css
@@ -2329,4 +2329,10 @@ img {
   resize: both;
 }
 
+/* % ######################################################### */
+/* % Jquery Confirmation UI styling */
+/* % ######################################################### */
+
+#dialog-confirm { color: red; }
+
 

From 7db51bfeaa2c9be2429400178285f0fc6933da90 Mon Sep 17 00:00:00 2001
From: Ehsan Afkhami <eafkhami@dhcp56-241.mni.mcgill.ca>
Date: Tue, 13 Oct 2015 16:34:21 -0400
Subject: [PATCH 65/85] changed dialog look

---
 .../app/views/layouts/application.html.erb    |  2 +-
 .../javascripts/custom-confirm-dialog.js      | 10 +++----
 BrainPortal/public/stylesheets/cbrain.css     | 26 ++++++++++++++++++-
 3 files changed, 31 insertions(+), 7 deletions(-)

diff --git a/BrainPortal/app/views/layouts/application.html.erb b/BrainPortal/app/views/layouts/application.html.erb
index 9f8768c77..7bd6e0473 100644
--- a/BrainPortal/app/views/layouts/application.html.erb
+++ b/BrainPortal/app/views/layouts/application.html.erb
@@ -54,7 +54,7 @@
     <%= javascript_include_tag "cbrain" %>
     <%= javascript_include_tag "dynamic-table" %>
     <%= javascript_include_tag "rails" %>
-	<%= javascript_include_tag "custom-confirm-dialog" %>
+    <%= javascript_include_tag "custom-confirm-dialog" %>
     <%= yield :scripts %>
 
     <!-- Dynamically Appended Body Elements Below This -->
diff --git a/BrainPortal/public/javascripts/custom-confirm-dialog.js b/BrainPortal/public/javascripts/custom-confirm-dialog.js
index 59b26855c..abef18616 100644
--- a/BrainPortal/public/javascripts/custom-confirm-dialog.js
+++ b/BrainPortal/public/javascripts/custom-confirm-dialog.js
@@ -6,18 +6,18 @@
 // The custom dialog box actually gets created in the function below
 function myCustomConfirmBox(message, callback) {
 
-	if ($('#dialog-confirm').length == 0){
-		$(document.body).append('<div id="dialog-confirm"></div>');
+	if ($('.cbrain-dialog-confirm').length == 0){
+		$(document.body).append('<div class="cbrain-dialog-confirm"></div>');
 	}
 
-	$("#dialog-confirm").html(message);
+	$(".cbrain-dialog-confirm").html(message);
+
 
 	// Define the Dialog and its properties.
-	$("#dialog-confirm").dialog({
+	$(".cbrain-dialog-confirm").dialog({
 		resizable: false,
 		modal: true,
 		title: "Confirmation",
-		height: 150,
 		width: 400,
 		buttons: {
 			"Yes": function () {
diff --git a/BrainPortal/public/stylesheets/cbrain.css b/BrainPortal/public/stylesheets/cbrain.css
index 037c926f6..bc5fed8e9 100644
--- a/BrainPortal/public/stylesheets/cbrain.css
+++ b/BrainPortal/public/stylesheets/cbrain.css
@@ -2333,6 +2333,30 @@ img {
 /* % Jquery Confirmation UI styling */
 /* % ######################################################### */
 
-#dialog-confirm { color: red; }
+.cbrain-dialog-confirm {
+	background-color: pink !important;
+	font-weight: bold !important;
+	border: 3px solid red !important;
+}
+
+.ui-dialog-titlebar-close {
+  visibility: hidden;
+}
+
+
+/*
+
+
+
+.ui-dialog-titlebar {
+  outline: red solid thick;
+  height: 20px;
+}
+.ui-dialog {
+  outline: #00FF00 dotted thick;
+}
+*/
+
+
 
 

From bd94292d632ba9a59c71077561bf60b2a56e6fe1 Mon Sep 17 00:00:00 2001
From: Ehsan Afkhami <eafkhami@dhcp56-241.mni.mcgill.ca>
Date: Tue, 13 Oct 2015 16:39:20 -0400
Subject: [PATCH 66/85] changed dialog look 2

---
 .../javascripts/custom-confirm-dialog.js      |  1 +
 BrainPortal/public/stylesheets/cbrain.css     | 19 ++-----------------
 2 files changed, 3 insertions(+), 17 deletions(-)

diff --git a/BrainPortal/public/javascripts/custom-confirm-dialog.js b/BrainPortal/public/javascripts/custom-confirm-dialog.js
index abef18616..396bbf652 100644
--- a/BrainPortal/public/javascripts/custom-confirm-dialog.js
+++ b/BrainPortal/public/javascripts/custom-confirm-dialog.js
@@ -17,6 +17,7 @@ function myCustomConfirmBox(message, callback) {
 	$(".cbrain-dialog-confirm").dialog({
 		resizable: false,
 		modal: true,
+		dialogClass: "no-close",
 		title: "Confirmation",
 		width: 400,
 		buttons: {
diff --git a/BrainPortal/public/stylesheets/cbrain.css b/BrainPortal/public/stylesheets/cbrain.css
index bc5fed8e9..e2e48af1f 100644
--- a/BrainPortal/public/stylesheets/cbrain.css
+++ b/BrainPortal/public/stylesheets/cbrain.css
@@ -2339,24 +2339,9 @@ img {
 	border: 3px solid red !important;
 }
 
-.ui-dialog-titlebar-close {
-  visibility: hidden;
-}
-
-
-/*
-
-
-
-.ui-dialog-titlebar {
-  outline: red solid thick;
-  height: 20px;
-}
-.ui-dialog {
-  outline: #00FF00 dotted thick;
+.no-close .ui-dialog-titlebar-close {
+  display: none;
 }
-*/
-
 
 
 

From 3070eb6009cefc3ed7ef8f008623bf0ca7cf5778 Mon Sep 17 00:00:00 2001
From: Ehsan Afkhami <eafkhami@dhcp56-200.mni.mcgill.ca>
Date: Wed, 21 Oct 2015 11:26:43 -0400
Subject: [PATCH 67/85] this is the fix for The site selection box is not
 sorted issue #241

---
 BrainPortal/app/helpers/select_box_helper.rb | 32 +++++++++++++++++++-
 BrainPortal/app/views/groups/_new.html.erb   |  4 +--
 BrainPortal/app/views/groups/show.html.erb   | 26 +++++++++-------
 BrainPortal/app/views/users/_new.html.erb    |  4 +--
 BrainPortal/app/views/users/show.html.erb    | 16 +++++-----
 5 files changed, 59 insertions(+), 23 deletions(-)

diff --git a/BrainPortal/app/helpers/select_box_helper.rb b/BrainPortal/app/helpers/select_box_helper.rb
index 02b455f3d..1d4a65898 100644
--- a/BrainPortal/app/helpers/select_box_helper.rb
+++ b/BrainPortal/app/helpers/select_box_helper.rb
@@ -60,6 +60,37 @@ def user_select(parameter_name = "user_id", options = {}, select_tag_options = {
     select_tag parameter_name, grouped_options, select_tag_options
   end
 
+  # Create a standard site select box for selecting a site id for a form.
+  # The +parameter_name+ argument will be the name of the parameter
+  # when the form is submitted and the +select_tag_options+ hash will be sent
+  # directly as options to the +select_tag+ helper method called to create the element.
+  # The +options+ hash can contain either or both of the following:
+  # [selector] used for default selection. This can be a Site object, a site id (String or Fixnum),
+  #            or any model that has a site_id attribute.
+  # [sites] the array of Site objects used to build the select box. Defaults to +Site.order(:name).all+.
+  # When calling site_select, set the :prompt option in select_tag_options hash, to the text you want
+  # displayed when no option is selected
+  def site_select(parameter_name = "site", options = {}, select_tag_options = {} )
+     options  = { :selector => options } unless options.is_a?(Hash)
+     sites = options[:sites] || Site.order(:name).all
+     selector = options[:selector]
+
+     if selector.respond_to?(:site_id)
+       selected = selector.site_id.to_s
+     elsif selector.is_a?(Site)
+       selected = selector.id.to_s
+     else
+       selected = selector.to_s
+     end
+
+     site_options = sites.map{ |s| [s.name, s.id]}
+
+     select_tag parameter_name, options_for_select(site_options, selected), select_tag_options
+  end
+
+
+
+
   # Create a standard groups select box for selecting a group id for a form.
   # The +parameter_name+ argument will be the name of the parameter
   # when the form is submitted and the +select_tag_options+ hash will be sent
@@ -468,7 +499,6 @@ def task_type_select(parameter_name = "task_type", options = {}, select_tag_opti
     type_select(parameter_name, options.dup.merge({:types => task_types, :generate_descendants => generate_descendants, :include_top => include_top}), select_tag_options)
   end
 
-
   # Create a standard types select box for selecting a types type for a form.
   # The +parameter_name+ argument will be the name of the parameter
   # when the form is submitted and the +select_tag_options+ hash will be sent
diff --git a/BrainPortal/app/views/groups/_new.html.erb b/BrainPortal/app/views/groups/_new.html.erb
index fed8a2eee..92d613939 100644
--- a/BrainPortal/app/views/groups/_new.html.erb
+++ b/BrainPortal/app/views/groups/_new.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 <http://www.gnu.org/licenses/>.  
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 -%>
 
@@ -40,7 +40,7 @@
       <% if current_user.has_role?(:admin_user) %>
         <p>
           <%= f.label :site_id, "Site:" %>
-          <%= f.collection_select :site_id, Site.all, :id, :name, {:include_blank  => true} %>
+		  <%= site_select "group[site_id]",{}, :prompt => "(Select a site)" %>
         </p>
         <p>
         Make this a system group invisible to normal users:
diff --git a/BrainPortal/app/views/groups/show.html.erb b/BrainPortal/app/views/groups/show.html.erb
index b5b76d7dd..182d9e2c6 100644
--- a/BrainPortal/app/views/groups/show.html.erb
+++ b/BrainPortal/app/views/groups/show.html.erb
@@ -18,19 +18,19 @@
 # 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/>.
 #
 -%>
 
 <% title "Project Info" %>
 
-<% if @group.is_a?(WorkGroup) %> 
+<% if @group.is_a?(WorkGroup) %>
   <div class="menu_bar">
     <% unless @group.creator_id == current_user.id %>
       <%= link_to 'Unregister', {:action => :unregister, :id => @group.id}, :class => "button", :method  => :post %>
     <% end %>
     <% if @group.can_be_edited_by?(current_user) %>
-    
+
         <%= link_to 'Switch', {:action => :switch, :id => @group.id}, :class => "button", :method  => :post %>
         <% if current_user.has_role?(:normal_user) && @group.can_be_edited_by?(current_user) && current_user.visible_users.present? %>
           <%= overlay_ajax_link "Invite Other Users", new_invitation_path(group_id: @group.id), class: "button" %>
@@ -44,7 +44,7 @@
 
 <%= error_messages_for @group, :header_message => "Project could not be updated." %>
 
-<div class="display_inline_block" style="min-width: 50%"> 
+<div class="display_inline_block" style="min-width: 50%">
 
   <%= show_table(@group, :edit_condition => @group.can_be_edited_by?(current_user)) do |t| %>
 
@@ -55,23 +55,27 @@
     <% t.cell("Creator") { @group.creator.try(:login)} %>
 
     <% t.edit_cell(:site_id, :content => link_to_site_if_accessible(@group.site), :disabled => !current_user.has_role?(:admin_user)) do %>
-      <%= select_tag "group[site_id]", options_for_select(Site.all.map{ |s| [s.name, s.id]}, :selected => @group.site_id), :include_blank => true %>
+
+	  <%= site_select "group[site_id]", @group.site_id, :prompt => "(Select a site)" %>
+
+
+
     <% end %>
 
     <% t.cell("Type") { @group.pretty_category_name(current_user) } %>
-    
+
     <% t.edit_cell(:description, :content =>  overlay_description(@group.description)) do %>
         <%= text_area_tag "group[description]", @group.description, :rows => 4, :cols => 40 %><br>
         <div class="field_explanation">The first line should be a short summary, and the rest are for details.</div><br>
     <% 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 %>
         <%= hidden_field_tag "group[invisible]", "0" %>
         <%= check_box_tag("group[invisible]", "1", @group.invisible?) %>
       <% end %>
     <% end %>
-    
+
     <% t.empty_cell %>
 
   <% end %>
@@ -91,7 +95,7 @@
 
   <% end %>
 
-  <% 
+  <%
     group_members  = @group.users
     open_invites   = Invitation.where(sender_id: current_user.id, group_id: @group.id, active: true)
   %>
@@ -112,12 +116,12 @@
         <div class="generalbox" style="width: 100%">
           <%= render :partial => 'users_form' %><br>
           <%= hidden_field_tag :update_users, true %>
-        </div> 
+        </div>
       <% end %>
     <% end %>
     <% if open_invites.present? %>
       <% default_text = array_to_table(open_invites.map(&:user).sort{ |a,b| a.login.casecmp(b.login)}, :table_class => 'simple bordered float_left', :cols => 20, :min_data => 20, :fill_by_columns => true ) { |u,r,c| u.login } %>
-    
+
       <% t.edit_cell(:invites, :show_width => 2,
                                :header  => 'Pending Invitations',
                                :content => default_text) do %>
diff --git a/BrainPortal/app/views/users/_new.html.erb b/BrainPortal/app/views/users/_new.html.erb
index dd73884a9..f6e105e1a 100644
--- a/BrainPortal/app/views/users/_new.html.erb
+++ b/BrainPortal/app/views/users/_new.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 <http://www.gnu.org/licenses/>.  
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 -%>
 
@@ -62,7 +62,7 @@
 
         <% if current_user.has_role? :admin_user %>
           <p><%= f.label :site_id, "Site" %><br/>
-          <%= f.collection_select :site_id, Site.all.sort { |a,b| a.name <=> b.name }, :id, :name, { :include_blank  => true } %></p>
+			 <%= site_select "user[site_id]",{}, :prompt => "(Select a site)" %>
         <% end %>
 
         <p><%= f.label :password, "Password" %><br/>
diff --git a/BrainPortal/app/views/users/show.html.erb b/BrainPortal/app/views/users/show.html.erb
index badf912fb..dc09f8da2 100644
--- a/BrainPortal/app/views/users/show.html.erb
+++ b/BrainPortal/app/views/users/show.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 <http://www.gnu.org/licenses/>.  
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 -%>
 
@@ -31,7 +31,7 @@
   <% end %>
 
   <%= link_to 'Report Maker', report_path, :class => "button" %>
-  
+
   <% if delete_permission?(@user) %>
     <%= link_to 'Delete', user_path(@user), { :confirm => "Are you sure you want to delete '#{@user.name}' ?", :method => :delete, :class => "button" } %>
   <% end %>
@@ -47,7 +47,7 @@
     <% t.attribute_cell(:login) %>
 
     <%
-      t.edit_cell(:type, :content => @user.type.underscore.titleize, :disabled => !((current_user.has_role?(:site_manager) || current_user.has_role?(:admin_user)) && not_admin_user(@user))) do 
+      t.edit_cell(:type, :content => @user.type.underscore.titleize, :disabled => !((current_user.has_role?(:site_manager) || current_user.has_role?(:admin_user)) && not_admin_user(@user))) do
         select_tag "user[type]", options_for_select(roles_for_user(current_user), :selected => @user.type)
       end
     %>
@@ -56,7 +56,9 @@
 
     <%
       t.edit_cell(:site_id, :content => link_to_site_if_accessible(@user.site), :disabled => !current_user.has_role?(:admin_user)) do
-        select_tag "user[site_id]", options_for_select(Site.all.map{ |s| [s.name, s.id]}, :selected => @user.site_id), :include_blank => true
+
+		  site_select "user[site_id]", @user.site_id, :prompt => "(Select a site)"
+
       end
     %>
 
@@ -94,7 +96,7 @@
         select_tag "user[time_zone]", time_zone_options_for_select(@user.time_zone, /canada/i), :include_blank => true
       end
     %>
-    
+
     <% t.edit_cell(:password, :content => "********") do %>
       <%= link_to "Change Password", change_password_user_path(@user) %>
     <% end %>
@@ -158,7 +160,7 @@
      <table class="resource_list">
         <tr>
           <th colspan="3">
-            Projects 
+            Projects
             <% if current_user.has_role?(:site_manager) || current_user.has_role?(:admin_user) %>
               <%= overlay_content_link "(Update)", :style => "text-decoration: underline; font-size: 0.9em", :enclosing_element => "span" do %>
                 <%= form_for @user, :as => :user, :url => { :action => "update" } do |f| -%>
@@ -192,7 +194,7 @@
     <P>
 
