Merge pull request #72 from sanger/devel

Merge devel into master

Gemfile

@@ -1,6 +1,5 @@
 source 'https://rubygems.org'
 
-
 # Bundle edge Rails instead: gem 'rails', github: 'rails/rails'
 gem 'rails', '4.2.3'
 # Use sqlite3 as the database for Active Record
@@ -41,7 +40,7 @@ gem 'kaminari'
 
 gem 'backbone-on-rails'
 
-gem 'rest-client'
+gem 'pmb-client', '0.1.0', :github => 'sanger/pmb-client'
 
 gem 'exception_notification'
 

Gemfile.lock

@@ -1,3 +1,10 @@
+GIT
+  remote: git://github.com/sanger/pmb-client.git
+  revision: 016f151a3bde84448ed64e528259c3511282dcdb
+  specs:
+    pmb-client (0.1.0)
+      json_api_client (~> 1.1)
+
 GEM
   remote: https://rubygems.org/
   specs:
@@ -78,8 +85,6 @@ GEM
     database_cleaner (1.4.1)
     debug_inspector (0.0.2)
     diff-lcs (1.2.5)
-    domain_name (0.5.25)
-      unf (>= 0.0.5, < 1.0.0)
     eco (1.0.0)
       coffee-script
       eco-source
@@ -96,13 +101,15 @@ GEM
     factory_girl_rails (4.5.0)
       factory_girl (~> 4.5.0)
       railties (>= 3.0.0)
+    faraday (0.9.2)
+      multipart-post (>= 1.2, < 3)
+    faraday_middleware (0.10.0)
+      faraday (>= 0.7.4, < 0.10)
     ffi (1.9.8)
     font-awesome-rails (4.5.0.0)
       railties (>= 3.2, < 5.0)
     globalid (0.3.6)
       activesupport (>= 4.1.0)
-    http-cookie (1.0.2)
-      domain_name (~> 0.5)
     i18n (0.7.0)
     jbuilder (2.3.1)
       activesupport (>= 3.0.0, < 5)
@@ -119,6 +126,12 @@ GEM
     json (1.8.3)
     json-schema (2.6.0)
       addressable (~> 2.3.8)
+    json_api_client (1.1.1)
+      activemodel (>= 3.2.0)
+      activesupport (>= 3.2.0)
+      addressable (~> 2.2)
+      faraday (~> 0.9)
+      faraday_middleware (~> 0.9)
     kaminari (0.16.3)
       actionpack (>= 3.0.0)
       activesupport (>= 3.0.0)
@@ -132,9 +145,9 @@ GEM
     mini_portile (0.6.2)
     minitest (5.8.3)
     multi_json (1.11.2)
+    multipart-post (2.0.0)
     mysql2 (0.3.20)
     net-ldap (0.12.0)
-    netrc (0.11.0)
     nokogiri (1.6.6.3)
       mini_portile (~> 0.6.0)
     phantomjs (1.9.8.0)
@@ -183,10 +196,6 @@ GEM
       uri_template (~> 0.7)
     rdoc (4.2.0)
     ref (2.0.0)
-    rest-client (1.8.0)
-      http-cookie (>= 1.0.2, < 2.0)
-      mime-types (>= 1.16, < 3.0)
-      netrc (~> 0.7)
     rouge (1.10.1)
     rspec-core (3.2.3)
       rspec-support (~> 3.2.0)
@@ -250,9 +259,6 @@ GEM
     uglifier (2.7.1)
       execjs (>= 0.3.0)
       json (>= 1.8.0)
-    unf (0.1.4)
-      unf_ext
-    unf_ext (0.0.7.1)
     uri_template (0.7.0)
     web-console (2.2.1)
       activemodel (>= 4.0)
@@ -290,12 +296,12 @@ DEPENDENCIES
   mysql2 (= 0.3.20)
   net-ldap
   phantomjs
+  pmb-client (= 0.1.0)!
   poltergeist
   puma
   rails (= 4.2.3)
   rake
   raml_ruby (~> 0.1.1)
-  rest-client
   rspec-rails (~> 3.1)
   sass-rails (~> 5.0)
   sdoc (~> 0.4.0)
@@ -310,4 +316,4 @@ DEPENDENCIES
   with_model
 
