iqvoc 3.5.3 → 3.5.4

data/CHANGELOG.md

@@ -1,3 +1,12 @@
+## 3.5.4 (2012-02-08)
+
+  * Top concepts<br>
+    From now on the hierarchical concept view only lists concepts marked as "top term".
+    This also includes a default concept scheme and support for top concepts in RDF views.
+  * Configurable navigation<br>
+    Use `Iqvoc.navigation_items` to inject additional navigation items.
+  * Bugfixes
+
 ## 3.5.1 (2012-02-01)
 
  * Bugfixes
@@ -22,7 +31,7 @@
  * Several asset pipeline related fixes
  * Largely simplified heroku setup
  * Improvements to engine mode
- 
+
 Detailed commit log: https://github.com/innoq/iqvoc/compare/v3.3.0...v3.3.3
 
 ## 3.3.0 (2012-01-10)
@@ -31,7 +40,7 @@ Detailed commit log: https://github.com/innoq/iqvoc/compare/v3.3.0...v3.3.3
  * Asset pipeline<br>
    [Detailed instructions](https://github.com/innoq/iqvoc/wiki/iQvoc-as-a-Rails-Engine)
    on how to use iQvoc as a Rails Engine (including the asset pipeline).
-   
+
 This is a big update. Detailed commit log: https://github.com/innoq/iqvoc/compare/v3.2.6...v3.3.0
 
 ## 3.2.6 (2012-01-10)

data/Gemfile

@@ -33,17 +33,16 @@ gem 'iq_rdf', '~> 0.1.2'
 gem 'json'
 gem 'rails_autolink'
 gem 'jruby-openssl', :platforms => :jruby
-gem 'blazing'
-gem 'blazing-passenger'
-gem 'blazing-rails'
+gem 'fastercsv', :platforms => :ruby_18
 
 group :development do
-  gem 'awesome_print'
   gem 'heroku'
   gem 'view_marker'
 end
 
 group :development, :test do
+  gem 'awesome_print'
+  
   platforms :ruby do
     gem 'mysql2'
     gem 'sqlite3'
@@ -65,8 +64,7 @@ group :test do
   gem 'capybara-webkit'
   gem 'database_cleaner'
   gem 'factory_girl_rails'
-  gem 'memory_test_fix'
-  gem 'turn'
+  gem 'minitest'
 end
 
 group :production do

data/Gemfile.lock

@@ -44,23 +44,11 @@ GEM
       i18n (~> 0.6)
       multi_json (~> 1.0)
     addressable (2.2.6)
-    ansi (1.4.2)
     arel (3.0.0)
     authlogic (3.1.0)
       activerecord (>= 3.0.7)
       activerecord (>= 3.0.7)
     awesome_print (1.0.2)
-    blazing (0.2.7)
-      activesupport
-      grit
-      i18n
-      logging
-    blazing-passenger (0.2.3)
-      blazing (>= 0.2.5)
-      httparty
-    blazing-rails (0.1.3)
-      blazing (>= 0.2.5)
-      httparty
     bouncy-castle-java (1.5.0146.1)
     builder (3.0.0)
     cancan (1.6.7)
@@ -77,7 +65,6 @@ GEM
     childprocess (0.3.0)
       ffi (~> 1.0.6)
     database_cleaner (0.7.1)
-    diff-lcs (1.1.3)
     erubis (2.7.0)
     execjs (1.3.0)
       multi_json (~> 1.0)
@@ -86,20 +73,15 @@ GEM
     factory_girl_rails (1.6.0)
       factory_girl (~> 2.5.0)
       railties (>= 3.0.0)
+    fastercsv (1.5.4)
     ffi (1.0.11)
     ffi (1.0.11-java)
-    grit (2.4.1)
-      diff-lcs (~> 1.1)
-      mime-types (~> 1.15)
     heroku (2.19.1)
       launchy (>= 0.3.2)
       rest-client (~> 1.6.1)
       rubyzip
       term-ansicolor (~> 1.0.5)
     hike (1.2.1)
-    httparty (0.8.1)
-      multi_json
-      multi_xml
     i18n (0.6.0)
     iq_rdf (0.1.2)
       builder
@@ -122,17 +104,13 @@ GEM
       ffi (~> 1.0.9)
       spoon (~> 0.0.1)
     libv8 (3.3.10.4)
-    little-plugger (1.1.3)
-    logging (1.6.2)
-      little-plugger (>= 1.1.3)
     mail (2.4.1)
       i18n (>= 0.4.0)
       mime-types (~> 1.16)
       treetop (~> 1.4.8)
-    memory_test_fix (0.2.0)
     mime-types (1.17.2)
+    minitest (2.11.1)
     multi_json (1.0.4)
-    multi_xml (0.4.1)
     mysql2 (0.3.11)
     nokogiri (1.5.0)
     nokogiri (1.5.0-java)
@@ -188,8 +166,6 @@ GEM
     treetop (1.4.10)
       polyglot
       polyglot (>= 0.3.1)
-    turn (0.8.3)
-      ansi
     tzinfo (0.3.31)
     uglifier (1.2.3)
       execjs (>= 0.3.0)
@@ -209,20 +185,18 @@ DEPENDENCIES
   activerecord-oracle_enhanced-adapter
   authlogic
   awesome_print
-  blazing
-  blazing-passenger
-  blazing-rails
   cancan
   capybara
   capybara-webkit
   database_cleaner
   factory_girl_rails
+  fastercsv
   heroku
   iq_rdf (~> 0.1.2)
   jruby-openssl
   json
   kaminari
-  memory_test_fix
+  minitest
   mysql2
   nokogiri (~> 1.5.0)
   pg
@@ -232,6 +206,5 @@ DEPENDENCIES
   spork-testunit!
   sqlite3
   therubyracer
-  turn
   uglifier (>= 1.0.3)
   view_marker