   <% end %>
-  
+
   <P>
   <%= render :partial => "layouts/log_report", :locals  => { :log  => @log, :title => 'User activity report' } %>
 </div>

From 26003c0f6bf8da48c253e37c21775517d24fdc55 Mon Sep 17 00:00:00 2001
From: Ehsan Afkhami <eafkhami@dhcp56-200.mni.mcgill.ca>
Date: Wed, 21 Oct 2015 11:39:24 -0400
Subject: [PATCH 68/85] issue 241 -- removed some empty lines

---
 BrainPortal/app/views/groups/show.html.erb | 4 ----
 BrainPortal/app/views/users/show.html.erb  | 2 --
 2 files changed, 6 deletions(-)

diff --git a/BrainPortal/app/views/groups/show.html.erb b/BrainPortal/app/views/groups/show.html.erb
index 182d9e2c6..bc05d0cda 100644
--- a/BrainPortal/app/views/groups/show.html.erb
+++ b/BrainPortal/app/views/groups/show.html.erb
@@ -55,11 +55,7 @@
     <% t.cell("Creator") { @group.creator.try(:login)} %>
 
     <% t.edit_cell(:site_id, :content => link_to_site_if_accessible(@group.site), :disabled => !current_user.has_role?(:admin_user)) do %>
-
 	  <%= site_select "group[site_id]", @group.site_id, :prompt => "(Select a site)" %>
-
-
-
     <% end %>
 
     <% t.cell("Type") { @group.pretty_category_name(current_user) } %>
diff --git a/BrainPortal/app/views/users/show.html.erb b/BrainPortal/app/views/users/show.html.erb
index dc09f8da2..95cd99053 100644
--- a/BrainPortal/app/views/users/show.html.erb
+++ b/BrainPortal/app/views/users/show.html.erb
@@ -56,9 +56,7 @@
 
     <%
       t.edit_cell(:site_id, :content => link_to_site_if_accessible(@user.site), :disabled => !current_user.has_role?(:admin_user)) do
-
 		  site_select "user[site_id]", @user.site_id, :prompt => "(Select a site)"
-
       end
     %>
 

From 22ea502633b80f67a3e4dd72f02626eefba9a41a Mon Sep 17 00:00:00 2001
From: Ehsan Afkhami <eafkhami@dhcp56-200.mni.mcgill.ca>
Date: Wed, 21 Oct 2015 14:42:40 -0400
Subject: [PATCH 69/85] Tag controller should check user_id and group_id, when
 creating and updating. #209

---
 BrainPortal/app/controllers/tags_controller.rb | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/BrainPortal/app/controllers/tags_controller.rb b/BrainPortal/app/controllers/tags_controller.rb
index 4f5c852b9..827eef284 100644
--- a/BrainPortal/app/controllers/tags_controller.rb
+++ b/BrainPortal/app/controllers/tags_controller.rb
@@ -17,7 +17,7 @@
 # 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 <http://www.gnu.org/licenses/>.  
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 
 #RESTful controller for the Tag resource.
@@ -41,12 +41,14 @@ def edit #:nodoc:
   # POST /tags.xml
   def create #:nodoc:
     @tag = Tag.new(params[:tag])
-    @tag.user_id = current_user.id
+
+     @tag.user_id = current_user.id if @tag.user_id.blank? || !current_user.available_users.raw_first_column(:user_id).include?(@tag.user_id)
+     @tag.group_id = current_user.own_group.id if @tag.user_id.blank? || !current_user.available_groups.map(&:id).include?(@tag.group_id)
 
     respond_to do |format|
       if @tag.save
         flash[:notice] = 'Tag was successfully created.'
-        format.html { redirect_to userfiles_path }        
+        format.html { redirect_to userfiles_path }
         format.xml  { render :xml => @tag, :status => :created, :location => @tag }
       else
         format.html { redirect_to userfiles_path }
@@ -61,6 +63,9 @@ def create #:nodoc:
   def update #:nodoc:
     @tag = current_user.tags.find(params[:id])
 
+    @tag.user_id = current_user.id if @tag.user_id.blank? || !current_user.available_users.raw_first_column(:user_id).include?(@tag.user_id)
+    @tag.group_id = current_user.own_group.id if @tag.user_id.blank? || !current_user.available_groups.map(&:id).include?(@tag.group_id)
+
     respond_to do |format|
       if @tag.update_attributes(params[:tag])
         flash[:notice] = 'Tag was successfully updated.'

From 1849de2ca5c298916752a1ea80fe71bf612c2546 Mon Sep 17 00:00:00 2001
From: Ehsan Afkhami <eafkhami@dhcp56-200.mni.mcgill.ca>
Date: Thu, 22 Oct 2015 12:17:04 -0400
Subject: [PATCH 70/85] updated fix for issue #209 and #241

---
 .../app/controllers/tags_controller.rb        | 20 ++++++++++++++-----
 BrainPortal/app/helpers/select_box_helper.rb  |  1 +
 2 files changed, 16 insertions(+), 5 deletions(-)

diff --git a/BrainPortal/app/controllers/tags_controller.rb b/BrainPortal/app/controllers/tags_controller.rb
index 827eef284..f00c79656 100644
--- a/BrainPortal/app/controllers/tags_controller.rb
+++ b/BrainPortal/app/controllers/tags_controller.rb
@@ -1,4 +1,3 @@
-
 #
 # CBRAIN Project
 #
@@ -26,6 +25,7 @@ class TagsController < ApplicationController
   Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
 
   before_filter :login_required
+  before_filter(:only => [:update]) { |c| c.authenticate_params }
   layout false
 
   def new #:nodoc:
@@ -43,7 +43,7 @@ def create #:nodoc:
     @tag = Tag.new(params[:tag])
 
      @tag.user_id = current_user.id if @tag.user_id.blank? || !current_user.available_users.raw_first_column(:user_id).include?(@tag.user_id)
-     @tag.group_id = current_user.own_group.id if @tag.user_id.blank? || !current_user.available_groups.map(&:id).include?(@tag.group_id)
+     @tag.group_id = current_user.own_group.id if @tag.group_id.blank? || !current_user.available_groups.map(&:id).include?(@tag.group_id)
 
     respond_to do |format|
       if @tag.save
@@ -63,9 +63,6 @@ def create #:nodoc:
   def update #:nodoc:
     @tag = current_user.tags.find(params[:id])
 
-    @tag.user_id = current_user.id if @tag.user_id.blank? || !current_user.available_users.raw_first_column(:user_id).include?(@tag.user_id)
-    @tag.group_id = current_user.own_group.id if @tag.user_id.blank? || !current_user.available_groups.map(&:id).include?(@tag.group_id)
-
     respond_to do |format|
       if @tag.update_attributes(params[:tag])
         flash[:notice] = 'Tag was successfully updated.'
@@ -94,4 +91,17 @@ def destroy #:nodoc:
       format.xml  { head :ok }
     end
   end
+
+
+
+  def authenticate_params
+    user_id = params[:tag][:user_id]
+    group_id = params[:tag][:group_id]
+
+    params[:tag][:user_id] = current_user.id if user_id.blank? || !current_user.available_users.raw_first_column(:id).include?(user_id)
+    params[:tag][:group_id] = current_user.own_group.id if group_id.blank? || !current_user.available_groups.raw_first_column(:id).include?(group_id)
+  end
+
+
+
 end
diff --git a/BrainPortal/app/helpers/select_box_helper.rb b/BrainPortal/app/helpers/select_box_helper.rb
index 1d4a65898..f7fec47e3 100644
--- a/BrainPortal/app/helpers/select_box_helper.rb
+++ b/BrainPortal/app/helpers/select_box_helper.rb
@@ -68,6 +68,7 @@ def user_select(parameter_name = "user_id", options = {}, select_tag_options = {
   # [selector] used for default selection. This can be a Site object, a site id (String or Fixnum),
   #            or any model that has a site_id attribute.
   # [sites] the array of Site objects used to build the select box. Defaults to +Site.order(:name).all+.
+  # +options+ need not be hash, the default selected item can be passed as an argument.
   # When calling site_select, set the :prompt option in select_tag_options hash, to the text you want
   # displayed when no option is selected
   def site_select(parameter_name = "site", options = {}, select_tag_options = {} )

From 78a4343617dce4d32dfeec47ed3d2dd7a24450ad Mon Sep 17 00:00:00 2001
From: Ehsan Afkhami <eafkhami@dhcp56-200.mni.mcgill.ca>
Date: Thu, 22 Oct 2015 13:01:18 -0400
Subject: [PATCH 71/85] second fix update to issue 209 and 241

---
 BrainPortal/app/controllers/tags_controller.rb | 14 ++++++--------
 1 file changed, 6 insertions(+), 8 deletions(-)

diff --git a/BrainPortal/app/controllers/tags_controller.rb b/BrainPortal/app/controllers/tags_controller.rb
index f00c79656..ec899d113 100644
--- a/BrainPortal/app/controllers/tags_controller.rb
+++ b/BrainPortal/app/controllers/tags_controller.rb
@@ -25,7 +25,7 @@ class TagsController < ApplicationController
   Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
 
   before_filter :login_required
-  before_filter(:only => [:update]) { |c| c.authenticate_params }
+  before_filter(:only => [:update, :create]) { |c| c.send :validate_params }
   layout false
 
   def new #:nodoc:
@@ -42,9 +42,6 @@ def edit #:nodoc:
   def create #:nodoc:
     @tag = Tag.new(params[:tag])
 
-     @tag.user_id = current_user.id if @tag.user_id.blank? || !current_user.available_users.raw_first_column(:user_id).include?(@tag.user_id)
-     @tag.group_id = current_user.own_group.id if @tag.group_id.blank? || !current_user.available_groups.map(&:id).include?(@tag.group_id)
-
     respond_to do |format|
       if @tag.save
         flash[:notice] = 'Tag was successfully created.'
@@ -92,14 +89,15 @@ def destroy #:nodoc:
     end
   end
 
+  private
 
-
-  def authenticate_params
+  # This method validates that the current user has access to the user and group being assigned to the created or updated tag
+  def validate_params #:nodoc:
     user_id = params[:tag][:user_id]
     group_id = params[:tag][:group_id]
 
-    params[:tag][:user_id] = current_user.id if user_id.blank? || !current_user.available_users.raw_first_column(:id).include?(user_id)
-    params[:tag][:group_id] = current_user.own_group.id if group_id.blank? || !current_user.available_groups.raw_first_column(:id).include?(group_id)
+    params[:tag][:user_id]  = current_user.id           if !current_user.available_users.raw_first_column(:id).include?(user_id)
+    params[:tag][:group_id] = current_user.own_group.id if !current_user.available_groups.raw_first_column(:id).include?(group_id)
   end
 
 

From dd783668bc287f169888b0138fd15d6df2f0590d Mon Sep 17 00:00:00 2001
From: Ehsan Afkhami <eafkhami@dhcp56-200.mni.mcgill.ca>
Date: Thu, 22 Oct 2015 14:18:20 -0400
Subject: [PATCH 72/85] removed some tabed lines

---
 BrainPortal/app/controllers/tags_controller.rb | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/BrainPortal/app/controllers/tags_controller.rb b/BrainPortal/app/controllers/tags_controller.rb
index ec899d113..01c235b5a 100644
--- a/BrainPortal/app/controllers/tags_controller.rb
+++ b/BrainPortal/app/controllers/tags_controller.rb
@@ -93,11 +93,11 @@ def destroy #:nodoc:
 
   # This method validates that the current user has access to the user and group being assigned to the created or updated tag
   def validate_params #:nodoc:
-    user_id = params[:tag][:user_id]
-    group_id = params[:tag][:group_id]
+   user_id = params[:tag][:user_id]
+   group_id = params[:tag][:group_id]
 
-    params[:tag][:user_id]  = current_user.id           if !current_user.available_users.raw_first_column(:id).include?(user_id)
-    params[:tag][:group_id] = current_user.own_group.id if !current_user.available_groups.raw_first_column(:id).include?(group_id)
+   params[:tag][:user_id]  = current_user.id           if !current_user.available_users.raw_first_column(:id).include?(user_id)
+   params[:tag][:group_id] = current_user.own_group.id if !current_user.available_groups.raw_first_column(:id).include?(group_id)
   end
 
 

From 129bd20d19f031b7db62c737f608c4a52a80d829 Mon Sep 17 00:00:00 2001
From: Ehsan Afkhami <eafkhami@dhcp56-200.mni.mcgill.ca>
Date: Thu, 22 Oct 2015 14:54:27 -0400
Subject: [PATCH 73/85] removed the block from before filter for issue 209

---
 BrainPortal/app/controllers/tags_controller.rb | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/BrainPortal/app/controllers/tags_controller.rb b/BrainPortal/app/controllers/tags_controller.rb
index 01c235b5a..477ff3d51 100644
--- a/BrainPortal/app/controllers/tags_controller.rb
+++ b/BrainPortal/app/controllers/tags_controller.rb
@@ -25,7 +25,7 @@ class TagsController < ApplicationController
   Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
 
   before_filter :login_required
-  before_filter(:only => [:update, :create]) { |c| c.send :validate_params }
+  before_filter :validate_params, :only => [:update, :create]
   layout false
 
   def new #:nodoc:
@@ -93,11 +93,11 @@ def destroy #:nodoc:
 
   # This method validates that the current user has access to the user and group being assigned to the created or updated tag
   def validate_params #:nodoc:
-   user_id = params[:tag][:user_id]
-   group_id = params[:tag][:group_id]
+    user_id = params[:tag][:user_id]
+    group_id = params[:tag][:group_id]
 
-   params[:tag][:user_id]  = current_user.id           if !current_user.available_users.raw_first_column(:id).include?(user_id)
-   params[:tag][:group_id] = current_user.own_group.id if !current_user.available_groups.raw_first_column(:id).include?(group_id)
+    params[:tag][:user_id]  = current_user.id           if !current_user.available_users.raw_first_column(:id).include?(user_id)
+    params[:tag][:group_id] = current_user.own_group.id if !current_user.available_groups.raw_first_column(:id).include?(group_id)
   end
 
 

From 0266c9a187c09d126b63c004bf057785a5ce05da Mon Sep 17 00:00:00 2001
From: Ehsan Afkhami <eafkhami@dhcp56-200.mni.mcgill.ca>
Date: Fri, 23 Oct 2015 09:49:49 -0400
Subject: [PATCH 74/85] issue 98, not yet complete

---
 .../app/views/layouts/_section_account.html.erb      |  5 ++++-
 BrainPortal/config/initializers/cbrain.rb            |  4 ++--
 BrainPortal/lib/cbrain_file_revision.rb              | 12 ++++++++++--
 3 files changed, 16 insertions(+), 5 deletions(-)

diff --git a/BrainPortal/app/views/layouts/_section_account.html.erb b/BrainPortal/app/views/layouts/_section_account.html.erb
index 989662564..d6653a4bb 100644
--- a/BrainPortal/app/views/layouts/_section_account.html.erb
+++ b/BrainPortal/app/views/layouts/_section_account.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 <http://www.gnu.org/licenses/>.  
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 -%>
 
@@ -57,6 +57,9 @@
       <% end %>
     <% end %>
     Rev:&nbsp;<%= $CBRAIN_StartTime_Revision %>
+    <%if current_user.has_role?(:admin_user) && !CbrainFileRevision.git_branch_name.blank? %>
+      &nbsp;<%= CbrainFileRevision.git_branch_name %>
+    <%end%>
   </span>
 