 BUNDLED WITH
-   1.11.2
+   1.12.1

app/assets/javascripts/batches.coffee

@@ -5,7 +5,7 @@ $ ->
     userFavouritesCollection  = new Mixtio.Collections.UserFavourites(Mixtio.Bootstrap.UserFavourites)
     consumableTypesCollection = new Mixtio.Collections.ConsumableTypes(Mixtio.Bootstrap.ConsumableTypes)
     kitchensCollection        = new Mixtio.Collections.Kitchens(Mixtio.Bootstrap.Kitchens)
-    ingredientsCollection     = new Mixtio.Collections.Ingredients()
+    ingredientsCollection     = new Mixtio.Collections.Ingredients(Mixtio.Bootstrap.Ingredients)
 
     # Create the Views
     consumableTypeView = new Mixtio.Views.ConsumableTypes(
@@ -48,7 +48,7 @@ $ ->
       favouritesStarView.update(model, options)
       expiryDateView.update(model)
       consumablesView.update(model)
-      
+
       ingredients = model?.get('latest_batch')?.ingredients?.map (ingredient) ->
         type = Mixtio.Bootstrap.ConsumableTypes.filter((type) -> type.id == ingredient.consumable_type_id)[0]
         {
@@ -66,5 +66,7 @@ $ ->
 
     # And finally render
     consumableTypeView.render()
+    consumableTypeView.setSelected(Mixtio.Bootstrap.SelectedConsumableType)
+    ingredientsView.render()
 
   $('[data-toggle="tooltip"]').tooltip()

app/assets/javascripts/views/consumable_types.coffee

@@ -1,7 +1,7 @@
 class Mixtio.Views.ConsumableTypes extends Backbone.View
 
   events:
-    change: 'setSelected'
+    change: 'onChange'
 
   initialize: (options) ->
     @favourites_collection = options.favourites
@@ -30,7 +30,10 @@ class Mixtio.Views.ConsumableTypes extends Backbone.View
       @$el.append(view)
     )
 
-  setSelected: () ->
+  setSelected: (val) ->
+    @$el.val(val)
+
+  onChange: () ->
     id = @$el.val()
 
     if id is ""

app/assets/javascripts/views/expiry_date.coffee

@@ -5,5 +5,5 @@ class Mixtio.Views.ExpiryDate extends Backbone.View
     @render()
 
   render: () ->
-    @$el.datepicker('setDate', @model?.get('days_to_keep'))
+    @$el.datepicker('setDate', @model?.get('days_to_keep') or 'today')
     this

app/models/concerns/has_volume.rb

@@ -4,7 +4,7 @@ module HasVolume
 
   included do
     enum unit: {
-        "μL": -6,
+        "µL": -6,
         "mL": -3,
         'L': 0,
     }
@@ -19,8 +19,4 @@ def display_volume
     end
   end
 
-  def simple_volume
-    display_volume ? display_volume.gsub('μ', 'u') : nil
-  end
-
 end

app/models/consumable_type.rb

@@ -20,10 +20,6 @@ class ConsumableType < ActiveRecord::Base
       "LN2":   5
   }
 
-  def simple_storage_condition
-    (storage_condition or "").gsub('°', '')
-  end
-
   def latest_batch
     batches.last
   end

app/views/api/v2/docs/index.html.erb

@@ -461,7 +461,7 @@ sort=-updated_at
             "created_at":"2016-04-08T11:19:44.440Z",
             "barcode":"RGNT_171",
             "volume":"51.8",
-            "unit":"μL",
+            "unit":"µL",
             "depleted":false
          },
          "relationships":{
@@ -486,7 +486,7 @@ sort=-updated_at
             "created_at":"2016-04-08T11:19:44.446Z",
             "barcode":"RGNT_172",
             "volume":"51.8",
-            "unit":"μL",
+            "unit":"µL",
             "depleted":false
          },
          "relationships":{
@@ -530,7 +530,7 @@ sort=-updated_at
          "created_at":"2016-04-08T11:19:44.440Z",
          "barcode":"RGNT_171",
          "volume":"51.8",
-         "unit":"μL",
+         "unit":"µL",
          "depleted":false
       },
       "relationships":{