data/README.md

@@ -42,7 +42,7 @@ heroku restart
 
 Remember to visit the Users section and change the default passwords!
 
-**Remarks:** 
+**Remarks:**
 For now iQvoc only supports the standard Bamboo stack. Cedar is not supported as we have `sqlite3` as a dependency
 in the Gemfile and Cedar does not support a custom `BUNDLE_WITHOUT` config like Bamboo at the moment.
 

data/app/assets/javascripts/iqvoc/iqvoc.js

@@ -1,4 +1,4 @@
-/*jslint vars: true, unparam: true, browser: true */
+/*jslint vars: true, unparam: true, browser: true, white: true */
 /*global jQuery */
 
 var IQVOC = (function($) {
@@ -188,6 +188,15 @@ jQuery(document).ready(function($) {
 		IQVOC.EntitySelector(node);
 	});
 
+	// hide broader relations for top terms (mutually exclusive in mono hierarchies)
+	var topTerm = $("#concept_top_term.exclusive");
+	var onTopTermToggle = function(ev) {
+		var broader = topTerm.closest("li").next(); // XXX: brittle
+		broader[topTerm.prop("checked") ? "slideUp" : "slideDown"]();
+	};
+	topTerm.on("change", onTopTermToggle);
+	onTopTermToggle();
+
 	// Label editing (inline notes)
 	$("fieldset.note_relation ol li.inline_note.new").hide();
 	$("fieldset.note_relation input[type=button]").click(function(ev) {
@@ -247,4 +256,3 @@ jQuery(document).ready(function($) {
 		});
 	});
 });
-

data/app/controllers/application_controller.rb

@@ -18,6 +18,6 @@ require "iqvoc/controller_extensions"
 
 class ApplicationController < ActionController::Base
   include Iqvoc::ControllerExtensions
-  
+
   protect_from_forgery
 end

