Merge pull request #35 from sanger/next_release

Release-1.10.00

.gitignore

@@ -5,3 +5,4 @@ tmp/
 public/stylesheets/*.css
 .DS_Store
 .sass-cache/
+*.orig

.rspec

@@ -0,0 +1,2 @@
+--color
+--require spec_helper

.rvmrc

@@ -1 +1 @@
-rvm use 1.9.2@illumina_c_pipeline --create
+rvm use 1.9.3@illumina_c_pipeline --create

Gemfile

@@ -8,7 +8,7 @@ gem 'state_machine', '~>1.0.1'
 gem 'hashie', '~>1.0.0'
 gem 'exception_notification'
 
-gem 'sequencescape-client-api', '>=0.2.6',
+gem 'sequencescape-client-api', '>=0.2.9',
   :github  => 'sanger/sequencescape-client-api',
   :branch  => 'production',
   :require => 'sequencescape'
@@ -19,15 +19,25 @@ gem 'sanger_barcode', '>= 0.2.0',
 # put test-only gems in this group so their generators
 # and rake tasks are available in development mode:
 group :test do
-  gem 'capybara'
-  gem 'cucumber-rails', :require => false
   gem 'launchy'
+  gem 'rspec-rails'
+  gem 'webmock'
+
+  gem 'capybara'
+  gem 'phantomjs'
+  gem 'poltergeist'
 end
+
 group :development do
   gem 'ruby-debug19', :require => 'ruby-debug'
+  gem 'ruby-debug-base19x'
+  gem 'pry'
 end
 
 group :deployment do
   gem 'thin'
   gem "psd_logger", :git => "git+ssh://[email protected]/sanger/psd_logger.git"
+  # Due to guar changes, can likely be fied with ruby updates
+  gem "rspec-legacy_formatters"
+  gem 'guard-rspec', require: false
 end

