Merge branch 'staging'

Gemfile.lock

@@ -49,20 +49,20 @@ GEM
     activesupport (3.2.16)
       i18n (~> 0.6, >= 0.6.4)
       multi_json (~> 1.0)
-    acts_as_tree (1.4.0)
+    acts_as_tree (1.5.0)
       activerecord (>= 3.0.0)
     addressable (2.3.5)
     arel (3.0.3)
     bcrypt-ruby (3.1.2)
-    better_errors (1.0.1)
+    better_errors (1.1.0)
       coderay (>= 1.0.0)
       erubis (>= 2.6.6)
     binding_of_caller (0.7.2)
       debug_inspector (>= 0.0.1)
-    bootstrap-sass (3.0.2.0)
+    bootstrap-sass (3.0.3.0)
       sass (~> 3.2)
     builder (3.0.4)
-    byebug (2.3.1)
+    byebug (2.5.0)
       columnize (~> 0.3.6)
       debugger-linecache (~> 1.2.0)
     cancan (1.6.10)
@@ -72,13 +72,13 @@ GEM
       net-sftp (>= 2.0.0)
       net-ssh (>= 2.0.14)
       net-ssh-gateway (>= 1.1.0)
-    capybara (2.1.0)
+    capybara (2.2.1)
       mime-types (>= 1.16)
       nokogiri (>= 1.3.3)
       rack (>= 1.0.0)
       rack-test (>= 0.5.4)
       xpath (~> 2.0)
-    capybara-webkit (1.0.0)
+    capybara-webkit (1.1.0)
       capybara (~> 2.0, >= 2.0.2)
       json
     celluloid (0.15.2)
@@ -103,7 +103,7 @@ GEM
     connection_pool (1.2.0)
     crack (0.4.1)
       safe_yaml (~> 0.9.0)
-    d3_rails (3.3.9)
+    d3_rails (3.3.13)
       railties (>= 3.1.0)
     dagnabit (3.0.1)
       activerecord (>= 2.3.0)
@@ -132,11 +132,11 @@ GEM
       i18n (~> 0.5)
     fattr (2.2.1)
     font_awesome (3.101.0)
-    foreigner (1.6.0)
+    foreigner (1.6.1)
       activerecord (>= 3.0.0)
     fssm (0.2.10)
     god (0.13.3)
-    haml (4.0.4)
+    haml (4.0.5)
       tilt
     haml-rails (0.4)
       actionpack (>= 3.1, < 4.1)
@@ -167,15 +167,15 @@ GEM
     jquery-rails (3.0.4)
       railties (>= 3.0, < 5.0)
       thor (>= 0.14, < 2.0)
-    jquery-ui-rails (4.1.0)
+    jquery-ui-rails (4.1.1)
       railties (>= 3.1.0)
     js-routes (0.9.4)
       rails (>= 3.2)
     json (1.8.1)
-    kaminari (0.14.1)
+    kaminari (0.15.0)
       actionpack (>= 3.0.0)
       activesupport (>= 3.0.0)
-    launchy (2.3.0)
+    launchy (2.4.2)
       addressable (~> 2.3)
     libv8 (3.16.14.3)
     mail (2.5.4)
@@ -201,7 +201,7 @@ GEM
       mini_portile (~> 0.5.0)
     options (2.3.0)
       fattr
-    orm_adapter (0.4.0)
+    orm_adapter (0.5.0)
     pg (0.17.1)
     polyglot (0.3.3)
     pr_geohash (1.0.0)
@@ -212,7 +212,7 @@ GEM
       coderay (~> 1.0)
       method_source (~> 0.8)
       slop (~> 3.4)
-    pry-byebug (1.2.0)
+    pry-byebug (1.2.1)
       byebug (~> 2.2)
       pry (~> 0.9.12)
     pry-rails (0.3.2)
@@ -284,8 +284,9 @@ GEM
     rspec-expectations (2.14.4)
       diff-lcs (>= 1.1.3, < 2.0)
     rspec-mocks (2.14.4)
-    rspec-rails (2.14.0)
+    rspec-rails (2.14.1)
       actionpack (>= 3.0)
+      activemodel (>= 3.0)
       activesupport (>= 3.0)
       railties (>= 3.0)
       rspec-core (~> 2.14.0)
@@ -346,7 +347,7 @@ GEM
       polyglot
       polyglot (>= 0.3.1)
     tzinfo (0.3.38)
-    uglifier (2.3.0)
+    uglifier (2.4.0)
       execjs (>= 0.3.0)
       json (>= 1.8.0)
     vcr (2.8.0)

app/controllers/ontologies_controller.rb

@@ -27,20 +27,12 @@ def index
 
   def new
     @ontology_version = build_resource.versions.build
-    @c_vertices = []
-    vert = Category.first
-    if vert
-      @c_vertices = vert.roots.first.children
-    end
+    @c_vertices = Category.first.roots.first.children rescue []
   end
 
   def edit
     @ontology = resource
-    @c_vertices = []
-    vert = Category.first
-    if vert
-      @c_vertices = vert.roots.first.children
-    end
+    @c_vertices = Category.first.roots.first.children rescue []
   end
 
   def update

app/models/ability.rb

@@ -105,6 +105,8 @@ def initialize(user)
         # TODO tests written?
         subject.user == user || subject.metadatable.permission?(:editor, user)
       end
+
+      can :read, Category
     else
       can :show, Repository do |subject|
         !subject.is_private