data/app/controllers/collections_controller.rb

@@ -48,8 +48,8 @@ class CollectionsController < ApplicationController
 
     # When in single query mode, AR handles ALL includes to be loaded by that
     # one query. We don't want that! So let's do it manually :-)
-    ActiveRecord::Associations::Preloader.new(@collection, 
-      [:pref_labels, 
+    ActiveRecord::Associations::Preloader.new(@collection,
+      [:pref_labels,
       {:subcollections => [:pref_labels, :subcollections]},
       {:concepts => [:pref_labels] + Iqvoc::Concept.base_class.default_includes}]).run
   end
@@ -84,10 +84,10 @@ class CollectionsController < ApplicationController
     # When in single query mode, AR handles ALL includes to be loaded by that
     # one query. We don't want that! So let's do it manually :-)
     ActiveRecord::Associations::Preloader.new(@collection, [
-      :pref_labels, 
-      {:subcollections => :pref_labels}, 
+      :pref_labels,
+      {:subcollections => :pref_labels},
       {:concepts => [:pref_labels] + Iqvoc::Concept.base_class.default_includes}]).run
-      
+
     build_note_relations
   end
 

data/app/controllers/concepts/versions_controller.rb

@@ -84,7 +84,7 @@ class Concepts::VersionsController < ApplicationController
 
     new_version.unlock
     new_version.save :validate => false
-    
+
     flash[:notice] = t("txt.controllers.versioning.unlocked")
     redirect_to concept_path(:published => 0, :id => new_version)
   end

data/app/controllers/concepts_controller.rb

@@ -22,11 +22,11 @@ class ConceptsController < ApplicationController
 
     respond_to do |format|
       format.json do # Search for widget
-        @concepts = Iqvoc::Concept.base_class.editor_selectable.with_pref_labels.merge(Label::Base.by_query_value("#{params[:query]}%")).all
-        response = []
-        @concepts.each { |concept| response << concept_widget_data(concept)}
-
-        render :json => response
+        scope = Iqvoc::Concept.base_class.editor_selectable.with_pref_labels.
+            merge(Label::Base.by_query_value("#{params[:query]}%"))
+        scope = scope.where(:top_term => false) if params[:exclude_top_terms]
+        @concepts = scope.all.map { |concept| concept_widget_data(concept) }
+        render :json => @concepts
       end
       format.all do # RDF full export
         authorize! :full_export, Concept::Base
@@ -55,7 +55,7 @@ class ConceptsController < ApplicationController
       format.html do
         # When in single query mode, AR handles ALL includes to be loaded by that
         # one query. We don't want that! So let's do it manually :-)
-        ActiveRecord::Associations::Preloader.new(@concept, 
+        ActiveRecord::Associations::Preloader.new(@concept,
           Iqvoc::Concept.base_class.default_includes + [:collection_members => {:collection => :labels},
           :broader_relations => {:target => [:pref_labels, :broader_relations]},
           :narrower_relations => {:target => [:pref_labels, :narrower_relations]}]).run
@@ -65,7 +65,7 @@ class ConceptsController < ApplicationController
       format.json do
         # When in single query mode, AR handles ALL includes to be loaded by that
         # one query. We don't want that! So let's do it manually :-)
-        ActiveRecord::Associations::Preloader.new(@concept, 
+        ActiveRecord::Associations::Preloader.new(@concept,
           [:labels,
           { :relations => { :target => [:labelings, :relations] } }]).run
 
@@ -83,7 +83,6 @@ class ConceptsController < ApplicationController
         }
         render :json => concept_data
       end
-      format.ttl
     end
   end
 

data/app/controllers/dashboard_controller.rb

@@ -18,7 +18,7 @@ class DashboardController < ApplicationController
 
   def index
     authorize! :use, :dashboard
-    
+
     @items = []
     Iqvoc.first_level_classes.each do |klass|
       @items += klass.for_dashboard.all

data/app/controllers/instance_configuration_controller.rb

@@ -14,7 +14,13 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-require 'csv'
+if RUBY_VERSION < "1.9"
+  require 'rubygems'
+  require 'faster_csv'
+  CSV = FCSV
+else
+  require 'csv'
+end
 
 class InstanceConfigurationController < ApplicationController
 
@@ -54,7 +60,7 @@ class InstanceConfigurationController < ApplicationController
 
     redirect_to instance_configuration_url
   end
-  
+
   private
 
   # default value determines value type

data/app/controllers/rdf_controller.rb

@@ -18,25 +18,35 @@ class RdfController < ApplicationController
 
   skip_before_filter :require_user
   skip_before_filter :set_locale
+  
+  def scheme
+    respond_to do |format|
+      format.html { redirect_to about_path }
+      format.any do
+        authorize! :read, Iqvoc::Concept.root_class.instance
+        @top_concepts = Iqvoc::Concept.base_class.tops.published.all
+      end
+    end
+  end
 