app/views/batches/_form.html.erb

@@ -3,7 +3,9 @@
     <script type="text/javascript">
       Mixtio.Bootstrap.UserFavourites  = <%= json_escape(ConsumableType.find_user_favourites(current_user).to_json.html_safe); %>
       Mixtio.Bootstrap.ConsumableTypes = <%= json_escape(ConsumableType.order_by_name.to_json(include: {latest_batch: {include: {ingredients: {}, consumables: {}}}, latest_lot: {}}).html_safe); %>
+      Mixtio.Bootstrap.SelectedConsumableType = <%= json_escape(@batch_form.consumable_type_id.to_json.html_safe) %>;
       Mixtio.Bootstrap.Kitchens        = <%= json_escape(Kitchen.order_by_name.to_json.html_safe) %>;
+      Mixtio.Bootstrap.Ingredients     = <%= json_escape(@batch_form.ingredients.to_json.html_safe) %>;
     </script>
 
     <div class="form-group">

config/api.raml

@@ -402,7 +402,7 @@ resourceTypes:
                           "created_at":"2016-04-08T11:19:44.440Z",
                           "barcode":"RGNT_171",
                           "volume":"51.8",
-                          "unit":"μL",
+                          "unit":"µL",
                           "depleted":false
                        },
                        "relationships":{
@@ -427,7 +427,7 @@ resourceTypes:
                           "created_at":"2016-04-08T11:19:44.446Z",
                           "barcode":"RGNT_172",
                           "volume":"51.8",
-                          "unit":"μL",
+                          "unit":"µL",
                           "depleted":false
                        },
                        "relationships":{
@@ -480,7 +480,7 @@ resourceTypes:
                          "created_at":"2016-04-08T11:19:44.440Z",
                          "barcode":"RGNT_171",
                          "volume":"51.8",
-                         "unit":"μL",
+                         "unit":"µL",
                          "depleted":false
                       },
                       "relationships":{

config/environments/development.rb

@@ -41,4 +41,6 @@
 
   # config.stub_ldap = true
 
+  # Print My Barcode api base
+  config.x.pmb_api_base = 'http://pmb.dev/api/v1'
 end

config/environments/production.rb

@@ -76,4 +76,7 @@
 
   # Do not dump schema after migrations.
   config.active_record.dump_schema_after_migration = false
+
+  # Print My Barcode api base
+  config.x.pmb_api_base = 'http://pmb.prod/api/v1'
 end

config/environments/test.rb

@@ -47,4 +47,7 @@
       exception_recipients: %w(#{Rails.configuration.mailer['smtp']['recipient']})
   }
 
+  # Print My Barcode api base
+  config.x.pmb_api_base = 'http://pmb.test/api/v1'
+
 end

config/initializers/print_my_barcode.rb

@@ -0,0 +1 @@
+PMB::Base.site = Rails.configuration.x.pmb_api_base

lib/labels.rb

@@ -0,0 +1,33 @@
+class Labels
+
+  attr_accessor :consumables
+
+  def initialize(batch)
+    @consumables = batch.single_barcode? ? [batch.consumables.first] : batch.consumables
+  end
+
+  def to_h
+    {
+      body: body
+    }
+  end
+
+private
+
+  def body
+    consumables.map do |consumable|
+      {
+        label_1: {
+          barcode_text: consumable.barcode,
+          reagent_name: consumable.batch.consumable_type.name,
+          batch_no: consumable.batch.number,
+          date: "Use by:#{consumable.batch.expiry_date}",
+          barcode: consumable.barcode,
+          volume: consumable.display_volume,
+          storage_condition: consumable.batch.consumable_type.storage_condition,
+        }
+      }
+    end
+  end
+
+end