   <span class="loggedas">
diff --git a/BrainPortal/config/initializers/cbrain.rb b/BrainPortal/config/initializers/cbrain.rb
index 1e10fad39..4cb962fb7 100644
--- a/BrainPortal/config/initializers/cbrain.rb
+++ b/BrainPortal/config/initializers/cbrain.rb
@@ -17,7 +17,7 @@
 # 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 <http://www.gnu.org/licenses/>.  
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 
 # CBRAIN constants and some global utility methods.
@@ -172,7 +172,7 @@ def self.spawn_with_active_records_if(condition,destination = nil, taskname = 'I
       end
     end
   end
-  
+
   # This method runs a Ruby block in the background, as a separate subprocess,
   # but without any access to the services provided by Rails (no ActiveRecords,
   # no DB, all filehandles closed except for STDIN, STDOUT and STDERR). If
diff --git a/BrainPortal/lib/cbrain_file_revision.rb b/BrainPortal/lib/cbrain_file_revision.rb
index 729a499fe..c25a1a2cf 100644
--- a/BrainPortal/lib/cbrain_file_revision.rb
+++ b/BrainPortal/lib/cbrain_file_revision.rb
@@ -17,7 +17,7 @@
 # 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 <http://www.gnu.org/licenses/>.  
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 
 # This class encapsulates an information record about
@@ -194,6 +194,14 @@ def self.git_available? #:nodoc:
     @_git_available == :yes
   end
 
+  def self.git_branch_name
+    return "" unless git_available?
+    IO.popen("git rev-parse --abbrev-ref HEAD") do |fh|
+      fh.gets.strip
+    end
+  end
+
+
   def self.for_relpath(relpath, mode = :auto) #:nodoc:
     cbrain_root = Pathname.new(Rails.root).parent
     rev = self.new("#{cbrain_root}/#{relpath}") # TODO: find the object originally registered IN its file?
@@ -320,7 +328,7 @@ def get_git_rev_info_from_static_file #:nodoc:
     end
 
     return self unless revinfo # not much else to do
-   
+
     @commit   = revinfo[0]
     datetime  = revinfo[1]
     if datetime =~ /(\d\d\d\d-\d\d-\d\dT?)\s*(\d\d:\d\d:\d\dZ?)(\s*[+-][\d:]+)?/

From 320775504eae0e2cda51ec36fe33e2f4b92f7d79 Mon Sep 17 00:00:00 2001
From: Ehsan Afkhami <eafkhami@dhcp56-200.mni.mcgill.ca>
Date: Fri, 23 Oct 2015 15:53:50 -0400
Subject: [PATCH 75/85] display git branch name feature #98

---
 BrainPortal/app/models/exception_log.rb              |  2 +-
 BrainPortal/app/models/remote_resource.rb            | 12 ++++++------
 .../app/views/bourreaux/_bourreaux_display.html.erb  |  2 +-
 .../app/views/layouts/_section_account.html.erb      |  8 ++++----
 .../active_record.rb                                 |  0
 .../array.rb                                         |  0
 .../exceptions.rb                                    |  0
 .../hash.rb                                          |  0
 .../kernel.rb                                        |  0
 .../object.rb                                        |  0
 .../string.rb                                        |  0
 .../symbol.rb                                        |  0
 .../traces_cbrain.rb                                 |  0
 BrainPortal/config/initializers/cbrain.rb            |  5 ++++-
 BrainPortal/lib/cbrain_system_checks.rb              |  5 +----
 15 files changed, 17 insertions(+), 17 deletions(-)
 rename BrainPortal/config/initializers/{core_extensions => added_core_extensions}/active_record.rb (100%)
 rename BrainPortal/config/initializers/{core_extensions => added_core_extensions}/array.rb (100%)
 rename BrainPortal/config/initializers/{core_extensions => added_core_extensions}/exceptions.rb (100%)
 rename BrainPortal/config/initializers/{core_extensions => added_core_extensions}/hash.rb (100%)
 rename BrainPortal/config/initializers/{core_extensions => added_core_extensions}/kernel.rb (100%)
 rename BrainPortal/config/initializers/{core_extensions => added_core_extensions}/object.rb (100%)
 rename BrainPortal/config/initializers/{core_extensions => added_core_extensions}/string.rb (100%)
 rename BrainPortal/config/initializers/{core_extensions => added_core_extensions}/symbol.rb (100%)
 rename BrainPortal/config/initializers/{core_extensions => added_core_extensions}/traces_cbrain.rb (100%)

diff --git a/BrainPortal/app/models/exception_log.rb b/BrainPortal/app/models/exception_log.rb
index ec9973a7f..93ae89a41 100644
--- a/BrainPortal/app/models/exception_log.rb
+++ b/BrainPortal/app/models/exception_log.rb
@@ -56,7 +56,7 @@ def self.log_exception(exception, user, request)
     e.session            = session.to_hash
     e.request_headers    = hdrs
     e.instance_name      = CBRAIN::Instance_Name rescue "(?)"
-    e.revision_no        = $CBRAIN_StartTime_Revision
+    e.revision_no        = CBRAIN::CBRAIN_StartTime_Revision
     e.save
 
     e
diff --git a/BrainPortal/app/models/remote_resource.rb b/BrainPortal/app/models/remote_resource.rb
index 25918748f..cbb7ee9af 100644
--- a/BrainPortal/app/models/remote_resource.rb
+++ b/BrainPortal/app/models/remote_resource.rb
@@ -551,11 +551,11 @@ def self.remote_resource_info
       :rails_time_zone    => time_zone_name,
 
       # Svn info
-      :revision           => @git_tag,                  # 'live' value
-      :lc_author          => @git_author,               # at process start
-      :lc_rev             => @git_commit,               # at process start
-      :lc_date            => @git_date,                 # at process start
-      :starttime_revision => $CBRAIN_StartTime_Revision # at process start
+      :revision           => @git_tag,                          # 'live' value
+      :lc_author          => @git_author,                       # at process start
+      :lc_rev             => @git_commit,                       # at process start
+      :lc_date            => @git_date,                         # at process start
+      :starttime_revision => CBRAIN::CBRAIN_StartTime_Revision  # at process start
 
     )
 
@@ -571,7 +571,7 @@ def self.remote_resource_ping
     info                    = RemoteResourceInfo.new
     info.id                 = rr.id
     info.name               = rr.name
-    info.starttime_revision = $CBRAIN_StartTime_Revision
+    info.starttime_revision = CBRAIN::CBRAIN_StartTime_Revision
     info.uptime             = Time.now.localtime - CBRAIN::Startup_LocalTime
     info
   end
diff --git a/BrainPortal/app/views/bourreaux/_bourreaux_display.html.erb b/BrainPortal/app/views/bourreaux/_bourreaux_display.html.erb
index c558a30c3..0f4acd5b9 100644
--- a/BrainPortal/app/views/bourreaux/_bourreaux_display.html.erb
+++ b/BrainPortal/app/views/bourreaux/_bourreaux_display.html.erb
@@ -66,7 +66,7 @@
     ) do |r|
       if loaded.(r)
         revision = r.info(:ping).starttime_revision
-        red_if(revision != '???' && revision != $CBRAIN_StartTime_Revision, revision, nil, :color2 => 'red')
+        red_if(revision != '???' && revision != CBRAIN::CBRAIN_StartTime_Revision, revision, nil, :color2 => 'red')
       else
         html_colorize("(...)", "magenta")
       end
diff --git a/BrainPortal/app/views/layouts/_section_account.html.erb b/BrainPortal/app/views/layouts/_section_account.html.erb
index d6653a4bb..a9a9236bd 100644
--- a/BrainPortal/app/views/layouts/_section_account.html.erb
+++ b/BrainPortal/app/views/layouts/_section_account.html.erb
@@ -56,10 +56,10 @@
         <% end %>
       <% end %>
     <% end %>
-    Rev:&nbsp;<%= $CBRAIN_StartTime_Revision %>
-    <%if current_user.has_role?(:admin_user) && !CbrainFileRevision.git_branch_name.blank? %>
-      &nbsp;<%= CbrainFileRevision.git_branch_name %>
-    <%end%>
+    Rev: <%= CBRAIN::CBRAIN_StartTime_Revision %>
+    <% if current_user.has_role?(:admin_user) %>
+      <%= "Branch: " + (CBRAIN::CBRAIN_Git_Branch.present? ? CBRAIN::CBRAIN_Git_Branch : "unknown") %>
+    <% end %>
   </span>
 
   <span class="loggedas">
diff --git a/BrainPortal/config/initializers/core_extensions/active_record.rb b/BrainPortal/config/initializers/added_core_extensions/active_record.rb
similarity index 100%
rename from BrainPortal/config/initializers/core_extensions/active_record.rb
rename to BrainPortal/config/initializers/added_core_extensions/active_record.rb
diff --git a/BrainPortal/config/initializers/core_extensions/array.rb b/BrainPortal/config/initializers/added_core_extensions/array.rb
similarity index 100%
rename from BrainPortal/config/initializers/core_extensions/array.rb
rename to BrainPortal/config/initializers/added_core_extensions/array.rb
diff --git a/BrainPortal/config/initializers/core_extensions/exceptions.rb b/BrainPortal/config/initializers/added_core_extensions/exceptions.rb
similarity index 100%
rename from BrainPortal/config/initializers/core_extensions/exceptions.rb
rename to BrainPortal/config/initializers/added_core_extensions/exceptions.rb
diff --git a/BrainPortal/config/initializers/core_extensions/hash.rb b/BrainPortal/config/initializers/added_core_extensions/hash.rb
similarity index 100%
rename from BrainPortal/config/initializers/core_extensions/hash.rb
rename to BrainPortal/config/initializers/added_core_extensions/hash.rb
diff --git a/BrainPortal/config/initializers/core_extensions/kernel.rb b/BrainPortal/config/initializers/added_core_extensions/kernel.rb
similarity index 100%
rename from BrainPortal/config/initializers/core_extensions/kernel.rb
rename to BrainPortal/config/initializers/added_core_extensions/kernel.rb
diff --git a/BrainPortal/config/initializers/core_extensions/object.rb b/BrainPortal/config/initializers/added_core_extensions/object.rb
similarity index 100%
rename from BrainPortal/config/initializers/core_extensions/object.rb
rename to BrainPortal/config/initializers/added_core_extensions/object.rb
diff --git a/BrainPortal/config/initializers/core_extensions/string.rb b/BrainPortal/config/initializers/added_core_extensions/string.rb
similarity index 100%
rename from BrainPortal/config/initializers/core_extensions/string.rb
rename to BrainPortal/config/initializers/added_core_extensions/string.rb
diff --git a/BrainPortal/config/initializers/core_extensions/symbol.rb b/BrainPortal/config/initializers/added_core_extensions/symbol.rb
similarity index 100%
rename from BrainPortal/config/initializers/core_extensions/symbol.rb
rename to BrainPortal/config/initializers/added_core_extensions/symbol.rb
diff --git a/BrainPortal/config/initializers/core_extensions/traces_cbrain.rb b/BrainPortal/config/initializers/added_core_extensions/traces_cbrain.rb
similarity index 100%
rename from BrainPortal/config/initializers/core_extensions/traces_cbrain.rb
rename to BrainPortal/config/initializers/added_core_extensions/traces_cbrain.rb
diff --git a/BrainPortal/config/initializers/cbrain.rb b/BrainPortal/config/initializers/cbrain.rb
index 4cb962fb7..2f0a37a80 100644
--- a/BrainPortal/config/initializers/cbrain.rb
+++ b/BrainPortal/config/initializers/cbrain.rb
@@ -48,7 +48,10 @@ class CBRAIN
   TasksPlugins_Dir           = "#{Plugins_Dir}/installed-plugins/cbrain_task" # singular; historical
   TaskDescriptorsPlugins_Dir = "#{Plugins_Dir}/installed-plugins/cbrain_task_descriptors"
 
-  $CBRAIN_StartTime_Revision = "???"  # Will be filled in by validation script
+  CBRAIN_StartTime_Revision = CbrainFileRevision.cbrain_head_tag
+
+  # Return current git branch for Cbrain, if no branch present resturn blank
+  CBRAIN_Git_Branch = CbrainFileRevision.git_branch_name
 
   # Some environment variables MUST be set for some subsystems to work.
   # In deployment at McGill, we run the rails application under control
diff --git a/BrainPortal/lib/cbrain_system_checks.rb b/BrainPortal/lib/cbrain_system_checks.rb
index 8da769e06..6b3034b0e 100644
--- a/BrainPortal/lib/cbrain_system_checks.rb
+++ b/BrainPortal/lib/cbrain_system_checks.rb
@@ -289,11 +289,8 @@ def self.a050_check_data_provider_cache_wipe
 
   def self.a080_ensure_set_starttime_revision
 
-    # Global for the whole Rails process
-    $CBRAIN_StartTime_Revision = RemoteResource.current_resource.info.revision
-
     #-----------------------------------------------------------------------------
-    puts "C> Current application tag or revision: #{$CBRAIN_StartTime_Revision}"
+    puts "C> Current application tag or revision: #{CBRAIN::CBRAIN_StartTime_Revision}"
     #-----------------------------------------------------------------------------
 
   end

From 3ed55ddd0c3e4b39446f3189329ff14e9c9af6b1 Mon Sep 17 00:00:00 2001
From: Ehsan Afkhami <eafkhami@dhcp56-200.mni.mcgill.ca>
Date: Fri, 23 Oct 2015 16:14:02 -0400
Subject: [PATCH 76/85] bug fix for issue 209

---
 BrainPortal/app/controllers/tags_controller.rb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/BrainPortal/app/controllers/tags_controller.rb b/BrainPortal/app/controllers/tags_controller.rb
index 477ff3d51..abf32f27b 100644
--- a/BrainPortal/app/controllers/tags_controller.rb
+++ b/BrainPortal/app/controllers/tags_controller.rb
@@ -96,8 +96,8 @@ def validate_params #:nodoc:
     user_id = params[:tag][:user_id]
     group_id = params[:tag][:group_id]
 
-    params[:tag][:user_id]  = current_user.id           if !current_user.available_users.raw_first_column(:id).include?(user_id)
-    params[:tag][:group_id] = current_user.own_group.id if !current_user.available_groups.raw_first_column(:id).include?(group_id)
+    params[:tag][:user_id]  = current_user.id           if !current_user.available_users.raw_first_column(:id).include?(user_id.to_i)
+    params[:tag][:group_id] = current_user.own_group.id if !current_user.available_groups.raw_first_column(:id).include?(group_id.to_i)
   end
 
 

From 1cb8efac11d90ec66aa7eb3acc628b73ebdbd13d Mon Sep 17 00:00:00 2001
From: Ehsan Afkhami <eafkhami@dhcp56-200.mni.mcgill.ca>
Date: Fri, 23 Oct 2015 16:44:05 -0400
Subject: [PATCH 77/85] added git branch to boot messages

---
 BrainPortal/lib/cbrain_system_checks.rb | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/BrainPortal/lib/cbrain_system_checks.rb b/BrainPortal/lib/cbrain_system_checks.rb
index 6b3034b0e..f19d64779 100644
--- a/BrainPortal/lib/cbrain_system_checks.rb
+++ b/BrainPortal/lib/cbrain_system_checks.rb
@@ -290,7 +290,9 @@ def self.a050_check_data_provider_cache_wipe
   def self.a080_ensure_set_starttime_revision
 
     #-----------------------------------------------------------------------------
-    puts "C> Current application tag or revision: #{CBRAIN::CBRAIN_StartTime_Revision}"
+    puts  "C> Current application tag or revision: #{CBRAIN::CBRAIN_StartTime_Revision}"
+    print "C> Current Git branch: "
+    CBRAIN::CBRAIN_Git_Branch.present? ? puts(CBRAIN::CBRAIN_Git_Branch) : puts("unknown")
     #-----------------------------------------------------------------------------
 
   end

From 79b006c232750af2f9295f37898e24ee2dc909ec Mon Sep 17 00:00:00 2001
From: Ehsan Afkhami <eafkhami@dhcp56-200.mni.mcgill.ca>
Date: Mon, 26 Oct 2015 13:57:40 -0400
Subject: [PATCH 78/85] simplifying code for issue 245