   def show
-    scope = if (params[:published] == "0")
-      Iqvoc::Concept.base_class.scoped.unpublished
+    scope = if params[:published] == "0"
+      Iqvoc::Concept.base_class.unpublished
     else
-      Iqvoc::Concept.base_class.scoped.published
+      Iqvoc::Concept.base_class.published
     end
     if @concept = scope.by_origin(params[:id]).with_associations.last
       respond_to do |format|
-        format.html {
+        format.html do
           redirect_to concept_url(:id => @concept.origin, :published => params[:published])
-        }
-        format.any {
+        end
+        format.any do
           authorize! :read, @concept
-          render "show_concept"
-        }
+          render :show_concept
+        end
       end
     else
-      raise ActiveRecord::RecordNotFound.new("Coulnd't find either a concept matching '#{params[:id]}'.")
+      raise ActiveRecord::RecordNotFound.new("Concept '#{params[:id]}' not found.")
     end
   end
 

data/app/controllers/user_sessions_controller.rb

@@ -15,7 +15,7 @@
 # limitations under the License.
 
 class UserSessionsController < ApplicationController
-  
+
   skip_before_filter :require_user, :only => [:new, :create]
 
   def new

data/app/helpers/application_helper.rb

@@ -16,6 +16,25 @@
 
 module ApplicationHelper
 
+  # expects an array of hashes with the following members:
+  # :content - usually a navigation link
+  # :active? - an optional function determining whether the respective item is
+  #     currently active
+  # :controller - an optional string, used instead of `active?` to check for a
+  #     specific controller
+  # :authorized? - an optional function determining whether the respective item
+  #     is available to the current user (defaults to true)
+  def nav_items(items)
+    items.map do |item|
+      if (not item[:authorized?]) || instance_eval(&item[:authorized?])
+        active = item[:controller] ? params[:controller] == item[:controller] :
+            (item[:active?] ? instance_eval(&item[:active?]) : false)
+        content_tag "li", instance_eval(&item[:content]),
+            :class => ("active" if active)
+      end
+    end.join.html_safe
+  end
+
   def iqvoc_default_rdf_namespaces
     Iqvoc.rdf_namespaces.merge({
         :default => root_url(:format => nil, :lang => nil, :trailing_slash => true).gsub(/\/\/$/, "/"), # gsub because of a Rails bug :-(

data/app/helpers/dashboard_helper.rb

@@ -34,9 +34,9 @@ module DashboardHelper
 
     content_tag :span, raw(msg), :class => css
   end
-  
+
   def link_to_dashboard_item(item)
-    if item.is_a?(Label::Base) 
+    if item.is_a?(Label::Base)
       item.published? ? label_path(:id => item.origin) : label_path(:published => 0, :id => item.origin)
     else
       item.published? ? concept_path(:id => item.origin) : concept_path(:published => 0, :id => item.origin)

data/app/helpers/rdf_helper.rb

@@ -18,7 +18,7 @@ module RdfHelper
 
   def render_concept(document, concept)
 
-    # You can not eager load polymorpihc associations. That's why we're loading
+    # You can not eager load polymorphic associations. That's why we're loading
     # the collections _one_ time and remember them for further _render_concept_
     # calls in the future.
     @rdf_helper_cached_collections ||= Iqvoc::Collection.base_class.select("id, origin").all.each_with_object({}) do |c, hash|
@@ -35,6 +35,8 @@ module RdfHelper
 
       c.Schema::expires(concept.expired_at) if concept.expired_at
       c.Owl::deprecated(true) if concept.expired_at and concept.expired_at <= Date.new
+      
+      c.Skos::topConceptOf IqRdf.build_uri(Iqvoc::Concept.root_class.instance.origin) if concept.top_term?
 
       concept.labelings.each do |labeling|
         labeling.build_rdf(document, c)

data/app/helpers/search_results_helper.rb

@@ -28,5 +28,5 @@ module SearchResultsHelper
     end
     text
   end
-  
+
 end

data/app/models/collection/member/base.rb

@@ -15,7 +15,7 @@
 # limitations under the License.
 
