spec maint

.gitignore

@@ -14,6 +14,7 @@
 
 .ruby-gemset
 .ruby-version
+.coveralls.yml
 .nvmrc
 .env
 /config/database.yml

.travis.yml

@@ -8,3 +8,7 @@ addons:
   postgresql: "9.3"
 services:
   - postgresql
+script:
+  - RAILS_ENV=test bundle exec rake db:migrate --trace
+  - bundle exec rake db:test:prepare
+  - bundle exec rake

Gemfile

@@ -54,7 +54,7 @@ gem 'roo', ">2.3.0"
 
 gem 'httparty'
 # Ketcher editor
-gem 'ketcherails', '0.1.3', github: 'ComPlat/ketcher-rails'
+gem 'ketcherails', github: 'ComPlat/ketcher-rails', branch: 'extrema_search_safe'#'0.1.3', github: 'ComPlat/ketcher-rails'
 
 # Free font icons
 gem "font-awesome-rails"
@@ -131,10 +131,10 @@ group :test do
   gem 'factory_girl_rails'
   gem 'database_cleaner'
 
-  gem "faker", "~> 1.4"
-  gem "capybara", "~> 2.4"
-  gem "launchy", "~> 2.4"
-  gem "selenium-webdriver", "~> 2.43"
+  gem "faker", "~> 1.6.6"
+  gem "capybara", "~> 2.7.1"
+  gem "launchy", "~> 2.4.3"
+  gem "selenium-webdriver", "~> 2.53.4"
 end
 
 # Chemotion plugins: lsit your chemotion specific plugin gems here

Gemfile.lock

 GIT
   remote: git://github.com/ComPlat/ketcher-rails.git
-  revision: 10772e248579cf96b4d2dd6dd66181b07d832a65
+  revision: 5b4a1cc0252cda98733771a96a7c3cce54494550
+  branch: extrema_search_safe
   specs:
     ketcherails (0.1.3)
       bootstrap-kaminari-views
@@ -196,7 +197,7 @@ GEM
     factory_girl_rails (4.7.0)
       factory_girl (~> 4.7.0)
       railties (>= 3.0.0)
-    faker (1.6.3)
+    faker (1.6.6)
       i18n (~> 0.5)
     ffi (1.9.10)
     font-awesome-rails (4.6.2.0)
@@ -387,7 +388,7 @@ GEM
     sdoc (0.4.1)
       json (~> 1.7, >= 1.7.7)
       rdoc (~> 4.0)
-    selenium-webdriver (2.53.0)
+    selenium-webdriver (2.53.4)
       childprocess (~> 0.5)
       rubyzip (~> 1.0)
       websocket (~> 1.0)
@@ -472,7 +473,7 @@ DEPENDENCIES
   capistrano-rails
   capistrano-rvm
   capistrano3-delayed-job
-  capybara (~> 2.4)
+  capybara (~> 2.7.1)
   coveralls
   daemons
   database_cleaner
@@ -480,7 +481,7 @@ DEPENDENCIES
   devise
   dotenv-rails
   factory_girl_rails
-  faker (~> 1.4)
+  faker (~> 1.6.6)
   font-awesome-rails
   fontcustom
   grape
@@ -492,8 +493,8 @@ DEPENDENCIES
   jbuilder (~> 2.0)
   jquery-rails
   kaminari
-  ketcherails (= 0.1.3)!
-  launchy (~> 2.4)
+  ketcherails!
+  launchy (~> 2.4.3)
   mailcatcher
   nokogiri
   openbabel (= 2.3.2.1)!
@@ -509,7 +510,7 @@ DEPENDENCIES
   sablon!
   sass-rails (~> 5.0)
   sdoc (~> 0.4.0)
-  selenium-webdriver (~> 2.43)
+  selenium-webdriver (~> 2.53.4)
   spring
   svg2pdf!
   thin

app/models/sample.rb

@@ -235,7 +235,7 @@ class Sample < ActiveRecord::Base
 
   def init_elemental_compositions
     residue = self.residues[0]
-    return unless m_formula = self.molecule.sum_formular
+    return unless m_formula = (self.molecule && self.molecule.sum_formular)
 
     if residue.present? && self.molfile.include?(' R# ')# case when residue will be deleted
       p_formula = residue.custom_info['formula']