---
 BrainPortal/app/views/layouts/_section_account.html.erb | 2 +-
 BrainPortal/lib/cbrain_system_checks.rb                 | 5 +----
 2 files changed, 2 insertions(+), 5 deletions(-)

diff --git a/BrainPortal/app/views/layouts/_section_account.html.erb b/BrainPortal/app/views/layouts/_section_account.html.erb
index a9a9236bd..c8da22c20 100644
--- a/BrainPortal/app/views/layouts/_section_account.html.erb
+++ b/BrainPortal/app/views/layouts/_section_account.html.erb
@@ -58,7 +58,7 @@
     <% end %>
     Rev: <%= CBRAIN::CBRAIN_StartTime_Revision %>
     <% if current_user.has_role?(:admin_user) %>
-      <%= "Branch: " + (CBRAIN::CBRAIN_Git_Branch.present? ? CBRAIN::CBRAIN_Git_Branch : "unknown") %>
+     "Branch: " <%=  CBRAIN::CBRAIN_Git_Branch.presence || "unknown" %>
     <% end %>
   </span>
 
diff --git a/BrainPortal/lib/cbrain_system_checks.rb b/BrainPortal/lib/cbrain_system_checks.rb
index f19d64779..b27d1740b 100644
--- a/BrainPortal/lib/cbrain_system_checks.rb
+++ b/BrainPortal/lib/cbrain_system_checks.rb
@@ -288,13 +288,10 @@ def self.a050_check_data_provider_cache_wipe
 
 
   def self.a080_ensure_set_starttime_revision
-
     #-----------------------------------------------------------------------------
     puts  "C> Current application tag or revision: #{CBRAIN::CBRAIN_StartTime_Revision}"
-    print "C> Current Git branch: "
-    CBRAIN::CBRAIN_Git_Branch.present? ? puts(CBRAIN::CBRAIN_Git_Branch) : puts("unknown")
+    puts  "C> Current Git branch: + #{CBRAIN::CBRAIN_Git_Branch.presence || "unknown"}"
     #-----------------------------------------------------------------------------
-
   end
 
   private

From f150d4d88b0290a5e23b6023d7ec664333fb872b Mon Sep 17 00:00:00 2001
From: Ehsan Afkhami <eafkhami@dhcp56-200.mni.mcgill.ca>
Date: Mon, 26 Oct 2015 14:15:45 -0400
Subject: [PATCH 79/85] look and feel change to issue 245 fix

---
 BrainPortal/app/views/layouts/_section_account.html.erb | 2 +-
 BrainPortal/lib/cbrain_system_checks.rb                 | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/BrainPortal/app/views/layouts/_section_account.html.erb b/BrainPortal/app/views/layouts/_section_account.html.erb
index c8da22c20..6cc78209d 100644
--- a/BrainPortal/app/views/layouts/_section_account.html.erb
+++ b/BrainPortal/app/views/layouts/_section_account.html.erb
@@ -58,7 +58,7 @@
     <% end %>
     Rev: <%= CBRAIN::CBRAIN_StartTime_Revision %>
     <% if current_user.has_role?(:admin_user) %>
-     "Branch: " <%=  CBRAIN::CBRAIN_Git_Branch.presence || "unknown" %>
+     &nbsp;Branch: <%=  CBRAIN::CBRAIN_Git_Branch.presence || "unknown" %>
     <% end %>
   </span>
 
diff --git a/BrainPortal/lib/cbrain_system_checks.rb b/BrainPortal/lib/cbrain_system_checks.rb
index b27d1740b..035ebecdb 100644
--- a/BrainPortal/lib/cbrain_system_checks.rb
+++ b/BrainPortal/lib/cbrain_system_checks.rb
@@ -290,7 +290,7 @@ def self.a050_check_data_provider_cache_wipe
   def self.a080_ensure_set_starttime_revision
     #-----------------------------------------------------------------------------
     puts  "C> Current application tag or revision: #{CBRAIN::CBRAIN_StartTime_Revision}"
-    puts  "C> Current Git branch: + #{CBRAIN::CBRAIN_Git_Branch.presence || "unknown"}"
+    puts  "C> Current Git branch: #{CBRAIN::CBRAIN_Git_Branch.presence || "unknown"}"
     #-----------------------------------------------------------------------------
   end
 

From 95fb0cc44e450aaa959c971c145dfcbeb156f0bf Mon Sep 17 00:00:00 2001
From: Pierre Rioux <pierre.rioux@mcgill.ca>
Date: Tue, 27 Oct 2015 12:21:37 -0400
Subject: [PATCH 80/85] Adjustments to 'dev' branch.

---
 BrainPortal/app/views/layouts/_section_account.html.erb | 4 ++--
 BrainPortal/db/schema.rb                                | 5 +++--
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/BrainPortal/app/views/layouts/_section_account.html.erb b/BrainPortal/app/views/layouts/_section_account.html.erb
index 6cc78209d..4d664a406 100644
--- a/BrainPortal/app/views/layouts/_section_account.html.erb
+++ b/BrainPortal/app/views/layouts/_section_account.html.erb
@@ -57,8 +57,8 @@
       <% end %>
     <% end %>
     Rev: <%= CBRAIN::CBRAIN_StartTime_Revision %>
-    <% if current_user.has_role?(:admin_user) %>
-     &nbsp;Branch: <%=  CBRAIN::CBRAIN_Git_Branch.presence || "unknown" %>
+    <% if current_user.present? && current_user.has_role?(:admin_user) %>
+      Branch: <%=  CBRAIN::CBRAIN_Git_Branch.presence || "unknown" %>
     <% end %>
   </span>
 
diff --git a/BrainPortal/db/schema.rb b/BrainPortal/db/schema.rb
index 022f3e81b..1509f51e4 100644
--- a/BrainPortal/db/schema.rb
+++ b/BrainPortal/db/schema.rb
@@ -11,7 +11,7 @@
 #
 # It's strongly recommended to check this file into your version control system.
 
-ActiveRecord::Schema.define(:version => 20150615174035) do
+ActiveRecord::Schema.define(:version => 20150929193957) do
 
   create_table "active_record_logs", :force => true do |t|
     t.integer  "ar_id"
@@ -236,6 +236,7 @@
     t.string   "support_email"
     t.string   "system_from_email"
     t.string   "external_status_page_url"
+    t.string   "docker_executable_name"
   end
 
   add_index "remote_resources", ["type"], :name => "index_remote_resources_on_type"
@@ -316,6 +317,7 @@
     t.integer  "group_id"
     t.integer  "ncpus"
     t.string   "docker_image"
+    t.string   "extra_qsub_args"
   end
 
   add_index "tool_configs", ["bourreau_id"], :name => "index_tool_configs_on_bourreau_id"
@@ -360,7 +362,6 @@
   add_index "userfiles", ["data_provider_id"], :name => "index_userfiles_on_data_provider_id"
   add_index "userfiles", ["group_id"], :name => "index_userfiles_on_group_id"
   add_index "userfiles", ["hidden", "id"], :name => "index_userfiles_on_hidden_and_id"
-  add_index "userfiles", ["hidden"], :name => "index_userfiles_on_hidden"
   add_index "userfiles", ["immutable", "id"], :name => "index_userfiles_on_immutable_and_id"
   add_index "userfiles", ["name"], :name => "index_userfiles_on_name"
   add_index "userfiles", ["type"], :name => "index_userfiles_on_type"

From cb68f893745f479e8c301b4deaecf6451f8e2c48 Mon Sep 17 00:00:00 2001
From: Pierre Rioux <pierre.rioux@mcgill.ca>
Date: Tue, 27 Oct 2015 13:09:11 -0400
Subject: [PATCH 81/85] Coloring of account bar based on GIT branch name.

---
 .../views/layouts/_section_account.html.erb   | 10 ++++++--
 BrainPortal/public/stylesheets/cbrain.css     | 23 ++++++++++++++++++-
 2 files changed, 30 insertions(+), 3 deletions(-)

diff --git a/BrainPortal/app/views/layouts/_section_account.html.erb b/BrainPortal/app/views/layouts/_section_account.html.erb
index 4d664a406..c760ce1b8 100644
--- a/BrainPortal/app/views/layouts/_section_account.html.erb
+++ b/BrainPortal/app/views/layouts/_section_account.html.erb
@@ -26,7 +26,13 @@
 <!-- PARTIAL: ACCOUNT SECTION -->
 <!-- ************************ -->
 
-<div class="account">
+<%
+  # We can colorize the CBRAIN interface based on the current GIT branch
+  # One only needs to define a CSS class 'account_git_branch_NAME'
+  git_branch = CBRAIN::CBRAIN_Git_Branch.presence || "unknown"
+%>
+
+<div class="account account_git_branch_<%= git_branch.gsub(/\W/,"_") %>">
 
   <span class="home_credits">
     <% if current_user %>
@@ -58,7 +64,7 @@
     <% end %>
     Rev: <%= CBRAIN::CBRAIN_StartTime_Revision %>
     <% if current_user.present? && current_user.has_role?(:admin_user) %>
-      Branch: <%=  CBRAIN::CBRAIN_Git_Branch.presence || "unknown" %>
+      Branch: <%= git_branch %>
     <% end %>
   </span>
 
diff --git a/BrainPortal/public/stylesheets/cbrain.css b/BrainPortal/public/stylesheets/cbrain.css
index e2e48af1f..005c0c867 100644
--- a/BrainPortal/public/stylesheets/cbrain.css
+++ b/BrainPortal/public/stylesheets/cbrain.css
@@ -905,7 +905,7 @@ pre {
 /* % ######################################################### */
 
 .account {
-  background: #0471B4;
+  background: #0471B4;  /* can be overridden in .account_git_branch_NNNN later in this file */
   color: #fff;
   height:1.8em;
   font-size: 0.9em;
@@ -935,6 +935,27 @@ pre {
   font-weight: bold;
 }
 
+/* ============================================================================== */
+/* Special coloring of the account section's background, based on GIT branch name */
+/* These should all be named .account_git_branch_NNNN where NNNN is a branch name */
+/* ============================================================================== */
+
+.account_git_branch_dev { /* used by devlopment team, obviously */
+  background: #AA04B4;
+}
+
+.account_git_branch_master {
+  background: #0471B4; /* same as in .account */
+}
+
+.account_git_branch_service {
+  background: #0471B4; /* same as in .account */
+}
+
+.account_git_branch_unknown {  /* when not deployed using GIT */
+  background: #0471B4; /* same as in .account */
+}
+
 
 
 /* % ######################################################### */

From 218a221e6f50afae62c48434cf917dfd7c0e0503 Mon Sep 17 00:00:00 2001
From: Pierre Rioux <pierre.rioux@mcgill.ca>
Date: Wed, 28 Oct 2015 13:16:20 -0400
Subject: [PATCH 82/85] Limit CSVFile viewability to size < 200K

---
 .../cbrain-plugins-base/userfiles/csv_file/csv_file.rb   | 9 ++++++++-
 BrainPortal/config/console_rc.rb                         | 4 ++--
 2 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/csv_file/csv_file.rb b/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/csv_file/csv_file.rb
index 8fae42223..176ec702c 100644
--- a/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/csv_file/csv_file.rb
+++ b/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/csv_file/csv_file.rb
@@ -27,7 +27,7 @@ class CSVFile < TextFile
 
   Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
 
-  has_viewer :name => 'CSV Viewer', :partial  => :csv_file, :if  => :is_locally_synced?
+  has_viewer :name => 'CSV Viewer', :partial  => :csv_file, :if  => :is_viewable
 
   def self.pretty_type #:nodoc:
     "CSV File"
@@ -37,6 +37,13 @@ def self.file_name_pattern #:nodoc:
     /\.csv$/i
   end
 
+  def is_viewable #:nodoc
+    return false unless is_locally_synced?
+    return false unless self.size.presence
+    return false unless self.size < 200_000
+    true
+  end
+
   # Tries to guess and return the quote character
   # and the separator character for the content of the CSV file.
   # This method invokes the class method of the same name,
diff --git a/BrainPortal/config/console_rc.rb b/BrainPortal/config/console_rc.rb
index 2b6bfbc7a..9e6733f66 100644
--- a/BrainPortal/config/console_rc.rb
+++ b/BrainPortal/config/console_rc.rb
@@ -117,7 +117,7 @@ def bb_bash(*bb)
 # cycle_bb :start,   [list of bourreaux]   # starts bourreaux
 # cycle_bb :stop,    [list of bourreaux]   # stops bourreaux (implies :workoff)
 # cycle_bb :workon,  [list of bourreaux]   # starts bourreau workers
-# cycle_bb :workoff, [list of bourreaux]   # starts bourreau workers
+# cycle_bb :workoff, [list of bourreaux]   # stops bourreau workers
 # cycle_bb :cycle,   [list of bourreaux]   # does 'workoff,stop,start,workon'
 def cycle_bb(*bb)
 
@@ -128,7 +128,7 @@ def cycle_bb(*bb)
 
 Usage: cycle_bb(what, bourreau_list = <online bourreaux>)
 where 'what' is "start", "stop", "workon", "workoff" or a combination,
-or the keyword "cycle" which means "stop start workon".
+or the keyword "cycle" which means "workoff stop start workon".
 
     USAGE
     return false

From 9ff9a53aa5617a4272939a543d341784647d9254 Mon Sep 17 00:00:00 2001
From: Pierre Rioux <pierre.rioux@mcgill.ca>
Date: Thu, 29 Oct 2015 11:20:31 -0400
Subject: [PATCH 83/85] Added size limit to view TextFiles

---
 .../cbrain-plugins-base/userfiles/csv_file/csv_file.rb   | 6 +++---
 .../cbrain-plugins-base/userfiles/text_file/text_file.rb | 9 ++++++++-
 2 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/csv_file/csv_file.rb b/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/csv_file/csv_file.rb
index 176ec702c..3d00c7813 100644
--- a/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/csv_file/csv_file.rb
+++ b/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/csv_file/csv_file.rb
@@ -27,7 +27,7 @@ class CSVFile < TextFile
 
   Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
 
-  has_viewer :name => 'CSV Viewer', :partial  => :csv_file, :if  => :is_viewable
+  has_viewer :name => 'CSV Viewer', :partial  => :csv_file, :if => :is_viewable
 
   def self.pretty_type #:nodoc:
     "CSV File"
@@ -38,9 +38,9 @@ def self.file_name_pattern #:nodoc:
   end
 
   def is_viewable #:nodoc
-    return false unless is_locally_synced?
     return false unless self.size.presence
-    return false unless self.size < 200_000
+    return false unless self.size < 200_000  # smaller than the limit in TextFile
+    return false unless is_locally_synced?
     true
   end
 
diff --git a/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/text_file/text_file.rb b/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/text_file/text_file.rb
index 962cd853b..a383727ab 100644
--- a/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/text_file/text_file.rb
+++ b/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/text_file/text_file.rb
@@ -25,10 +25,17 @@ class TextFile < SingleFile
 
   Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
 
-  has_viewer :name => 'Text File', :partial  => :text_file, :if  => :is_locally_synced?
+  has_viewer :name => 'Text File', :partial  => :text_file, :if => :is_viewable?
 
   def self.file_name_pattern #:nodoc:
     /\.txt$/i
   end
 
+  def is_viewable? #:nodoc
+    return false unless self.size.presence
+    return false unless self.size < 500_000
+    return false unless is_locally_synced?
+    true
+  end
+
 end

From 6082312dae05915865a7d2bb592d556cb306b9bf Mon Sep 17 00:00:00 2001
From: Pierre Rioux <pierre.rioux@mcgill.ca>
Date: Thu, 29 Oct 2015 14:36:28 -0400
Subject: [PATCH 84/85] Fixed missing or spurious code documentation.