app/models/ontology/categories.rb

@@ -8,24 +8,28 @@ module Ontology::Categories
 
 
   def create_categories 
-    if !self.is?('OWL')
-      raise Exception.new('Error: No OWL')
-    end
-    # Delete previous set of categories
-    [ Category.all, CEdge.all ].flatten.each { |c| c.destroy }
+    raise Exception.new('Error: No OWL') unless self.is? 'OWL'
+
+    # Delete previous set of categories.
+    [Category, CEdge].map(&:destroy_all)
+
     classes = self.entities.select { |e| e.kind == 'Class' }
-    subclasses = self.sentences.select { |e| e.text.include?('SubClassOf')}
-    classes.each { |c| categorify(c) }
+    classes.map! { |c| categorify(c) }
 
+    subclasses = self.sentences.select { |e| e.text.include?('SubClassOf')}
     subclasses.each do |s|
-      c1,c2 = s.hierarchical_class_names
+      c1, c2 = s.hierarchical_class_names
+
       e1 = self.entities.where('name = ? OR iri = ?', c1, c1).first
       e2 = self.entities.where('name = ? OR iri = ?', c2, c2).first
-      CEdge.create!(:child_id => categorify(e1).id, :parent_id => categorify(e2).id)
+
+      CEdge.create!(child_id: categorify(e1).id, parent_id: categorify(e2).id)
     end
   end
 
+
   protected
+
   def categorify(entity)
     return if entity.kind != 'Class'
     Category.where(name: entity.display_name || entity.name).

app/models/ontology/entities.rb

@@ -49,8 +49,8 @@ def delete_edges
   end
 
   def create_entity_tree
-    if !self.is?('OWL2')
-      raise Exception.new('Error: No OWL2')
+    if !self.is?('OWL')
+      raise Exception.new('Error: No OWL')
     end
 
     # Delete previous set of categories

app/views/categories/_category.html.haml

@@ -1,6 +1,6 @@
 - if category then
-  %li{ :id => category.id }
+  %li{:id => category.id}
     %a
-      =link_to "#{category.name.gsub(/_/, ' ')} (#{category.related_ontologies.count})", category
+      = link_to "#{category.name.gsub(/_/, ' ')} (#{category.related_ontologies.count})", category
     %ul
       = render :partial => 'category', :collection => category.children.to_a

app/views/categories/show.html.haml

@@ -1,6 +1,6 @@
-%h2= @category.name
+%h2= @category.name.gsub(/_/, ' ')
 
 Following ontologies are in this category
 %ul.ontology_list
   -@ontologies.each do |ontology|
-    %li= fancy_link ontology
+    %li= fancy_link ontology

app/views/shared/_form_errors.html.haml

@@ -0,0 +1,8 @@
+- if resource.errors.any?
+  .flash.alert.alert-danger
+    %strong
+      = pluralize resource.errors.count, 'error'
+      prohibited this resource from being saved:
+    %ul
+      - resource.errors.full_messages.each do |msg|
+        %li= msg

db/seeds/003-git.rb

@@ -18,7 +18,7 @@
 
 # Import ontologies
 ontologies = %w[
-  owl/Domain_Fields_Extension.owl
+  owl/Domain_Fields_Core.owl
   casl/partial_order.casl
   casl/test1.casl
   casl/test2.casl

db/seeds/007-metadata.rb

@@ -0,0 +1,2 @@
+# Create metadata objects (FormalityLevel, LicenseModel, OntologyType, Task).
+Rake::Task['generate:metadata'].invoke

db/seeds/008-categories.rb

@@ -0,0 +1,2 @@
+# Create categories from Domain_Fields_Core ontology.
+Rake::Task['generate:categories'].invoke

lib/tasks/generate.rake

@@ -1,7 +1,7 @@
 namespace :generate do
   desc 'Import the categories for the ontologies'
   task :categories => :environment do
-    Ontology.find_by_name('Domain_fields_core').create_categories
+    Ontology.where("name ilike 'Domain_Fields_Core'").first.create_categories
   end
 
   desc 'Generate entity trees for ALL OWL ontologies'

spec/models/category.rb

@@ -2,7 +2,7 @@
 
 describe Category do
 
-  context "get ontologies of a category and subcategories" do
+  context 'get ontologies of a category and subcategories' do
     before do
       edge = FactoryGirl.create(:c_edge)
 
@@ -28,4 +28,22 @@
     end
   end
 
+  context 'creation of categories from ontology' do
+    before do
+      @user = FactoryGirl.create :user
+      @ontology = FactoryGirl.create :single_ontology
+      @ontology.import_xml_from_file fixture_file('Domain_Fields_Core.xml'),
+        fixture_file('Domain_Fields_Core.pp.xml'), @user
+      @ontology.create_categories
+    end
+
+    it 'should be the correct categories count' do
+      Category.count.should == 123
+    end
+
+    it 'should be the correct category edges count' do
+      CEdge.count.should == 122
+    end
+  end
+
 end

spec/spec_helper.rb

@@ -19,6 +19,10 @@ def query_string
 
 end
 
+def fixture_file(name)
+  Rails.root + 'test/fixtures/ontologies/xml/' + name
+end
+
 RSpec.configure do |config|
   # ## Mock Framework
   # config.mock_with :mocha