config/database.yml.travis

@@ -3,4 +3,5 @@ test:
   encoding: unicode
   database: travis_ci_test
   username: postgres
-
+  pool: 5
+  host: localhost

lib/svg/reaction_composer.rb

@@ -6,9 +6,9 @@ module SVG
 
     def initialize(materials_svg_paths, options = {})
       @svg_path = File.join(File.dirname(__FILE__), '..', '..', 'public', 'images', 'molecules')
-      @starting_materials = materials_svg_paths[:starting_materials]
-      @reactants = materials_svg_paths[:reactants]
-      @products = materials_svg_paths[:products]
+      @starting_materials = materials_svg_paths[:starting_materials] || []
+      @reactants = materials_svg_paths[:reactants] || []
+      @products = materials_svg_paths[:products] || []
       number_of_reactants = (@reactants.size == 0 && @starting_materials.size != 0) ? 1 : @reactants.size
       number_of_starting_materials = @starting_materials.size
       number_of_products = @products.size
@@ -16,7 +16,7 @@ module SVG
       @word_size = is_report ? 4 + (number_of_reactants + number_of_starting_materials + number_of_products) : 8
       @arrow_width = number_of_reactants * 50 + 60
       width = (@starting_materials.size + @products.size) * 100 + @arrow_width
-      @solvents = options[:solvents]
+      @solvents = options[:solvents] || []
       @temperature = options[:temperature]
       @arrow_y_shift = @solvents.count > 3 ? (@solvents.count - 3) * 12 : 0
 

spec/api/molecule_api_spec.rb

@@ -44,7 +44,7 @@ M  END"
         let!(:params) {
           {
             inchistring: "InChI=1S/C8H8/c1-2-5-3(1)7-4(1)6(2)8(5)7/h1-8H",
-            molecule_svg_file: "TXWRERCHRDBNLG-UHFFFAOYSA-N.svg",
+            #molecule_svg_file: "TXWRERCHRDBNLG-UHFFFAOYSA-N.svg",
             inchikey: "TXWRERCHRDBNLG-UHFFFAOYSA-N",
             molecular_weight: 104.14912,
             sum_formular: "C8H8",
@@ -62,7 +62,7 @@ M  END"
           params.each do |k, v|
             expect(m.attributes.symbolize_keys[k]).to eq(v)
           end
-
+          expect(m.molecule_svg_file).to match(/\w{128}\.svg/)
         end
 
       end

spec/api/sample_api_spec.rb

@@ -221,7 +221,7 @@ describe Chemotion::SampleAPI do
             solvent: '',
             impurities: '',
             location: '',
-            molecule: FactoryGirl.create(:molecule),
+          #  molecule: FactoryGirl.create(:molecule),
             molfile: '',
             is_top_secret: false
           }

spec/api/user_api_spec.rb

@@ -3,7 +3,7 @@ require 'rails_helper'
 describe Chemotion::UserAPI do
   let(:json_options) {
     {
-      only: [:id,:is_templates_moderator],
+      only: [:id,:is_templates_moderator,:type],
       methods: [:name, :initials]
     }
   }

spec/controllers/pages_controller_spec.rb

 require 'rails_helper'
 
 RSpec.describe PagesController do
+  #login_user
   let(:user)    { create(:person) }
-  let (:group) {create(:group,users: [user])}
+  let (:g1) {create(:group)}
+  let (:g2) {create(:group)}
+  let(:json_options) {
+    {
+      only: [:id],
+      methods: [:name, :initials]
+    }
+  }
   before do
-    #allow_any_instance_of(WardenAuthentication).to receive(:current_user).and_return(user)
-    allow(request.env['warden']).to receive(:authenticate!).and_return(user)
-    allow(controller).to receive(:current_user).and_return(user)
+    sign__in(user)
   end
 
   describe "GET groups" do
 
 
     it "assigns @groups" do
-
+      g1.users << user
+      g1.save
+      g2.admins << user
+      g2.save
       get :groups
-      expect(assigns(:groups)).to match_array([group])
+      groups=assigns(:groups).map{|g| g.select{|k| k.match(/id|name|initials/)}}
+      expect(groups).to match_array([g1.as_json(json_options),g2.as_json(json_options)])
     end
 