Gemfile.lock

@@ -13,10 +13,10 @@ GIT
 
 GIT
   remote: git://github.com/sanger/sequencescape-client-api.git
-  revision: e39210258080d2011b2391d44055a849494097c6
+  revision: 79a7e0818410acb62f5befcc24eb4d72f092abca
   branch: production
   specs:
-    sequencescape-client-api (0.2.6)
+    sequencescape-client-api (0.2.9)
       activemodel (~> 3.0.0)
       activesupport (~> 3.0.0)
       i18n
@@ -56,68 +56,83 @@ GEM
     archive-tar-minitar (0.5.2)
     arel (2.0.10)
     builder (2.1.2)
-    capybara (1.1.1)
+    capybara (2.9.0)
+      addressable
       mime-types (>= 1.16)
       nokogiri (>= 1.3.3)
       rack (>= 1.0.0)
       rack-test (>= 0.5.4)
-      selenium-webdriver (~> 2.0)
-      xpath (~> 0.1.4)
-    childprocess (0.2.2)
-      ffi (~> 1.0.6)
+      xpath (~> 2.0)
     chunky_png (1.2.4)
+    cliver (0.3.2)
+    coderay (1.1.1)
     columnize (0.3.4)
     compass (0.11.5)
       chunky_png (~> 1.2)
       fssm (>= 0.2.7)
       sass (~> 3.1)
-    cucumber (1.0.6)
-      builder (>= 2.1.2)
-      diff-lcs (>= 1.1.2)
-      gherkin (~> 2.4.18)
-      json (>= 1.4.6)
-      term-ansicolor (>= 1.0.6)
-    cucumber-rails (1.0.5)
-      capybara (>= 1.1.1)
-      cucumber (~> 1.0.6)
-      nokogiri (>= 1.5.0)
-    daemons (1.1.4)
-    diff-lcs (1.1.3)
+    crack (0.4.3)
+      safe_yaml (~> 1.0.0)
+    daemons (1.2.4)
+    debugger-ruby_core_source (1.3.8)
+    diff-lcs (1.2.5)
     erubis (2.6.6)
       abstract (>= 1.0.0)
-    eventmachine (0.12.10)
+    eventmachine (1.2.0.1)
     exception_notification (2.5.2)
       actionmailer (>= 3.0.4)
-    ffi (1.0.9)
+    ffi (1.9.14)
+    formatador (0.2.5)
     formtastic (1.2.4)
       actionpack (>= 2.3.7)
       activesupport (>= 2.3.7)
       i18n (~> 0.4)
     fssm (0.2.7)
-    gherkin (2.4.18)
-      json (>= 1.4.6)
+    guard (1.8.3)
+      formatador (>= 0.2.4)
+      listen (~> 1.3)
+      lumberjack (>= 1.0.2)
+      pry (>= 0.9.10)
+      thor (>= 0.14.6)
+    guard-rspec (1.2.2)
+      guard (>= 1.1)
     gyoku (1.2.2)
       builder (>= 2.1.2)
+    hashdiff (0.3.0)
     hashie (1.0.0)
     httpi (2.2.7)
       rack
     i18n (0.5.4)
     json (1.6.0)
-    json_pure (1.6.0)
     launchy (2.0.5)
       addressable (~> 2.2.6)
     linecache19 (0.5.12)
       ruby_core_source (>= 0.1.4)
+    listen (1.3.1)
+      rb-fsevent (>= 0.9.3)
+      rb-inotify (>= 0.9)
+      rb-kqueue (>= 0.2)
+    lumberjack (1.0.10)
     mail (2.2.19)
       activesupport (>= 2.3.6)
       i18n (>= 0.4.0)
       mime-types (~> 1.16)
       treetop (~> 1.4.8)
+    method_source (0.8.2)
     mime-types (1.19)
     nokogiri (1.5.0)
     nori (2.4.0)
+    phantomjs (2.1.1.0)
+    poltergeist (1.10.0)
+      capybara (~> 2.1)
+      cliver (~> 0.3.1)
+      websocket-driver (>= 0.2.0)
     polyglot (0.3.3)
-    rack (1.2.6)
+    pry (0.10.4)
+      coderay (~> 1.1.0)
+      method_source (~> 0.8.1)
+      slop (~> 3.4)
+    rack (1.2.8)
     rack-mount (0.6.14)
       rack (>= 1.0.0)
     rack-test (0.5.7)
@@ -137,43 +152,76 @@ GEM
       rdoc (~> 3.4)
       thor (~> 0.14.4)
     rake (0.9.6)
+    rb-fsevent (0.9.7)
+    rb-inotify (0.9.7)
+      ffi (>= 0.5.0)
+    rb-kqueue (0.2.4)
+      ffi (>= 0.5.0)
     rdoc (3.12)
       json (~> 1.4)
+    rspec (3.5.0)
+      rspec-core (~> 3.5.0)
+      rspec-expectations (~> 3.5.0)
+      rspec-mocks (~> 3.5.0)
+    rspec-core (3.5.3)
+      rspec-support (~> 3.5.0)
+    rspec-expectations (3.5.0)
+      diff-lcs (>= 1.2.0, < 2.0)
+      rspec-support (~> 3.5.0)
+    rspec-legacy_formatters (1.0.1)
+      rspec (~> 3.0)
+    rspec-mocks (3.5.0)
+      diff-lcs (>= 1.2.0, < 2.0)
+      rspec-support (~> 3.5.0)
+    rspec-rails (3.5.2)
+      actionpack (>= 3.0)
+      activesupport (>= 3.0)
+      railties (>= 3.0)
+      rspec-core (~> 3.5.0)
+      rspec-expectations (~> 3.5.0)
+      rspec-mocks (~> 3.5.0)
+      rspec-support (~> 3.5.0)
+    rspec-support (3.5.0)
     ruby-debug-base19 (0.11.25)
       columnize (>= 0.3.1)
       linecache19 (>= 0.5.11)
       ruby_core_source (>= 0.1.4)
+    ruby-debug-base19x (0.11.31)
+      debugger-ruby_core_source (> 0)
+      rake (>= 0.8.1)
     ruby-debug19 (0.11.6)
       columnize (>= 0.3.1)
       linecache19 (>= 0.5.11)
       ruby-debug-base19 (>= 0.11.19)
     ruby_core_source (0.1.5)
       archive-tar-minitar (>= 0.5.2)
-    rubyzip (0.9.4)
+    safe_yaml (1.0.4)
     sass (3.1.7)
     savon (0.9.2)
       builder (>= 2.1.2)
       gyoku (>= 0.4.0)
       httpi (>= 0.7.8)
       nokogiri (>= 1.4.0)
       nori (>= 0.2.0)
-    selenium-webdriver (2.6.0)
-      childprocess (>= 0.2.1)
-      ffi (>= 1.0.7)
-      json_pure
-      rubyzip
+    slop (3.6.0)
     state_machine (1.0.2)
-    term-ansicolor (1.0.6)
-    thin (1.2.11)
-      daemons (>= 1.0.9)
-      eventmachine (>= 0.12.6)
-      rack (>= 1.0.0)
+    thin (1.7.0)
+      daemons (~> 1.0, >= 1.0.9)
+      eventmachine (~> 1.0, >= 1.0.4)
+      rack (>= 1, < 3)
     thor (0.14.6)
     treetop (1.4.12)
       polyglot
       polyglot (>= 0.3.1)
     tzinfo (0.3.35)
-    xpath (0.1.4)
+    webmock (1.22.5)
+      addressable (< 2.4.0)
+      crack (>= 0.3.2)
+      hashdiff
+    websocket-driver (0.6.4)
+      websocket-extensions (>= 0.1.0)
+    websocket-extensions (0.1.2)
+    xpath (2.0.0)
       nokogiri (~> 1.3)
     yajl-ruby (1.1.0)
 