---
 BrainPortal/app/helpers/ajax_widget_helper.rb |  3 +-
 BrainPortal/app/helpers/rich_ui_helper.rb     | 16 +++---
 BrainPortal/app/helpers/userfiles_helper.rb   |  4 +-
 BrainPortal/app/models/cluster_task.rb        | 14 ++++-
 BrainPortal/app/models/data_provider.rb       |  3 +-
 BrainPortal/app/models/exception_log.rb       |  9 ++--
 BrainPortal/app/models/ssh_data_provider.rb   |  7 ++-
 BrainPortal/app/models/userfile.rb            | 12 +++--
 BrainPortal/app/models/worker.rb              | 13 +++--
 .../cb_serializer/common/cb_serializer.rb     |  2 +-
 .../userfiles/csv_file/csv_file.rb            |  4 +-
 .../userfiles/text_file/text_file.rb          |  2 +-
 BrainPortal/lib/authenticated_system.rb       |  8 +--
 BrainPortal/lib/cbrain_file_revision.rb       |  2 +-
 BrainPortal/lib/scir.rb                       | 51 ++++++++++---------
 BrainPortal/lib/scir_moab.rb                  | 20 ++++----
 BrainPortal/lib/scir_pbs.rb                   | 20 ++++----
 BrainPortal/lib/scir_sge.rb                   | 20 ++++----
 BrainPortal/lib/scir_sharcnet.rb              | 20 ++++----
 BrainPortal/lib/scir_unix.rb                  | 22 ++++----
 .../lib/smart_data_provider_interface.rb      |  6 +--
 BrainPortal/lib/subpath_format_validator.rb   |  4 +-
 22 files changed, 144 insertions(+), 118 deletions(-)

diff --git a/BrainPortal/app/helpers/ajax_widget_helper.rb b/BrainPortal/app/helpers/ajax_widget_helper.rb
index 103e26e13..a169ae719 100644
--- a/BrainPortal/app/helpers/ajax_widget_helper.rb
+++ b/BrainPortal/app/helpers/ajax_widget_helper.rb
@@ -100,7 +100,8 @@ def ajax_element(url, options ={}, &block)
     html.html_safe
   end
 
-  def ajax_refresh_link(text, target, options = {})
+  # This doesn't seem to be used anymore? PR OCT 2015
+  def ajax_refresh_link(text, target, options = {}) #:nodoc:
     options["data-target"] = target
 
     options[:class] ||= ""
diff --git a/BrainPortal/app/helpers/rich_ui_helper.rb b/BrainPortal/app/helpers/rich_ui_helper.rb
index 2660d1bc4..fc95b3ae8 100644
--- a/BrainPortal/app/helpers/rich_ui_helper.rb
+++ b/BrainPortal/app/helpers/rich_ui_helper.rb
@@ -104,9 +104,9 @@ def build_tabs(options = {}, &block)
   # Utility class for the build_tabs method (see above).
   #
   #############################################################
-  class TabBuilder
+  class TabBuilder #:nodoc:
 
-    def initialize
+    def initialize #:nodoc:
       @tab_titles = "".html_safe
       @tab_divs   = "".html_safe
     end
@@ -115,9 +115,7 @@ def tab_titles #:nodoc:
       ("<ul>\n" + @tab_titles + "\n</ul>\n").html_safe
     end
 
-
-
-    attr_reader :tab_divs
+    attr_reader :tab_divs #:nodoc:
 
     # This creates an individual tab, it either takes a block and/or a partial as an option (:partial => "partial")
     def tab(name, &block)
@@ -134,7 +132,7 @@ def tab(name, &block)
       @tab_divs += "<div id=\"tb_#{random_id}\">\n".html_safe +
                    capture.call(&block) +
                    "</div>\n".html_safe
-      return "" # in case invoked with <%= instead <% 
+      return "" # in case invoked with <%= instead <%
     end
   end
 
@@ -172,8 +170,9 @@ def build_accordion(options = {}, &block)
   # Utility class for the build_accordion method (see above).
   #
   #############################################################
-  class AccordionBuilder
-    def section(header, &block)
+  class AccordionBuilder #:nodoc:
+
+    def section(header, &block) #:nodoc:
       capture     = eval("method(:capture)", block.binding)
       head = "<h3><a href=\"#\">#{header}</a></h3>".html_safe
       body = "<div style=\"display: none\">".html_safe +
@@ -181,6 +180,7 @@ def section(header, &block)
              "</div>".html_safe
       return head + body
     end
+
   end
 
   # Create a tooltip that displays html when mouseovered.
diff --git a/BrainPortal/app/helpers/userfiles_helper.rb b/BrainPortal/app/helpers/userfiles_helper.rb
index 48f630556..ece789812 100644
--- a/BrainPortal/app/helpers/userfiles_helper.rb
+++ b/BrainPortal/app/helpers/userfiles_helper.rb
@@ -48,7 +48,7 @@ def filename_listing(userfile, link_options={})
     html.join.html_safe
   end
 
-  def neighbor_file_link(neighbor, index, dir, options = {})
+  def neighbor_file_link(neighbor, index, dir, options = {}) #:nodoc:
     return "" unless neighbor
 
     if dir == :previous
@@ -63,6 +63,8 @@ def neighbor_file_link(neighbor, index, dir, options = {})
     link_to text, {:action  => action, :id  => neighbor.id, :sort_index => index}, link_options
   end
 
+  # Generates a set of two links, one for a 'previous' file and one for a 'next' file.
+  # The argument +sort_index+ is the index of the 'current' file.
   def file_link_table(previous_userfile, next_userfile, sort_index, options = {})
     (
     "<div class=\"display_table\" style=\"width:100%\">" +
diff --git a/BrainPortal/app/models/cluster_task.rb b/BrainPortal/app/models/cluster_task.rb
index df3f3690e..296b8b9f7 100644
--- a/BrainPortal/app/models/cluster_task.rb
+++ b/BrainPortal/app/models/cluster_task.rb
@@ -1638,15 +1638,26 @@ def update_size_of_cluster_workdir
     return nil
   end
 
+
+
+  ##################################################################
+  # Docker support methods
+  ##################################################################
+
+  # Returns true if the task's ToolConfig is configured to point to a docker image
+  # for the task's processing.
   def use_docker?
     return self.tool_config.docker_image.present?
   end
 
+  # Return the 'docker' command to be used for the task; this is fetched
+  # from the Bourreau's own attribute. Default: "docker".
   def docker_executable_name
     return RemoteResource.current_resource.docker_executable_name.presence || "docker"
   end
 
-  # Returns the command line(s) associated with the task, wrapped in a Docker call if a Docker image has to be used.
+  # Returns the command line(s) associated with the task, wrapped in
+  # a Docker call if a Docker image has to be used.
   def docker_commands
     commands = self.cluster_commands
     commands_joined=commands.join("\n");
@@ -1664,6 +1675,7 @@ def docker_commands
   end
 
 
+
   ##################################################################
   # Lifecycle hooks
   ##################################################################
diff --git a/BrainPortal/app/models/data_provider.rb b/BrainPortal/app/models/data_provider.rb
index 3eafe2bf7..158049746 100644
--- a/BrainPortal/app/models/data_provider.rb
+++ b/BrainPortal/app/models/data_provider.rb
@@ -1000,12 +1000,11 @@ def provider_full_path(userfile)
   def self.pretty_type #:nodoc:
     self.to_s
   end
-  
+
   # This is a method that will return category type for this data provider
   # in the case of this class (abstract) it will not be invoked.
   # Returning a nil is the convention that we'll use to HIDE a data provider class from the interface.
   # So we'll return nil if the data provider class is not appriopriate for the users to view.
-  
   def self.pretty_category_name
     nil
   end
diff --git a/BrainPortal/app/models/exception_log.rb b/BrainPortal/app/models/exception_log.rb
index 93ae89a41..afcb84613 100644
--- a/BrainPortal/app/models/exception_log.rb
+++ b/BrainPortal/app/models/exception_log.rb
@@ -62,10 +62,13 @@ def self.log_exception(exception, user, request)
     e
   end
 
-  after_find :replace_attributes_too_big
-  attr_accessor :truncated_attributes
+  # This next section is handling the case where reports (trace dumps etc)
+  # are too long, so they are truncated explicitely.
 
-  def replace_attributes_too_big
+  after_find    :replace_attributes_too_big
+  attr_accessor :truncated_attributes #:nodoc:
+
+  def replace_attributes_too_big #:nodoc:
     raw = {}
     self.class.serialized_attributes.keys.each do |att|
       att = att.to_sym
diff --git a/BrainPortal/app/models/ssh_data_provider.rb b/BrainPortal/app/models/ssh_data_provider.rb
index 4709cef8c..af91708a3 100644
--- a/BrainPortal/app/models/ssh_data_provider.rb
+++ b/BrainPortal/app/models/ssh_data_provider.rb
@@ -39,12 +39,11 @@ class SshDataProvider < DataProvider
 
   Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
 
-  
-  # this returns the category of the data provider -- used in view for admins
+  # This returns the category of the data provider -- used in view for admins
   def self.pretty_category_name
     "Single Level Types"
   end
-  
+
   def impl_is_alive? #:nodoc:
     return false unless self.master.is_alive?
     remote_cmd = "test -d #{self.remote_dir.bash_escape} && echo OK-Dir 2>&1"
@@ -281,7 +280,7 @@ def impl_provider_report #:nodoc:
     issues
   end
 
-  def impl_provider_repair(issue) #:nodoc
+  def impl_provider_repair(issue) #:nodoc:
     raise "No automatic repair possible. Register or delete the file manually." if issue[:type] == :unregistered
 
     super(issue)
diff --git a/BrainPortal/app/models/userfile.rb b/BrainPortal/app/models/userfile.rb
index b3493bf6e..ac515337a 100644
--- a/BrainPortal/app/models/userfile.rb
+++ b/BrainPortal/app/models/userfile.rb
@@ -220,6 +220,7 @@ def is_valid_file_type?(type)
     self.valid_file_types.include? type
   end
 
+  # Returns a suggested file type for the current userfile, based on its extension.
   def suggested_file_type
     @suggested_file_type ||= self.valid_file_classes.find{|ft| self.name =~ ft.file_name_pattern}
   end
@@ -625,7 +626,8 @@ def available?
 
   public
 
-  class Viewer
+  class Viewer #:nodoc:
+
     attr_reader :userfile_class, :name, :partial
 
     def initialize(userfile_class, viewer) #:nodoc:
@@ -636,7 +638,7 @@ def initialize(userfile_class, viewer) #:nodoc:
       initialize_from_hash(atts.merge(:userfile_class => userfile_class))
     end
 
-    def initialize_from_hash(atts = {})
+    def initialize_from_hash(atts = {}) #:nodoc:
       userfile_class = atts.delete(:userfile_class) # e.g. TextFile (the class)
       unless userfile_class.present? && userfile_class.is_a?(Class) && userfile_class < Userfile
         cb_error("Viewer =#{userfile_class}= must be associated with a Userfile class.")
@@ -663,17 +665,17 @@ def initialize_from_hash(atts = {})
       end
     end
 
-    def valid_for?(userfile)
+    def valid_for?(userfile) #:nodoc:
       return true if @conditions.empty?
       @conditions.all? { |condition| condition.call(userfile) }
     end
 
-    def ==(other)
+    def ==(other) #:nodoc:
       return false unless other.is_a? Viewer
       self.name == other.name
     end
 
-    def partial_path(alternate_partial=nil)
+    def partial_path(alternate_partial=nil) #:nodoc:
       @userfile_class.view_path(alternate_partial.presence || @partial)
     end
   end
diff --git a/BrainPortal/app/models/worker.rb b/BrainPortal/app/models/worker.rb
index 2cce708e7..9ea77c31c 100644
--- a/BrainPortal/app/models/worker.rb
+++ b/BrainPortal/app/models/worker.rb
@@ -721,22 +721,25 @@ def initialize_from_pidfile(pidfile) #:nodoc:
 
 end
 
+# This class pretends to be a logger object, but simply prefix
+# all the log messages with a constant string before passing it to
+# a real logger.
 class LoggerPrefixer #:nodoc:
   attr_accessor :true_logger
   attr_accessor :prefix
-  def debug(message)
+  def debug(message) #:nodoc:
     true_logger.debug(prefix + message)
   end
-  def info(message)
+  def info(message) #:nodoc:
     true_logger.info(prefix + message)
   end
-  def warn(message)
+  def warn(message) #:nodoc:
     true_logger.warn(prefix + message)
   end
-  def error(message)
+  def error(message) #:nodoc:
     true_logger.error(prefix + message)
   end
-  def fatal(message)
+  def fatal(message) #:nodoc:
     true_logger.fatal(prefix + message)
   end
 end
diff --git a/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/cb_serializer/common/cb_serializer.rb b/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/cb_serializer/common/cb_serializer.rb
index f1413636c..99a75a19b 100644
--- a/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/cb_serializer/common/cb_serializer.rb
+++ b/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/cb_serializer/common/cb_serializer.rb
@@ -27,7 +27,7 @@ def self.pretty_type #:nodoc:
     return "CBRAIN Serializer"
   end
 
-  # Returns the list of tasks parallelized;
+  # Returns the list of tasks serialized;
   # this list includes only the tasks that have been
   # 'enabled' (disabling can be triggered using the
   # interface).
diff --git a/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/csv_file/csv_file.rb b/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/csv_file/csv_file.rb
index 3d00c7813..cf92b2268 100644
--- a/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/csv_file/csv_file.rb
+++ b/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/csv_file/csv_file.rb
@@ -27,7 +27,7 @@ class CSVFile < TextFile
 
   Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
 
-  has_viewer :name => 'CSV Viewer', :partial  => :csv_file, :if => :is_viewable
+  has_viewer :name => 'CSV Viewer', :partial  => :csv_file, :if => :is_viewable?
 
   def self.pretty_type #:nodoc:
     "CSV File"
@@ -37,7 +37,7 @@ def self.file_name_pattern #:nodoc:
     /\.csv$/i
   end
 
-  def is_viewable #:nodoc
+  def is_viewable? #:nodoc:
     return false unless self.size.presence
     return false unless self.size < 200_000  # smaller than the limit in TextFile
     return false unless is_locally_synced?
diff --git a/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/text_file/text_file.rb b/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/text_file/text_file.rb
index a383727ab..4095fac23 100644
--- a/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/text_file/text_file.rb
+++ b/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/text_file/text_file.rb
@@ -31,7 +31,7 @@ def self.file_name_pattern #:nodoc:
     /\.txt$/i
   end
 
-  def is_viewable? #:nodoc
+  def is_viewable? #:nodoc:
     return false unless self.size.presence
     return false unless self.size < 500_000
     return false unless is_locally_synced?
diff --git a/BrainPortal/lib/authenticated_system.rb b/BrainPortal/lib/authenticated_system.rb
index 9a6b7614a..21b1501e4 100644
--- a/BrainPortal/lib/authenticated_system.rb
+++ b/BrainPortal/lib/authenticated_system.rb
@@ -56,15 +56,17 @@ def login_required
       authorized? || access_denied
     end
 
+    # Filter method to enforce a site requirement for a controller action.
+    # A NormalUser must be a member of a site to proceed.
     def site_membership_required
       (!current_user.site.nil? || access_error(401)) if current_user.has_role?(:normal_user)
     end
-      
-    
+
+
     ##########################################################
     #NEXT TWO ADDED BY TAREK
     ##########################################################
-    
+
     # Before filter to ensure that logged in User is an admin user.
     def admin_role_required
       current_user.has_role?(:admin_user) || access_error(401)
diff --git a/BrainPortal/lib/cbrain_file_revision.rb b/BrainPortal/lib/cbrain_file_revision.rb
index c25a1a2cf..3ee6f025b 100644
--- a/BrainPortal/lib/cbrain_file_revision.rb
+++ b/BrainPortal/lib/cbrain_file_revision.rb
@@ -194,6 +194,7 @@ def self.git_available? #:nodoc:
     @_git_available == :yes
   end
 
+  # If the current app was deployed using GIT, returns the current GIT branch name.
   def self.git_branch_name
     return "" unless git_available?
     IO.popen("git rev-parse --abbrev-ref HEAD") do |fh|
@@ -201,7 +202,6 @@ def self.git_branch_name
     end
   end
 
-
   def self.for_relpath(relpath, mode = :auto) #:nodoc:
     cbrain_root = Pathname.new(Rails.root).parent
     rev = self.new("#{cbrain_root}/#{relpath}") # TODO: find the object originally registered IN its file?
diff --git a/BrainPortal/lib/scir.rb b/BrainPortal/lib/scir.rb
index b3768c52d..75aecf174 100644
--- a/BrainPortal/lib/scir.rb
+++ b/BrainPortal/lib/scir.rb
@@ -36,17 +36,18 @@ def self.revision_info
   end
 
   # These constants are the same as the ones used for DRMAA
-  STATE_UNDETERMINED          = 0x00
-  STATE_QUEUED_ACTIVE         = 0x10
-  STATE_SYSTEM_ON_HOLD        = 0x11
-  STATE_USER_ON_HOLD          = 0x12
-  STATE_USER_SYSTEM_ON_HOLD   = 0x13
-  STATE_RUNNING               = 0x20
-  STATE_SYSTEM_SUSPENDED      = 0x21
-  STATE_USER_SUSPENDED        = 0x22
-  STATE_USER_SYSTEM_SUSPENDED = 0x23
-  STATE_DONE                  = 0x30
-  STATE_FAILED                = 0x40
+
+  STATE_UNDETERMINED          = 0x00 #:nodoc:
+  STATE_QUEUED_ACTIVE         = 0x10 #:nodoc:
+  STATE_SYSTEM_ON_HOLD        = 0x11 #:nodoc:
+  STATE_USER_ON_HOLD          = 0x12 #:nodoc:
+  STATE_USER_SYSTEM_ON_HOLD   = 0x13 #:nodoc:
+  STATE_RUNNING               = 0x20 #:nodoc:
+  STATE_SYSTEM_SUSPENDED      = 0x21 #:nodoc:
+  STATE_USER_SUSPENDED        = 0x22 #:nodoc:
+  STATE_USER_SYSTEM_SUSPENDED = 0x23 #:nodoc:
+  STATE_DONE                  = 0x30 #:nodoc:
+  STATE_FAILED                = 0x40 #:nodoc:
 