 class Collection::Member::Base < ActiveRecord::Base
-  
+
   self.table_name = 'collection_members'
 
   belongs_to :collection, :class_name => 'Collection::Base'

data/app/models/concept/base.rb

@@ -38,13 +38,15 @@ class Concept::Base < ActiveRecord::Base
     :on => :update
 
   validate :ensure_no_pref_labels_share_the_same_language
+  validate :ensure_exclusive_top_term
+  validate :ensure_rooted_top_terms
 
   Iqvoc::Concept.include_modules.each do |mod|
     include mod
   end
 
   # ********** Hooks
-  
+
   after_initialize do
     @full_validation = false
   end
@@ -125,7 +127,7 @@ class Concept::Base < ActiveRecord::Base
   # *** Concept2Concept relations
 
   # Broader
-  # Actually this is not needed anymore.
+  # FIXME: Actually this is not needed anymore.
   # BUT: the include in scope :tops doesn't work with
   # 'Iqvoc::Concept.broader_relation_class_name'!?!?! (Rails Bug????)
   has_many :broader_relations,
@@ -134,7 +136,7 @@ class Concept::Base < ActiveRecord::Base
     :extend => Concept::Relation::ReverseRelationExtension
 
   # Narrower
-  # Actually this is not needed anymore.
+  # FIXME: Actually this is not needed anymore.
   # BUT: the include in scope :tops doesn't work with
   # 'Iqvoc::Concept.broader_relation_class_name'!?!?! (Rails Bug????)
   has_many :narrower_relations,
@@ -226,26 +228,26 @@ class Concept::Base < ActiveRecord::Base
   # ********** Relation Stuff
 
   @nested_relations.each do |relation|
-    accepts_nested_attributes_for relation, :allow_destroy => true, :reject_if => Proc.new {|attrs| attrs[:value].blank? }
+    accepts_nested_attributes_for relation, :allow_destroy => true, :reject_if => Proc.new { |attrs| attrs[:value].blank? }
   end
 
   # ********** Scopes
 
-  scope :tops, includes(:broader_relations).
-    where(:concept_relations => {:id => nil})
+  scope :tops, where(:top_term => true)
 
   scope :broader_tops, includes(:narrower_relations, :pref_labels).
-    where(:concept_relations => {:id => nil}, :labelings => {:type => Iqvoc::Concept.pref_labeling_class_name}).
+    where(:concept_relations => { :id => nil },
+        :labelings => { :type => Iqvoc::Concept.pref_labeling_class_name }).
     order("LOWER(#{Label::Base.table_name}.value)")
 
   scope :with_associations, includes([
-      {:labelings => :target}, :relations, :matches, :notes
+      { :labelings => :target }, :relations, :matches, :notes
     ])
 
   scope :with_pref_labels,
     includes(:pref_labels).
     order("LOWER(#{Label::Base.table_name}.value)").
-    where(:labelings => {:type => Iqvoc::Concept.pref_labeling_class_name}) # This line is just a workaround for a Rails Bug. TODO: Delete it when the Bug is fixed
+    where(:labelings => { :type => Iqvoc::Concept.pref_labeling_class_name }) # This line is just a workaround for a Rails Bug. TODO: Delete it when the Bug is fixed
 
   scope :for_dashboard, lambda {
     unpublished_or_follow_up.
@@ -331,7 +333,7 @@ class Concept::Base < ActiveRecord::Base
   def related_concepts_for_relation_class(relation_class, only_published = true)
     relation_class = relation_class.name if relation_class < ActiveRecord::Base # Use the class name string
     relations.select { |rel| rel.class.name == relation_class }.map(&:target).
-      select { |c| c.published? || !only_published }
+        select { |c| c.published? || !only_published }
   end
 
   def matches_for_class(match_class)
@@ -390,6 +392,26 @@ class Concept::Base < ActiveRecord::Base
     end
   end
 