@@ -183,16 +231,26 @@ PLATFORMS
 DEPENDENCIES
   capybara
   compass (>= 0.11.1)
-  cucumber-rails
   exception_notification
   formtastic (~> 1.2.3)
+  guard-rspec
   hashie (~> 1.0.0)
   launchy
+  phantomjs
+  poltergeist
+  pry
   psd_logger!
   rails (~> 3.0.19)
   rake (~> 0.9.2)
+  rspec-legacy_formatters
+  rspec-rails
+  ruby-debug-base19x
   ruby-debug19
   sanger_barcode (>= 0.2.0)!
-  sequencescape-client-api (>= 0.2.6)!
+  sequencescape-client-api (>= 0.2.9)!
   state_machine (~> 1.0.1)
   thin
+  webmock
+
+BUNDLED WITH
+   1.13.6

Guardfile

@@ -0,0 +1,24 @@
+# A sample Guardfile
+# More info at https://github.com/guard/guard#readme
+
+guard 'rspec', :version => 2 do
+  watch(%r{^spec/.+_spec\.rb$})
+  watch(%r{^lib/(.+)\.rb$})     { |m| "spec/lib/#{m[1]}_spec.rb" }
+  watch('spec/spec_helper.rb')  { "spec" }
+
+  # Rails example
+  watch(%r{^app/(.+)\.rb$})                           { |m| "spec/#{m[1]}_spec.rb" }
+  watch(%r{^app/(.*)(\.erb|\.haml)$})                 { |m| "spec/#{m[1]}#{m[2]}_spec.rb" }
+  watch(%r{^app/controllers/(.+)_(controller)\.rb$})  { |m| ["spec/routing/#{m[1]}_routing_spec.rb", "spec/#{m[2]}s/#{m[1]}_#{m[2]}_spec.rb", "spec/acceptance/#{m[1]}_spec.rb"] }
+  watch(%r{^spec/support/(.+)\.rb$})                  { "spec" }
+  watch('config/routes.rb')                           { "spec/routing" }
+  watch('app/controllers/application_controller.rb')  { "spec/controllers" }
+
+  # Capybara request specs
+  watch(%r{^app/views/(.+)/.*\.(erb|haml)$})          { |m| "spec/requests/#{m[1]}_spec.rb" }
+
+  # Turnip features and steps
+  watch(%r{^spec/acceptance/(.+)\.feature$})
+  watch(%r{^spec/acceptance/steps/(.+)_steps\.rb$})   { |m| Dir[File.join("**/#{m[1]}.feature")][0] || 'spec/acceptance' }
+end
+

app/controllers/creation_controller.rb

@@ -54,9 +54,12 @@ def create
 
     respond_to do |format|
       format.html do
+        alert = [ "Cannot create the plate: #{exception.message}"]
+        alert.concat << exception.resource.errors.full_messages.join('; ') if exception.respond_to?(:resource)
+
         redirect_to(
           illumina_c_plate_path(@creation_form.parent),
-          :alert => [ "Cannot create the plate: #{exception.message}", *exception.resource.errors.full_messages ]
+          :alert => alert
         )
       end
     end

app/controllers/labware_controller.rb

@@ -4,7 +4,7 @@ class LabwareController < ApplicationController
   before_filter :check_for_current_user!, :only => [ :update ]
 
   def locate_labware
-     @labware = locate_labware_identified_by(params[:id])
+    @labware = locate_labware_identified_by(params[:id])
   end
   private :locate_labware
 

app/controllers/metadata_controller.rb

@@ -0,0 +1,20 @@
+class MetadataController < ApplicationController
+
+  def create
+    metadata = metadata_hash
+    api.custom_metadatum_collection.create!(user: current_user_uuid, asset: params[:asset_id], metadata: metadata)
+    redirect_to(:back, notice: "Metadata was added successfully")
+  end
+
+  def update
+    metadata = metadata_hash
+    api.custom_metadatum_collection.find(params[:id]).update_attributes!(metadata: metadata)
+    redirect_to(:back, notice: "Metadata was updated successfully")
+  end
+
+  def metadata_hash
+    key_values = params[:metadata].map {|metadatum| [metadatum[:key], metadatum[:value]]}
+    Hash[key_values.reject {|k, v| k.blank? || v.blank? }]
+  end
+
+end

app/controllers/multiple_target_state_change_controller.rb

@@ -0,0 +1,29 @@
+class MultipleTargetStateChangeController < ApplicationController
+
+  def create
+
+    if params[:tubes]
+      tubes_uuid = params[:tubes].keys
+      tubes_uuid.each do |uuid|
+        purpose_uuid = api.multiplexed_library_tube.find(uuid).purpose.uuid
+        state_changer_for(purpose_uuid, uuid).move_to!("passed")
+      end
+      tubes_ean13_barcodes = params[:tubes].values
+      redirect_to(search_path, :notice => "Labware: #{tubes_ean13_barcodes.join(", ")} have been changed to a state of Passed")
+    else
+      redirect_to(search_path, :notice => "Nothing to pass")
+    end
+
+    rescue StateChangers::StateChangeError => exception
+    respond_to do |format|
+      format.html { redirect_to(search_path, :alert=> exception.message) }
+      format.csv
+    end
+  end
+
+  def state_changer_for(purpose_uuid, labware_uuid)
+    StateChangers.lookup_for(purpose_uuid).new(api, labware_uuid, current_user_uuid)
+  end
+  private :state_changer_for
+
+end