   # Returns the file name for the implementation.
   def self.drmaa_implementation
@@ -122,7 +123,7 @@ def initialize(job_ps_cache_delay = 30.seconds) #:nodoc:
       reset_job_info_cache
     end
 
-    def run(job)
+    def run(job) #:nodoc:
       reset_job_info_cache
       command = job.qsub_command
       qsubout = ""
@@ -130,17 +131,17 @@ def run(job)
       return qsubout_to_jid(qsubout)
     end
 
-    def update_job_info_cache
+    def update_job_info_cache #:nodoc:
       # sets @job_info_cache to a hash: { jid => drmaa_status, ... }
       raise "This method must be provided in a subclass."
     end
 
-    def reset_job_info_cache
+    def reset_job_info_cache #:nodoc:
       @job_info_cache     = nil
       @cache_last_updated = (100*@job_ps_cache_delay).seconds.ago
     end
 
-    def job_ps(jid,caller_updated_at = nil)
+    def job_ps(jid,caller_updated_at = nil) #:nodoc:
       caller_updated_at ||= (5*@job_ps_cache_delay).seconds.ago
       if @job_info_cache.nil? || @cache_last_updated < @job_ps_cache_delay.ago || caller_updated_at > @job_ps_cache_delay.ago
         update_job_info_cache
@@ -151,27 +152,27 @@ def job_ps(jid,caller_updated_at = nil)
       Scir::STATE_UNDETERMINED
     end
 
-    def hold(jid)
+    def hold(jid) #:nodoc:
       raise "This method must be provided in a subclass"
     end
 
-    def release(jid)
+    def release(jid) #:nodoc:
       raise "This method must be provided in a subclass"
     end
 
-    def suspend(jid)
+    def suspend(jid) #:nodoc:
       raise "This method must be provided in a subclass"
     end
 
-    def resume(jid)
+    def resume(jid) #:nodoc:
       raise "This method must be provided in a subclass"
     end
 
-    def terminate(jid)
+    def terminate(jid) #:nodoc:
       raise "This method must be provided in a subclass"
     end
 
-    def queue_tasks_tot_max
+    def queue_tasks_tot_max #:nodoc:
       [ "nyi", "nyi" ]
     end
 
@@ -208,23 +209,23 @@ def revision_info #:nodoc:
       Class.const_get(self.class.to_s.sub(/::JobTemplate/,"")).revision_info
     end
 
-    def self.new_jobtemplate(params = {})
+    def self.new_jobtemplate(params = {}) #:nodoc:
       job_template = self.new(params)
       job_template.queue = Scir.cbrain_config[:default_queue] if ( ! Scir.cbrain_config[:default_queue].blank? ) && ( job_template.queue.blank? )
       return job_template
     end
 
-    def initialize(params = {})
+    def initialize(params = {}) #:nodoc:
       params.each_pair { |m,v| self.send("#{m}=",v) }
     end
 
-    def qsub_command
+    def qsub_command #:nodoc:
       raise "Method qsub_command() must be provided in a subclass."
     end
 
     protected
 
-    def shell_escape(s)
+    def shell_escape(s) #:nodoc:
       "'" + s.gsub(/'/,"'\\\\''") + "'"
     end
 
diff --git a/BrainPortal/lib/scir_moab.rb b/BrainPortal/lib/scir_moab.rb
index 33a016079..92bc77211 100644
--- a/BrainPortal/lib/scir_moab.rb
+++ b/BrainPortal/lib/scir_moab.rb
@@ -30,7 +30,7 @@ class ScirMoab < Scir
 
   class Session < Scir::Session #:nodoc:
 
-    def update_job_info_cache
+    def update_job_info_cache #:nodoc:
       #xmltext, showqerr = bash_this_and_capture_out_err("showq --blocking --xml")
       xmltext, showqerr = bash_this_and_capture_out_err("showq --xml")
       xmltext.force_encoding('ASCII-8BIT') # THE STUPID MOAB XML DUMP CAN CONTAIN BINARY DATA!
@@ -64,7 +64,7 @@ def update_job_info_cache
       true
     end
 
-    def statestring_to_stateconst(state)
+    def statestring_to_stateconst(state) #:nodoc:
       return Scir::STATE_RUNNING        if state.match(/Run|Starting/i)
       return Scir::STATE_QUEUED_ACTIVE  if state.match(/Idle|Queue|Defer|Staged/i)
       return Scir::STATE_USER_ON_HOLD   if state.match(/H[oe]ld/i)
@@ -72,7 +72,7 @@ def statestring_to_stateconst(state)
       return Scir::STATE_UNDETERMINED
     end
 
-    def hold(jid)
+    def hold(jid) #:nodoc:
       IO.popen("mjobctl -h user #{shell_escape(jid)} 2>&1","r") do |i|
         p = i.read
         raise "Error holding: #{p.join("\n")}" unless p =~ /holds modified for job/i
@@ -80,7 +80,7 @@ def hold(jid)
       end
     end
 
-    def release(jid)
+    def release(jid) #:nodoc:
       IO.popen("mjobctl -u user #{shell_escape(jid)} 2>&1","r") do |i|
         p = i.read
         raise "Error releasing: #{p.join("\n")}" unless p =~ /holds modified for job/i
@@ -88,15 +88,15 @@ def release(jid)
       end
     end
 
-    def suspend(jid)
+    def suspend(jid) #:nodoc:
       raise "There is no 'suspend' action available for MOAB clusters"
     end
 
-    def resume(jid)
+    def resume(jid) #:nodoc:
       raise "There is no 'resume' action available for MOAB clusters"
     end
 
-    def terminate(jid)
+    def terminate(jid) #:nodoc:
       #IO.popen("mjobctl -c #{shell_escape(jid)} 2>&1","r") do |i|
       IO.popen("canceljob #{shell_escape(jid)} 2>&1","r") do |i|
         p = i.read
@@ -105,7 +105,7 @@ def terminate(jid)
       end
     end
 
-    def queue_tasks_tot_max
+    def queue_tasks_tot_max #:nodoc:
       job_ps("!dummy!") # trigger refresh if necessary
       moab_cluster_info = @job_info_cache["!moab_cluster_info!"]
       #<cluster LocalActiveNodes="43" LocalAllocProcs="270" LocalConfigNodes="49" LocalIdleNodes="4"
@@ -126,7 +126,7 @@ def queue_tasks_tot_max
 
     private
 
-    def qsubout_to_jid(txt)
+    def qsubout_to_jid(txt) #:nodoc:
       if txt && txt =~ /^(\S+)/
         val = Regexp.last_match[1]
         return val unless val =~ /error/i
@@ -138,7 +138,7 @@ def qsubout_to_jid(txt)
 
   class JobTemplate < Scir::JobTemplate #:nodoc:
 
-    def qsub_command
+    def qsub_command #:nodoc:
       raise "Error, this class only handle 'command' as /bin/bash and a single script in 'arg'" unless
         self.command == "/bin/bash" && self.arg.size == 1
       raise "Error: stdin not supported" if self.stdin
diff --git a/BrainPortal/lib/scir_pbs.rb b/BrainPortal/lib/scir_pbs.rb
index 1e9bf90b3..ae033d977 100644
--- a/BrainPortal/lib/scir_pbs.rb
+++ b/BrainPortal/lib/scir_pbs.rb
@@ -30,7 +30,7 @@ class ScirPbs < Scir
 
   class Session < Scir::Session #:nodoc:
 
-    def update_job_info_cache
+    def update_job_info_cache #:nodoc:
       out, err = bash_this_and_capture_out_err("qstat -f")
       raise "Cannot get output of 'qstat -f' ?!?" if out.blank? && ! err.blank?
       jid = 'Dummy'
@@ -51,7 +51,7 @@ def update_job_info_cache
       true
     end
 
-    def statestring_to_stateconst(state)
+    def statestring_to_stateconst(state) #:nodoc:
       return Scir::STATE_RUNNING        if state.match(/R/i)
       return Scir::STATE_QUEUED_ACTIVE  if state.match(/Q/i)
       return Scir::STATE_USER_ON_HOLD   if state.match(/H/i)
@@ -59,7 +59,7 @@ def statestring_to_stateconst(state)
       return Scir::STATE_UNDETERMINED
     end
 
-    def hold(jid)
+    def hold(jid) #:nodoc:
       IO.popen("qhold #{shell_escape(jid)} 2>&1","r") do |i|
         p = i.readlines
         raise "Error holding: #{p.join("\n")}" if p.size > 0
@@ -67,7 +67,7 @@ def hold(jid)
       end
     end
 
-    def release(jid)
+    def release(jid) #:nodoc:
       IO.popen("qrls #{shell_escape(jid)} 2>&1","r") do |i|
         p = i.readlines
         raise "Error releasing: #{p.join("\n")}" if p.size > 0
@@ -75,15 +75,15 @@ def release(jid)
       end
     end
 
-    def suspend(jid)
+    def suspend(jid) #:nodoc:
       raise "There is no 'suspend' action available for PBS clusters"
     end
 
-    def resume(jid)
+    def resume(jid) #:nodoc:
       raise "There is no 'resume' action available for PBS clusters"
     end
 
-    def terminate(jid)
+    def terminate(jid) #:nodoc:
       IO.popen("qdel #{shell_escape(jid)} 2>&1","r") do |i|
         p = i.readlines
         raise "Error deleting: #{p.join("\n")}" if p.size > 0
@@ -91,7 +91,7 @@ def terminate(jid)
       end
     end
 
-    def queue_tasks_tot_max
+    def queue_tasks_tot_max #:nodoc:
       queue = Scir.cbrain_config[:default_queue]
       queue = "default" if queue.blank?
       queueinfo = `qstat -Q #{shell_escape(queue)} | tail -1`
@@ -106,7 +106,7 @@ def queue_tasks_tot_max
 
     private
 
-    def qsubout_to_jid(txt)
+    def qsubout_to_jid(txt) #:nodoc:
       if txt && txt =~ /^(\d+)/
         return Regexp.last_match[1]
       end
@@ -117,7 +117,7 @@ def qsubout_to_jid(txt)
 
   class JobTemplate < Scir::JobTemplate #:nodoc:
 
-    def qsub_command
+    def qsub_command #:nodoc:
       raise "Error, this class only handle 'command' as /bin/bash and a single script in 'arg'" unless
         self.command == "/bin/bash" && self.arg.size == 1
       raise "Error: stdin not supported" if self.stdin
diff --git a/BrainPortal/lib/scir_sge.rb b/BrainPortal/lib/scir_sge.rb
index c4595a16b..d7ddfe689 100644
--- a/BrainPortal/lib/scir_sge.rb
+++ b/BrainPortal/lib/scir_sge.rb
@@ -30,7 +30,7 @@ class ScirSge < Scir
 
   class Session < Scir::Session #:nodoc:
 
-    def update_job_info_cache
+    def update_job_info_cache #:nodoc:
       out, err = bash_this_and_capture_out_err("qstat -xml")
       raise "Cannot get output of 'qstat -xml' ?!?" if out.blank? && ! err.blank?
       @job_info_cache = {}
@@ -47,7 +47,7 @@ def update_job_info_cache
       true
     end
 
-    def statestring_to_stateconst(state)
+    def statestring_to_stateconst(state) #:nodoc:
       return Scir::STATE_RUNNING        if state =~ /r/i
       return Scir::STATE_USER_SUSPENDED if state =~ /s/i
       return Scir::STATE_USER_ON_HOLD   if state =~ /h/i
@@ -55,7 +55,7 @@ def statestring_to_stateconst(state)
       return Scir::STATE_UNDETERMINED
     end
 
-    def hold(jid)
+    def hold(jid) #:nodoc:
       IO.popen("qhold #{shell_escape(jid)} 2>&1") do |i|
         p = i.read
         raise "Error holding: #{p}" unless p =~ /modified hold of/i
@@ -63,7 +63,7 @@ def hold(jid)
       end
     end
 
-    def release(jid)
+    def release(jid) #:nodoc:
       IO.popen("qrls #{shell_escape(jid)} 2>&1") do |i|
         p = i.read
         raise "Error releasing: #{p}" unless p =~ /modified hold of/i
@@ -71,15 +71,15 @@ def release(jid)
       end
     end
 
-    def suspend(jid)
+    def suspend(jid) #:nodoc:
       raise "There is no 'suspend' action implemented yet for SGE clusters"
     end
 
-    def resume(jid)
+    def resume(jid) #:nodoc:
       raise "There is no 'resume' action implemented yet for SGE clusters"
     end
 
-    def terminate(jid)
+    def terminate(jid) #:nodoc:
       IO.popen("qdel #{shell_escape(jid)} 2>&1") do |i|
         p = i.read
         raise "Error deleting: #{p}" unless p =~ /has deleted job|has registered/i
@@ -87,7 +87,7 @@ def terminate(jid)
       end
     end
 
-    def queue_tasks_tot_max
+    def queue_tasks_tot_max #:nodoc:
       queue = Scir.cbrain_config[:default_queue] || ""
       queueopt = queue.blank? ? "" : "-q #{shell_escape(queue)}"
       tot = max = nil
@@ -115,7 +115,7 @@ def queue_tasks_tot_max
 
     private
 
-    def qsubout_to_jid(txt)
+    def qsubout_to_jid(txt) #:nodoc:
       if txt && txt =~ /Your job (\d+)/i
         return Regexp.last_match[1]
       end
@@ -126,7 +126,7 @@ def qsubout_to_jid(txt)
 
   class JobTemplate < Scir::JobTemplate #:nodoc:
 
-    def qsub_command
+    def qsub_command #:nodoc:
       raise "Error, this class only handle 'command' as /bin/bash and a single script in 'arg'" unless
         self.command == "/bin/bash" && self.arg.size == 1
       raise "Error: stdin not supported" if self.stdin
diff --git a/BrainPortal/lib/scir_sharcnet.rb b/BrainPortal/lib/scir_sharcnet.rb
index 2fef15ae9..c10dbd6f7 100644
--- a/BrainPortal/lib/scir_sharcnet.rb
+++ b/BrainPortal/lib/scir_sharcnet.rb
@@ -31,7 +31,7 @@ class ScirSharcnet < Scir
 
   class Session < Scir::Session #:nodoc:
 
-    def update_job_info_cache
+    def update_job_info_cache #:nodoc:
       @job_info_cache = {}
       jid = 'Dummy'
       IO.popen("sqjobs -u #{CBRAIN::Rails_UserName.to_s.bash_escape} 2>/dev/null;sqjobs -n","r") do |fh|
@@ -58,7 +58,7 @@ def update_job_info_cache
       end
     end
 
-    def statestring_to_stateconst(state)
+    def statestring_to_stateconst(state) #:nodoc:
       return Scir::STATE_RUNNING        if state.match(/R/i)
       return Scir::STATE_QUEUED_ACTIVE  if state.match(/Q/i)
       return Scir::STATE_USER_ON_HOLD   if state.match(/H/i)
@@ -66,15 +66,15 @@ def statestring_to_stateconst(state)
       return Scir::STATE_UNDETERMINED
     end
 
-    def hold(jid)
+    def hold(jid) #:nodoc:
       raise "There is no 'hold' action available on Sharcnet clusters."
     end
 
-    def release(jid)
+    def release(jid) #:nodoc:
       raise "There is no 'release' action available on Sharcnet clusters."
     end
 
-    def suspend(jid)
+    def suspend(jid) #:nodoc:
       raise "There is no 'suspend' action available on Sharcnet clusters."
       # does not work on sharcnet (they have bugs...)
       IO.popen("sqsuspend #{shell_escape(jid)} 2>&1","r") do |i|
@@ -84,7 +84,7 @@ def suspend(jid)
       end
     end
 