+  # top term and broader relations are mutually exclusive
+  def ensure_exclusive_top_term
+    if @full_validation
+      if top_term && broader_relations.any?
+        errors.add :base, I18n.t("txt.models.concept.top_term_exclusive_error")
+      end
+    end
+  end
+
+  # top terms must never be used as descendants (narrower relation targets)
+  # NB: for top terms themselves, this is covered by `ensure_exclusive_top_term`
+  def ensure_rooted_top_terms
+    if @full_validation
+      if narrower_relations.includes(:target). # XXX: inefficient?
+          select { |rel| rel.target.top_term? }.any?
+        errors.add :base, I18n.t("txt.models.concept.top_term_rooted_error")
+      end
+    end
+  end
+
   def ensure_a_pref_label_in_the_primary_thesaurus_language
     if @full_validation
       labels = pref_labels.select{|l| l.published?}

data/app/models/concept/skos/scheme.rb

@@ -0,0 +1,46 @@
+# encoding: UTF-8
+
+# Copyright 2011 innoQ Deutschland GmbH
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+require 'singleton'
+
+# virtual root node
+# NB:
+# * does not inherit from Concept::Base to avoid being included in all
+#   queries based on that class, including indirect ones (e.g. relations)
+# * persistence (i.e. a database record) is not required since this is a
+#   singleton and merely a static, virtual node
+class Concept::SKOS::Scheme
+  include Singleton
+  
+  def self.rdf_class
+    :ConceptScheme
+  end
+  
+  def self.rdf_namespace
+    :skos
+  end
+  
+  def origin
+    :scheme
+  end
+
+  def build_rdf_subject(document, controller, &block)
+    ns = IqRdf::Namespace.find_namespace_class(self.class.rdf_namespace.to_sym)
+    raise "Namespace '#{rdf_namespace}' is not defined in IqRdf document." unless ns
+    IqRdf.build_uri(origin, ns.build_uri(self.class.rdf_class), &block)
+  end
+  
+end

data/app/models/labeling/skos/base.rb

@@ -63,7 +63,7 @@ class Labeling::SKOS::Base < Labeling::Base
       end
     end
     scope = scope.includes(:owner)
-    
+
     scope = case params[:for]
     when "concept"
       scope.where("concepts.type" => Iqvoc::Concept.base_class_name).merge(Concept::Base.published)
@@ -73,7 +73,7 @@ class Labeling::SKOS::Base < Labeling::Base
       # no additional conditions
       scope
     end
-    
+
     scope
   end
 
@@ -84,7 +84,7 @@ class Labeling::SKOS::Base < Labeling::Base
   def self.build_from_rdf(subject, predicate, object)
     raise "Labeling::SKOS::Base#build_from_rdf: Subject (#{subject}) must be a Concept." unless subject.is_a?(Concept::Base)
     raise "Labeling::SKOS::Base#build_from_rdf: Object (#{object}) must be a string literal" unless object =~ /^"(.+)"(@(.+))$/
-    
+
     lang = $3
     value = JSON.parse(%Q{["#{$1}"]})[0].gsub("\\n", "\n") # Trick to decode \uHHHHH chars
 

data/app/models/note/skos/base.rb

@@ -25,7 +25,7 @@ class Note::SKOS::Base < Note::Base
     unless object =~ /^"(.+)"(@(.+))$/
       raise "Note::SKOS::Base#build_from_rdf: Object (#{object}) must be a string literal"
     end
-    
+
     lang = $3
     value = JSON.parse(%Q{["#{$1}"]})[0].gsub("\\n", "\n") # Trick to decode \uHHHHH chars
 

data/app/models/note/skos/change_note.rb

@@ -21,11 +21,11 @@ class Note::SKOS::ChangeNote < Note::SKOS::Base
   def self.edit_partial_name(obj)
     "partials/note/skos/edit_change_note"
   end
-  
+
   def self.search_result_partial_name
     'partials/note/skos/change_note/search_result'
   end
-  
+
   def self.single_query(params = {})
     query_str = build_query_string(params)
 

data/app/models/search_extension.rb

@@ -22,7 +22,7 @@ module SearchExtension
   end
 
   module ClassMethods
-    
+
     def multi_query(params = {})
       query_terms = params[:query].split(/\r\n/)
       results     = []