     it "renders the groups template" do

spec/features/pages_spec.rb

 require 'rails_helper'
 
 feature 'Pages' do
-  let(:john) { create(:user) }
+  let(:john) { create(:person) }
 
   background do
     sign_in(john)

spec/models/sample_spec.rb

@@ -88,10 +88,27 @@ M  END
 MOLFILE
     }
     let(:sample) { build(:sample, molfile: molfile) }
+    let(:mol_attributes){
+      {
+        "boiling_point" => nil,
+              "density" => nil,
+             "inchikey" => "XLYOFNOQVPJJNP-UHFFFAOYSA-N",
+        "inchistring" => "InChI=1S/H2O/h1H2",
+          "iupac_name" => "oxidane",
+       "melting_point" => nil,
+   "molecular_weight" => 18.01528,
+  #  "molecule_svg_file" => "XLYOFNOQVPJJNP-UHFFFAOYSA-N.svg", #todo
+            "molfile" => molfile.rstrip,
+              "names" => ["water", "oxidane"],
+       "sum_formular" => "H2O"
+     }
+    }
+
     before do
       sample.collections << FactoryGirl.build(:collection)
       sample.creator = FactoryGirl.build(:person)
     end
+
     it 'should create a molecule' do
       sample.save!
       molecule = sample.molecule
@@ -101,20 +118,11 @@ MOLFILE
     it 'should retrieve molecule information' do
       sample.save
       molecule = sample.molecule
+      mol_attributes.each do |k, v|
+        expect(molecule.attributes[k]).to eq(v)
+      end
+
 
-      expect(molecule.attributes).to include(
-        "boiling_point" => nil,
-              "density" => nil,
-             "inchikey" => "XLYOFNOQVPJJNP-UHFFFAOYSA-N",
-        "inchistring" => "InChI=1S/H2O/h1H2",
-          "iupac_name" => "oxidane",
-       "melting_point" => nil,
-   "molecular_weight" => 18.01528,
-  #  "molecule_svg_file" => "XLYOFNOQVPJJNP-UHFFFAOYSA-N.svg", #todo
-            "molfile" => molfile,
-              "names" => ["water", "oxidane"],
-       "sum_formular" => "H2O",
-      )
     end
 
     ##Fixme : now file are anonymised

spec/rails_helper.rb

@@ -3,6 +3,8 @@ ENV['RAILS_ENV'] ||= 'test'
 require 'spec_helper'
 require File.expand_path('../../config/environment', __FILE__)
 require 'rspec/rails'
+
+require 'devise'
 # Add additional requires below this line. Rails is not loaded until this point!
 
 # Requires supporting ruby files with custom matchers and macros, etc, in
@@ -26,8 +28,9 @@ RSpec.configure do |config|
 
   config.infer_spec_type_from_file_location!
 
-  config.include Devise::TestHelpers, type: :controller
-  config.extend ControllerMacros, type: :controller
+  #config.include Devise::TestHelpers, type: :controller
+  #config.extend ControllerMacros, type: :controller
+  config.include ControllerHelpers, type: :controller
 
   config.include LoginMacros
 end

spec/support/controller_helpers.rb

+module ControllerHelpers
+  def sign__in(user = FactoryGirl.create(:person))
+    if user.nil?
+      allow(request.env['warden']).to receive(:authenticate!).and_throw(:warden, {:scope => :user})
+      allow(controller).to receive(:current_user).and_return(nil)
+    else
+      allow(request.env['warden']).to receive(:authenticate!).and_return(user)
+      allow(controller).to receive(:current_user).and_return(user)
+    end
+  end
+end

spec/support/controller_macros.rb

 module ControllerMacros
-  def login_admin
-    before(:each) do
-      @request.env["devise.mapping"] = Devise.mappings[:admin]
-      sign_in FactoryGirl.create(:admin) # Using factory girl as an example
-    end
-  end
-
   def login_user
     before(:each) do
       @request.env["devise.mapping"] = Devise.mappings[:user]
-      user = FactoryGirl.create(:user)
-      user.confirm! # or set a confirmed_at inside the factory. Only necessary if you are using the "confirmable" module
+      user = FactoryGirl.create(:person)
+      #user.confirm! # or set a confirmed_at inside the factory. Only necessary if you are using the "confirmable" module
       sign_in user
     end
   end