-    def resume(jid)
+    def resume(jid) #:nodoc:
       raise "There is no 'resume' action available on Sharcnet clusters."
       # does not work on sharcnet (they have bugs...)
       IO.popen("sqresume #{shell_escape(jid)} 2>&1","r") do |i|
@@ -94,7 +94,7 @@ def resume(jid)
       end
     end
 
-    def terminate(jid)
+    def terminate(jid) #:nodoc:
       IO.popen("sqkill #{shell_escape(jid)} 2>&1","r") do |i|
         p = i.readlines
         raise "Error deleting: #{p.join("\n")}" unless p =~ /is being terminated/
@@ -102,7 +102,7 @@ def terminate(jid)
       end
     end
 
-    def queue_tasks_tot_max
+    def queue_tasks_tot_max #:nodoc:
       job_ps('!dummy!') # to trigger refresh of @job_ps_cache if necessary
       tot_max = @job_info_cache['!sharcnet_load!'] || [ 'unknown', 'unknown' ]
       tot_max
@@ -112,7 +112,7 @@ def queue_tasks_tot_max
 
     private
 
-    def qsubout_to_jid(txt)
+    def qsubout_to_jid(txt) #:nodoc:
       if txt && txt =~ /as jobid\s+(\S+)/
         return Regexp.last_match[1]
       end
@@ -123,7 +123,7 @@ def qsubout_to_jid(txt)
 
   class JobTemplate < Scir::JobTemplate #:nodoc:
 
-    def qsub_command
+    def qsub_command #:nodoc:
       raise "Error, this class only handle 'command' as /bin/bash and a single script in 'arg'" unless
         self.command == "/bin/bash" && self.arg.size == 1
       raise "Error: stdin not supported" if self.stdin
diff --git a/BrainPortal/lib/scir_unix.rb b/BrainPortal/lib/scir_unix.rb
index 19916490c..047993157 100644
--- a/BrainPortal/lib/scir_unix.rb
+++ b/BrainPortal/lib/scir_unix.rb
@@ -31,7 +31,7 @@ class ScirUnix < Scir
 
   class Session < Scir::Session #:nodoc:
 
-    def update_job_info_cache
+    def update_job_info_cache #:nodoc:
       @job_info_cache = {}
       ps_command = case CBRAIN::System_Uname
         when /Linux/i
@@ -54,33 +54,33 @@ def update_job_info_cache
       true
     end
 
-    def statestring_to_stateconst(state)
+    def statestring_to_stateconst(state) #:nodoc:
       return Scir::STATE_USER_SUSPENDED if state.match(/[t]/i)
       return Scir::STATE_RUNNING        if state.match(/[sruz]/i)
       return Scir::STATE_UNDETERMINED
     end
 
-    def hold(jid)
+    def hold(jid) #:nodoc:
       true
     end
 
-    def release(jid)
+    def release(jid) #:nodoc:
       true
     end
 
-    def suspend(jid)
+    def suspend(jid) #:nodoc:
       Process.kill("-STOP",Process.getpgid(jid.to_i)) rescue true  # A negative signal name kills a GROUP
     end
 
-    def resume(jid)
+    def resume(jid) #:nodoc:
       Process.kill("-CONT",Process.getpgid(jid.to_i)) rescue true  # A negative signal name kills a GROUP
     end
 
-    def terminate(jid)
+    def terminate(jid) #:nodoc:
       Process.kill("-TERM",Process.getpgid(jid.to_i)) rescue true  # A negative signal name kills a GROUP
     end
 
-    def queue_tasks_tot_max
+    def queue_tasks_tot_max #:nodoc:
       loadav = `uptime`.strip
       loadav.match(/averages?:\s*([\d\.]+)/i)
       loadtxt = Regexp.last_match[1] || "unknown"
@@ -101,7 +101,7 @@ def queue_tasks_tot_max
       [ "exception", "exception" ]
     end
 
-    def run(job)
+    def run(job) #:nodoc:
       reset_job_info_cache
       command = job.qsub_command
       pid = Process.fork do
@@ -116,7 +116,7 @@ def run(job)
 
     private
 
-    def qsubout_to_jid(txt)
+    def qsubout_to_jid(txt) #:nodoc:
       raise "Not used in this implementation."
     end
 
@@ -125,7 +125,7 @@ def qsubout_to_jid(txt)
   class JobTemplate < Scir::JobTemplate #:nodoc:
 
     # NOTE: We use a custom 'run' method in the Session, instead of Scir's version.
-    def qsub_command
+    def qsub_command #:nodoc:
       raise "Error, this class only handle 'command' as /bin/bash and a single script in 'arg'" unless
         self.command == "/bin/bash" && self.arg.size == 1
       raise "Error: stdin not supported" if self.stdin
diff --git a/BrainPortal/lib/smart_data_provider_interface.rb b/BrainPortal/lib/smart_data_provider_interface.rb
index d1ada2491..a30b69484 100644
--- a/BrainPortal/lib/smart_data_provider_interface.rb
+++ b/BrainPortal/lib/smart_data_provider_interface.rb
@@ -17,7 +17,7 @@
 # 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 <http://www.gnu.org/licenses/>.  
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 
 require 'socket'
@@ -182,11 +182,11 @@ def provider_collection_index(userfile, directory = :all, allowed_types = :regul
     @provider.provider_collection_index(userfile, directory, allowed_types)
   end
 
-  def provider_report(force_reload=nil)
+  def provider_report(force_reload=nil) #:nodoc:
     @provider.provider_report(force_reload)
   end
 
-  def provider_repair(issue)
+  def provider_repair(issue) #:nodoc:
     @provider.provider_repair(issue)
   end
 
diff --git a/BrainPortal/lib/subpath_format_validator.rb b/BrainPortal/lib/subpath_format_validator.rb
index 49b3db4e0..2b00bdbe8 100644
--- a/BrainPortal/lib/subpath_format_validator.rb
+++ b/BrainPortal/lib/subpath_format_validator.rb
@@ -24,10 +24,12 @@ class SubpathFormatValidator < ActiveModel::EachValidator #:nodoc:
 
   Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
 
-  def validate_each(object, attribute, value)
+  def validate_each(object, attribute, value) #:nodoc:
     # FIXME currenly, hidden files and directories are not supported
     unless value.blank? || value =~ /^(?:[^.\/][^\/]*\/?)+$/
       object.errors[attribute] << (options[:message] || "contains invalid characters")
     end
   end
+
 end
+

From 1a3dd1860815114528c56712d3fdc96a73a96558 Mon Sep 17 00:00:00 2001
From: Pierre Rioux <pierre.rioux@mcgill.ca>
Date: Fri, 30 Oct 2015 14:48:29 -0400
Subject: [PATCH 85/85] Added flatfile revisions for 4.2.0

---
 cbrain_file_revisions.csv | 269 ++++++++++++++++++++------------------
 generate_rev_list.sh      |  37 ++++--
 2 files changed, 169 insertions(+), 137 deletions(-)

diff --git a/cbrain_file_revisions.csv b/cbrain_file_revisions.csv
index 165887a40..ce1d7e667 100644
--- a/cbrain_file_revisions.csv
+++ b/cbrain_file_revisions.csv
@@ -1,7 +1,7 @@
-4.1.0 -#- 2015-08-13 15:31:45 -0400 -#- CBRAIN Team -#- __CBRAIN_TAG__
-30a096a4ad781959b522ba3ece03aa7fb58f9a8a -#- 2015-08-13 15:02:48 -0400 -#- Pierre Rioux -#- __CBRAIN_HEAD__
+4.2.0 -#- 2015-10-30 12:19:56 -0400 -#- CBRAIN Team -#- __CBRAIN_TAG__
+6082312dae05915865a7d2bb592d556cb306b9bf -#- 2015-10-29 14:36:28 -0400 -#- Pierre Rioux -#- __CBRAIN_HEAD__
 d6f728be5bffe7343f99fcb27f7079f4414bc2c1 -#- 2015-05-21 14:03:58 -0400 -#- Ehsan Afkhami -#- Bourreau/.gitignore
-1caeb815694c44bafe2d082ba1682a0a80dbb193 -#- 2015-03-11 15:46:46 -0400 -#- Pierre Rioux -#- Bourreau/Gemfile
+b0eff7b5443f01744f3d158e8c7bd0fff9587ead -#- 2015-07-24 16:05:37 -0400 -#- Remi Bernard -#- Bourreau/Gemfile
 bc10f836fd930c034bc5a1af6375987587524a8f -#- 2015-08-07 13:14:41 -0400 -#- Remi Bernard -#- Bourreau/README
 d0e6e910a147a24e467236e93314c0b46ea406ba -#- 2012-08-30 11:35:20 -0400 -#- Pierre Rioux -#- Bourreau/Rakefile
 03df55efbefa7e89a08594b7b16befd28e38fae1 -#- 2014-12-04 20:42:56 -0500 -#- Pierre Rioux -#- Bourreau/app/controllers/application_controller.rb
@@ -59,7 +59,7 @@ e1987bf86b98100c87b6e038352b07673b7a5bda -#- 2013-09-03 15:39:13 -0400 -#- Natac
 31d70e8c1a243a3b7513e5d64e3c7a89dfcc6fb5 -#- 2011-04-26 22:21:12 +0000 -#- prioux -#- Bourreau/cbrain_plugins
 de3216d5876d326eab6a0b190e4ec24f4c054626 -#- 2011-07-18 17:16:57 -0400 -#- Pierre Rioux -#- Bourreau/config.ru
 73d1908294f5d0a218c07e2ce6428e273fb600d1 -#- 2015-04-01 15:24:59 -0400 -#- Natacha Beck -#- Bourreau/config/.gitignore
-41562bbad4c91100c05a806e0d1eee779dff1783 -#- 2015-01-28 18:35:17 -0500 -#- Pierre Rioux -#- Bourreau/config/application.rb
+b0eff7b5443f01744f3d158e8c7bd0fff9587ead -#- 2015-07-24 16:05:37 -0400 -#- Remi Bernard -#- Bourreau/config/application.rb
 de3216d5876d326eab6a0b190e4ec24f4c054626 -#- 2011-07-18 17:16:57 -0400 -#- Pierre Rioux -#- Bourreau/config/boot.rb
 81c9cb67a35c5ca1912c57e0e7ef1f752b1230dd -#- 2012-10-30 17:17:39 -0400 -#- Tarek Sherif -#- Bourreau/config/console_rc.rb
 953373139898fc0724dad1ffe6f3fe6f51b4c02f -#- 2009-03-31 20:41:45 +0000 -#- tsherif -#- Bourreau/config/daemons.yml
@@ -95,6 +95,7 @@ f3e1362e37f4f4395c88a7bd1d95ef830bd5e32c -#- 2012-04-24 19:57:20 -0400 -#- Pierr
 6c03e90867b0d46ba4e63decb2a58383854eb946 -#- 2011-07-05 16:00:45 -0400 -#- Pierre Rioux -#- Bourreau/lib/cbrain_file_revision.rb
 df10525ea5250f8328a3f867968b6238f1f78dbb -#- 2011-09-07 11:25:47 -0400 -#- Pierre Rioux -#- Bourreau/lib/cbrain_notice.rb
 81744bf3522320596acc7802c5991e64d97d3cb6 -#- 2010-10-19 19:24:57 +0000 -#- prioux -#- Bourreau/lib/cbrain_system_checks.rb
+b0eff7b5443f01744f3d158e8c7bd0fff9587ead -#- 2015-07-24 16:05:37 -0400 -#- Remi Bernard -#- Bourreau/lib/cbrain_task_generators
 7f01c8c96e4a6c26011e43a47adeef3f19c0ccdb -#- 2010-03-03 19:35:45 +0000 -#- prioux -#- Bourreau/lib/cbrain_transition_exception.rb
 d14bb5a958f674c4281eb56a2ef91364952e1e74 -#- 2015-06-04 15:51:58 -0400 -#- Remi Bernard -#- Bourreau/lib/consistency_checks.rb
 4551c18d1922bbd8cc3200c69cba1033c16bb24a -#- 2012-10-31 16:54:43 -0400 -#- Tarek Sherif -#- Bourreau/lib/core_models.rb
@@ -136,108 +137,109 @@ a9db076d944b822b8b5328b3d7c7cd4ddfc6c1a9 -#- 2012-08-02 14:19:46 -0400 -#- Tarek
 2e05b96e11956878ff65cc3a2728bd669c52873a -#- 2010-01-18 20:28:00 +0000 -#- nkassis -#- BrainPortal/.autotest
 b5593e0920aab26b2cac1a7569b7e16f7e5ad301 -#- 2015-06-03 17:37:07 -0400 -#- Remi Bernard -#- BrainPortal/.gitignore
 4ae88132ae49c202d5363fe1648d1f4861c81920 -#- 2015-04-29 16:40:11 -0400 -#- Natacha Beck -#- BrainPortal/.rspec
-4ae88132ae49c202d5363fe1648d1f4861c81920 -#- 2015-04-29 16:40:11 -0400 -#- Natacha Beck -#- BrainPortal/Gemfile
+9c42e72a65f837f1c3a1d5e1914e44da02ff8089 -#- 2015-09-09 14:56:58 -0400 -#- Remi Bernard -#- BrainPortal/Gemfile
 bc10f836fd930c034bc5a1af6375987587524a8f -#- 2015-08-07 13:14:41 -0400 -#- Remi Bernard -#- BrainPortal/README
 0a45d2c18a3e5b4bfcd2251e77b3ea00f05133b1 -#- 2015-01-26 14:43:49 -0500 -#- Pierre Rioux -#- BrainPortal/Rakefile
-1d69a39bb6ab8df149a792963670d3b2d4d47275 -#- 2015-06-09 13:33:12 -0400 -#- Remi Bernard -#- BrainPortal/app/controllers/application_controller.rb
-4ab0df1815e2fe8ffbe9dc837fa05861027a703c -#- 2015-07-29 14:40:56 -0400 -#- Pierre Rioux -#- BrainPortal/app/controllers/bourreaux_controller.rb
+ae450150e4767317062513ca0027778616d78684 -#- 2015-08-21 16:35:13 -0400 -#- Remi Bernard -#- BrainPortal/app/controllers/application_controller.rb
+3a42fd7db2bf64ee3acc7c9163de6c8ac376343b -#- 2015-09-21 15:27:17 -0400 -#- Remi Bernard -#- BrainPortal/app/controllers/bourreaux_controller.rb
 ce746f2e862f3f8538b5ab7580a7338eef3877ff -#- 2014-10-07 19:32:05 -0400 -#- Pierre Rioux -#- BrainPortal/app/controllers/controls_controller.rb
-70403d4a9074bc93d2028f67d66b459719a75cb4 -#- 2015-05-06 15:23:08 -0400 -#- Natacha Beck -#- BrainPortal/app/controllers/custom_filters_controller.rb
-cf2c835d3a4cbaa49c07b9ee67b2ae20c7701fb8 -#- 2015-06-17 14:35:57 -0400 -#- Remi Bernard -#- BrainPortal/app/controllers/data_providers_controller.rb
-4b901999b2220df048ef1296967a28118d7e11cc -#- 2012-08-30 16:31:00 -0400 -#- Tarek Sherif -#- BrainPortal/app/controllers/exception_logs_controller.rb
-ff28ae45e27417463a39d17b532c8f7ae7289658 -#- 2012-08-07 14:58:59 -0400 -#- Tarek Sherif -#- BrainPortal/app/controllers/feedbacks_controller.rb
-0e3793e391ead5fd3f7fd6236ad8cfd88621b2ab -#- 2015-05-19 18:14:51 -0400 -#- Pierre Rioux -#- BrainPortal/app/controllers/groups_controller.rb
+a7c9771ef11c05817e5626942f9cb060f3549ae4 -#- 2015-09-16 10:11:07 -0400 -#- Remi Bernard -#- BrainPortal/app/controllers/custom_filters_controller.rb
+a5bafa8c01b857e358d6cbad182e6f9e0cf66a3b -#- 2015-09-28 14:16:46 -0400 -#- Remi Bernard -#- BrainPortal/app/controllers/data_providers_controller.rb
+3a42fd7db2bf64ee3acc7c9163de6c8ac376343b -#- 2015-09-21 15:27:17 -0400 -#- Remi Bernard -#- BrainPortal/app/controllers/exception_logs_controller.rb
+3a42fd7db2bf64ee3acc7c9163de6c8ac376343b -#- 2015-09-21 15:27:17 -0400 -#- Remi Bernard -#- BrainPortal/app/controllers/feedbacks_controller.rb
+2fa60c7afe2c0ab74860c720286325f1267a845e -#- 2015-09-23 14:04:05 -0400 -#- Remi Bernard -#- BrainPortal/app/controllers/groups_controller.rb
 d896141b70f2c0704655d8c53c66efda5a736f26 -#- 2015-05-25 10:39:50 -0400 -#- Remi Bernard -#- BrainPortal/app/controllers/help_documents_controller.rb
 70403d4a9074bc93d2028f67d66b459719a75cb4 -#- 2015-05-06 15:23:08 -0400 -#- Natacha Beck -#- BrainPortal/app/controllers/invitations_controller.rb
-70403d4a9074bc93d2028f67d66b459719a75cb4 -#- 2015-05-06 15:23:08 -0400 -#- Natacha Beck -#- BrainPortal/app/controllers/messages_controller.rb
-19b1ab65da0769a687576878833172ebed0f196b -#- 2015-07-29 14:13:24 -0400 -#- Natacha Beck -#- BrainPortal/app/controllers/portal_controller.rb
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+1ddadd6b8b0098ada75f973f681cdec40fb73054 -#- 2015-10-07 12:10:45 -0400 -#- Remi Bernard -#- BrainPortal/app/controllers/portal_controller.rb
 9ecd53a7c71655c8ca325b6b2b1d58fd26384317 -#- 2015-04-15 17:01:28 -0400 -#- Natacha Beck -#- BrainPortal/app/controllers/service_controller.rb
-57141a2354ce3975fd4558029af17d33c8bf15a3 -#- 2015-08-07 18:06:15 -0400 -#- Remi Bernard -#- BrainPortal/app/controllers/sessions_controller.rb
-28264d2526142c37b9aa47d4319370f38b505e20 -#- 2015-06-18 13:31:56 -0400 -#- Ehsan Afkhami -#- BrainPortal/app/controllers/sites_controller.rb
-970fd506142f19c2b27feb929ff285174556bf47 -#- 2012-08-07 14:59:21 -0400 -#- Tarek Sherif -#- BrainPortal/app/controllers/tags_controller.rb
-4ab0df1815e2fe8ffbe9dc837fa05861027a703c -#- 2015-07-29 14:40:56 -0400 -#- Pierre Rioux -#- BrainPortal/app/controllers/tasks_controller.rb
-9b800a081b3085326001af2005c10befbdec5b02 -#- 2015-06-16 18:14:06 -1000 -#- Tristan Glatard -#- BrainPortal/app/controllers/tool_configs_controller.rb
-cb39bdfe9a9a17886505f76affc01dd5a4a032fa -#- 2015-07-14 12:12:21 -0400 -#- Natacha Beck -#- BrainPortal/app/controllers/tools_controller.rb
-e3a7cb5c2baa09dd26a9c284a8a1819cdfd7fdd9 -#- 2015-08-13 10:40:49 -0400 -#- Remi Bernard -#- BrainPortal/app/controllers/userfiles_controller.rb
-f558a185e90cc9fe86308147f0cafa03480398e0 -#- 2015-08-10 12:57:19 -0400 -#- Remi Bernard -#- BrainPortal/app/controllers/users_controller.rb
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+e2b1c2208d0609b38a2d2dc51fcbeb650d9ef893 -#- 2015-10-02 14:51:23 -0400 -#- Remi Bernard -#- BrainPortal/app/controllers/tasks_controller.rb
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-6b795c542757f61f288628e20edaf811416ee9e7 -#- 2015-05-15 17:24:03 -0400 -#- Natacha Beck -#- BrainPortal/app/helpers/ajax_widget_helper.rb
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 0597b7a834fbd9fb7738ad291f45c83de2be5516 -#- 2015-06-30 11:46:19 -0400 -#- Remi Bernard -#- BrainPortal/app/helpers/basic_helper.rb
 70403d4a9074bc93d2028f67d66b459719a75cb4 -#- 2015-05-06 15:23:08 -0400 -#- Natacha Beck -#- BrainPortal/app/helpers/data_providers_helper.rb
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 ff28ae45e27417463a39d17b532c8f7ae7289658 -#- 2012-08-07 14:58:59 -0400 -#- Tarek Sherif -#- BrainPortal/app/helpers/disk_usage_report_helper.rb
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+0c3a032f4414535a331b15da9d0f26464f400bbe -#- 2015-09-09 13:44:31 -0400 -#- Remi Bernard -#- BrainPortal/app/models/cbrain_session.rb
 077511bc3a7a9c3674df2d6eee186c2741b3ee9e -#- 2015-01-05 16:56:36 -0500 -#- Pierre Rioux -#- BrainPortal/app/models/cbrain_task.rb
-b2dfe4981d5f5a780720c348bc0062f12cbf82d3 -#- 2015-07-30 18:13:59 -0400 -#- Tristan Glatard -#- BrainPortal/app/models/cluster_task.rb
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-db851a8f83b24e2909986e97ef968c3507c41d6e -#- 2015-05-14 12:21:55 -0400 -#- Remi Bernard -#- BrainPortal/public/javascripts/cbrain.js
+97d8c876f3b07b4800eb87b62fbacc59e7b512ce -#- 2015-08-24 16:23:40 -0400 -#- Remi Bernard -#- BrainPortal/public/javascripts/cbrain.js
 151f5958d1202e06df847e9ebf2b4fe421d4d1b8 -#- 2015-05-20 17:01:09 -0400 -#- Remi Bernard -#- BrainPortal/public/javascripts/codemirror-5.2.min.js
 151f5958d1202e06df847e9ebf2b4fe421d4d1b8 -#- 2015-05-20 17:01:09 -0400 -#- Remi Bernard -#- BrainPortal/public/javascripts/codemirror.js
-ffe2de57bc21e1683cd79125bfe56cdd6b138c7a -#- 2015-07-30 18:00:18 -0400 -#- Remi Bernard -#- BrainPortal/public/javascripts/dynamic-table.js
+bd94292d632ba9a59c71077561bf60b2a56e6fe1 -#- 2015-10-13 16:39:20 -0400 -#- Ehsan Afkhami -#- BrainPortal/public/javascripts/custom-confirm-dialog.js
+2408e08b13343fd759a0d1b5d6b678a19b905310 -#- 2015-08-17 16:05:06 -0400 -#- Pierre Rioux -#- BrainPortal/public/javascripts/dynamic-table.js
 813ba210de8e01a086a76ca67cbc6f8bc1b717f5 -#- 2014-07-14 12:03:03 -0400 -#- Natacha Beck -#- BrainPortal/public/javascripts/exception_logger.js
 7dc8ea20593868e53a87448062193df96e1d480b -#- 2012-07-09 13:15:07 -0400 -#- Tarek Sherif -#- BrainPortal/public/javascripts/jquery-1.6.4.min.js
 c804034536cb6b366a5346b68b3254f28e6db21a -#- 2010-04-07 18:08:22 +0000 -#- nkassis -#- BrainPortal/public/javascripts/jquery-ui-1.8.custom.min.js
@@ -805,11 +819,11 @@ dcc9f546f0359d737a04feb3ce372da09cee829d -#- 2012-06-28 16:00:14 -0400 -#- Pierr
 f2136717fbeb4a5ce0c30ea421d0960ba040a7db -#- 2015-03-23 18:20:40 -0400 -#- Pierre Rioux -#- BrainPortal/public/licenses/.gitignore
 f2136717fbeb4a5ce0c30ea421d0960ba040a7db -#- 2015-03-23 18:20:40 -0400 -#- Pierre Rioux -#- BrainPortal/public/licenses/README.txt
 216116284996dc3abe068a46270fdf50d2aca68b -#- 2009-07-14 20:01:12 +0000 -#- prioux -#- BrainPortal/public/robots.txt
-e3a7cb5c2baa09dd26a9c284a8a1819cdfd7fdd9 -#- 2015-08-13 10:40:49 -0400 -#- Remi Bernard -#- BrainPortal/public/stylesheets/cbrain.css
+cb68f893745f479e8c301b4deaecf6451f8e2c48 -#- 2015-10-27 13:09:11 -0400 -#- Pierre Rioux -#- BrainPortal/public/stylesheets/cbrain.css
 151f5958d1202e06df847e9ebf2b4fe421d4d1b8 -#- 2015-05-20 17:01:09 -0400 -#- Remi Bernard -#- BrainPortal/public/stylesheets/codemirror-5.2.css
 151f5958d1202e06df847e9ebf2b4fe421d4d1b8 -#- 2015-05-20 17:01:09 -0400 -#- Remi Bernard -#- BrainPortal/public/stylesheets/codemirror-neo.css
 151f5958d1202e06df847e9ebf2b4fe421d4d1b8 -#- 2015-05-20 17:01:09 -0400 -#- Remi Bernard -#- BrainPortal/public/stylesheets/codemirror.css
-e5b27eff9f6bf40cb7e9c17c1cd5bd914af79723 -#- 2015-07-30 17:53:32 -0400 -#- Remi Bernard -#- BrainPortal/public/stylesheets/dynamic-table.css
+02cb4903d2b6c28d27f374f6af66e65bd379164d -#- 2015-09-21 15:35:25 -0400 -#- Remi Bernard -#- BrainPortal/public/stylesheets/dynamic-table.css
 a72870bbedd7d777e9836aa630c6e568116ab2c2 -#- 2010-05-07 18:18:32 +0000 -#- prioux -#- BrainPortal/public/stylesheets/images/ui-bg_flat_0_aaaaaa_40x100.png
 a72870bbedd7d777e9836aa630c6e568116ab2c2 -#- 2010-05-07 18:18:32 +0000 -#- prioux -#- BrainPortal/public/stylesheets/images/ui-bg_flat_0_eeeeee_40x100.png
 a72870bbedd7d777e9836aa630c6e568116ab2c2 -#- 2010-05-07 18:18:32 +0000 -#- prioux -#- BrainPortal/public/stylesheets/images/ui-bg_flat_55_ffffff_40x100.png
@@ -891,6 +905,7 @@ f742c66daa62920f604790e93ef52a81fe24eedf -#- 2015-06-08 15:13:45 -0400 -#- Ehsan
 4ae88132ae49c202d5363fe1648d1f4861c81920 -#- 2015-04-29 16:40:11 -0400 -#- Natacha Beck -#- BrainPortal/spec/modules/core_models_spec.rb
 4ae88132ae49c202d5363fe1648d1f4861c81920 -#- 2015-04-29 16:40:11 -0400 -#- Natacha Beck -#- BrainPortal/spec/modules/resource_access_spec.rb
 4ae88132ae49c202d5363fe1648d1f4861c81920 -#- 2015-04-29 16:40:11 -0400 -#- Natacha Beck -#- BrainPortal/spec/modules/ssh_agent_spec.rb
+ae450150e4767317062513ca0027778616d78684 -#- 2015-08-21 16:35:13 -0400 -#- Remi Bernard -#- BrainPortal/spec/modules/view_scopes_spec.rb
 4ae88132ae49c202d5363fe1648d1f4861c81920 -#- 2015-04-29 16:40:11 -0400 -#- Natacha Beck -#- BrainPortal/spec/rails_helper.rb
 d52d418e53ff4b8fe4162a4c9b51a0e74fc14239 -#- 2010-01-14 21:28:55 +0000 -#- nkassis -#- BrainPortal/spec/rcov.opts
 4ae88132ae49c202d5363fe1648d1f4861c81920 -#- 2015-04-29 16:40:11 -0400 -#- Natacha Beck -#- BrainPortal/spec/spec_helper.rb
@@ -907,6 +922,6 @@ df3e2af099c3247e5b7c350de3afc8f99b0253d8 -#- 2012-01-25 13:10:16 -0500 -#- Pierr
 8c0d044038ede0b706ed465a2d14006c8accf1ca -#- 2015-03-09 20:29:40 -0400 -#- Pierre Rioux -#- README.md
 b7a704897dd9406489be2a675a7d0c9144005faf -#- 2015-05-20 10:27:43 -0400 -#- Pierre Rioux -#- Release-Notes.md
 d0e6e910a147a24e467236e93314c0b46ea406ba -#- 2012-08-30 11:35:20 -0400 -#- Pierre Rioux -#- alldoc.sh
-c0ac75cca188fd5f196309ce0a4e80d8751d917a -#- 2015-05-19 16:33:31 -0400 -#- Pierre Rioux -#- cbrain_file_revisions.csv
+1a44b0b82ef7a8a12bdfe4dbfc430e2ff989be4a -#- 2015-08-13 15:32:25 -0400 -#- Pierre Rioux -#- cbrain_file_revisions.csv
 2eceeb92afa749dd8c5c28082493fcdc0111af95 -#- 2012-01-26 13:46:35 -0500 -#- Pierre Rioux -#- generate_rev_list.sh
 9cb6e6130c771f2b343ce959b3f5d3dfdcd8afd5 -#- 2015-02-05 14:58:06 -0500 -#- Pierre Rioux -#- license_header.txt
diff --git a/generate_rev_list.sh b/generate_rev_list.sh
index 36f06ce27..315632c5c 100644
--- a/generate_rev_list.sh
+++ b/generate_rev_list.sh
@@ -18,33 +18,50 @@
 # 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/>. 
 #
 
+# This script examines all files in the CBRAIN project and creates
+# a CSV file with the date, author and latest commit IDs for each one.
+# This CSV file is used instead of GIT commands when CBRAIN is deployed
+# without GIT (using a tarball, for instance).
+
+STATIC_REV_FILE="cbrain_file_revisions.csv"
+CSV_SEP=" -#- " # careful, this is what is expected of cbrain_file_revision.rb !
+
+# Make sure we have GIT.
 GIT_EXEC=`which git 2>/dev/null`
 if test -z "$GIT_EXEC" ; then
   echo "You need access to GIT to run this script!"
   exit 10
 fi
 
-STATIC_REV_FILE="cbrain_file_revisions.csv"
-CSV_SEP=" -#- " # careful, this is what is expected of cbrain_file_revision.rb !
-
-cd `$GIT_EXEC rev-parse --show-toplevel` || exit 10
-
+# Make sure the cwd is OK.
 if ! test -d BrainPortal -a -d Bourreau ; then
   echo "You must run this script from the ROOT of the CBRAIN project."
   exit 10
 fi
 
+# Make sure we are deployed with GIT.
+cd `$GIT_EXEC rev-parse --show-toplevel` || exit 10
+
 echo "Generating the static list of revisions for all CBRAIN files..."
 cp /dev/null "$STATIC_REV_FILE"
 CBRAIN_REV_NUM="`BrainPortal/script/show_cbrain_rev`"
 CURRENT_DATE="`date \"+%F %T %z\"`"  # must be same ISO format as %ai of git log command below
+
+# This block's output is sent to the CSV file
 {
-echo "${CBRAIN_REV_NUM}${CSV_SEP}${CURRENT_DATE}${CSV_SEP}CBRAIN Team${CSV_SEP}__CBRAIN_TAG__"
-git log -n1 --format="%H${CSV_SEP}%ai${CSV_SEP}%an${CSV_SEP}__CBRAIN_HEAD__" -- .
-for n in `$GIT_EXEC ls-files` ; do $GIT_EXEC log -n1 --format="%H${CSV_SEP}%ai${CSV_SEP}%an${CSV_SEP}$n" -- "$n" | cat ; done
+  # These two statements generates the first entry, an artifical __CBRAIN_TAG__ for the whole project.
+  echo "${CBRAIN_REV_NUM}${CSV_SEP}${CURRENT_DATE}${CSV_SEP}CBRAIN Team${CSV_SEP}__CBRAIN_TAG__"
+  git log -n1 --format="%H${CSV_SEP}%ai${CSV_SEP}%an${CSV_SEP}__CBRAIN_HEAD__" -- .
+
+  # This loop generates one entry per file in the project.
+  for file in `$GIT_EXEC ls-files | sort` ; do
+    $GIT_EXEC log -n1 --format="%H${CSV_SEP}%ai${CSV_SEP}%an${CSV_SEP}$file" -- "$file" | cat
+  done
+
 } | tee -a "$STATIC_REV_FILE"
-echo "Done."
+
+echo "All done."