From 8b1677a5e07f771d0f520b624f20ddd0bd05fcd1 Mon Sep 17 00:00:00 2001
From: Katy Taylor <kt17@sanger.ac.uk>
Date: Mon, 15 Jun 2020 17:19:12 +0100
Subject: [PATCH 01/21] Start on the front end - Be able to display responses
 from lighthouse / wrangler in a table - change to 'render' not 'redirect_to'
 to allow updating view with results without using flash (flash can't handle a
 lot of data) - new view for this called 'results' - problem with rendering
 the 'new' view/form underneath is that the URL still says /process_plates,
 not /process_plates/new (due to render not redirect), so page won't work if
 you refresh it - TODO - have broken existing flash messages, fix them - TODO
 - show red failure flash if some of the service calls failed - TODO - modify
 the services to return me more information that I can display in my table

---
 app/controllers/process_plates_controller.rb | 81 +++++++++++++++++---
 app/views/process_plates/new.html.haml       | 55 ++++++-------
 app/views/process_plates/results.html.haml   | 20 +++++
 config/environments/development.rb           |  2 +-
 4 files changed, 118 insertions(+), 40 deletions(-)
 create mode 100644 app/views/process_plates/results.html.haml

diff --git a/app/controllers/process_plates_controller.rb b/app/controllers/process_plates_controller.rb
index 4b35b1c1..bdaadbfe 100644
--- a/app/controllers/process_plates_controller.rb
+++ b/app/controllers/process_plates_controller.rb
@@ -16,7 +16,7 @@ def new
   end
 
   def create
-    respond_to do |format|
+    # respond_to do |format|
       bed_verification_model = InstrumentProcessesInstrument.get_bed_verification_type(params[:instrument_barcode], params[:instrument_process])
       if bed_verification_model.nil?
         flash[:error] = 'Invalid instrument or process'
@@ -33,33 +33,46 @@ def create
           # find out if the 'receive_plates' process was executed
           receive_plates_process = InstrumentProcess.find_by(id: params[:instrument_process]).key.eql?('slf_receive_plates')
 
-          call_external_services(barcodes) if barcodes && receive_plates_process
+          message = ''
+          if barcodes && receive_plates_process
+            call_external_services(barcodes)
 
-          # add a flash on the page for the number of unique barcodes scanned in
-          num_unique_barcodes = bed_layout_verification.process_plate&.barcodes.uniq.length
-          if num_unique_barcodes
-            flash[:notice] = "Success - #{num_unique_barcodes} unique plate(s) scanned"
-          else
-            flash[:notice] = "Success"
+            message = @lighthouse_responses.concat(@wrangler_responses)
           end
+
+          # TODO: display the responses from the services in a partial, not a flash
+          # TODO: sort out original flash code below
+          flash[:notice] = message
+
+          # add a flash on the page for the number of unique barcodes scanned in
+          # num_unique_barcodes = bed_layout_verification.process_plate&.barcodes.uniq.length
+          # if num_unique_barcodes
+          #   flash[:notice] = "Success - #{num_unique_barcodes} unique plate(s) scanned"
+          # else
+          #   flash[:notice] = "Success"
+          # end
         else
           flash[:error] = bed_layout_verification.errors.values.flatten.join("\n")
         end
       end
-      format.html { redirect_to(new_process_plate_path) }
-    end
+      @results = parse_responses
+      render :results
+    # end
   end
 
   # Call any external services - currently lighthouse service for plates from Lighthouse Labs and
   #   wrangler for tube racks. If no samples are found in the lighthouse service, try the wrangler
   def call_external_services(barcodes)
+    puts "DEBUG: call_external_services"
     # call the lighthouse service first as we are assuming that most labware scanned will be
     #   plates from Lighthouse Labs
-    lighthouse_responses = Lighthouse.call_api(barcodes)
+    @lighthouse_responses = Lighthouse.call_api(barcodes)
+    puts "DEBUG: lighthouse_responses: #{@lighthouse_responses}"
 
     # keeping it simple for now, if all the responses are not CREATED, send ALL the barcodes
     #   to the wrangler
-    wrangler_responses = Wrangler.call_api(barcodes) unless all_created?(lighthouse_responses)
+    @wrangler_responses = Wrangler.call_api(barcodes) unless all_created?(@lighthouse_responses)
+    puts "DEBUG: wrangler_responses: #{@wrangler_responses}"
   end
 
   # Returns a list of unique barcodes by removing blanks and duplicates
@@ -73,4 +86,48 @@ def all_created?(responses)
 
     responses.all? { |response| response[:code] == "201" }
   end
+
+  def parse_responses
+    output = []
+
+    @lighthouse_responses.each do |r|
+
+      barcode = r[:barcode]
+      success = if r[:code] == '201'
+                  'Yes'
+                else
+                  'No'
+                end
+      purpose = r[:purpose]
+      study = r[:study]
+
+      output << {
+        :barcode => barcode,
+        :success => success,
+        :purpose => purpose,
+        :study => study
+      }
+    end
+
+    @wrangler_responses.each do |r|
+
+      barcode = r[:barcode]
+      success = if r[:code] == '201'
+                  'Yes'
+                else
+                  'No'
+                end
+      purpose = r[:purpose]
+      study = r[:study]
+
+      output << {
+        :barcode => barcode,
+        :success => success,
+        :purpose => purpose,
+        :study => study
+      }
+    end
+
+    output
+  end
 end
diff --git a/app/views/process_plates/new.html.haml b/app/views/process_plates/new.html.haml
index e438fa74..5c110530 100644
--- a/app/views/process_plates/new.html.haml
+++ b/app/views/process_plates/new.html.haml
@@ -1,42 +1,43 @@
 %h2 Activity Logging
 %div{:id => "info_box"}
+
 = form_for :process_plate, :url => process_plates_path , :html => {:class => "submit-once"} do |form|
- %fieldset
-  %ul
-   %li
-    %label{ :for => "user_barcode" } User barcode
-    = text_field_tag "user_barcode"
-    .live_results#user_barcode_results
+  %fieldset
+    %ul
+      %li
+        %label{ :for => "user_barcode" } User barcode
+        = text_field_tag "user_barcode"
+        .live_results#user_barcode_results
 
-   %li
-    %label{ :for => "instrument_barcode" } Instrument barcode
-    = text_field_tag "instrument_barcode"
-    .live_results#instrument_barcode_results
+      %li
+        %label{ :for => "instrument_barcode" } Instrument barcode
+        = text_field_tag "instrument_barcode"
+        .live_results#instrument_barcode_results
 
 
-   %li
-    %label{ :for => "instrument_process" } Instrument process
-    %select#instrument_process{ :name => "instrument_process" }
-     %option{ :value => -1 } Select a process...
-     - for process_name, process_id in InstrumentProcess.sorted_by_name.map { |x| [x.name, x.id]}
-      %option{ :value => process_id } #{process_name}
+      %li
+        %label{ :for => "instrument_process" } Instrument process
+        %select#instrument_process{ :name => "instrument_process" }
+          %option{ :value => -1 } Select a process...
+          - for process_name, process_id in InstrumentProcess.sorted_by_name.map { |x| [x.name, x.id]}
+            %option{ :value => process_id } #{process_name}
 
-   %li
-    #source_plates_results
+      %li
+        #source_plates_results
 
-   %li.hidden#visual_check_input
-    %label{ :for => "visual_check"} Visual check performed
-    = check_box_tag "visual_check"
+      %li.hidden#visual_check_input
+        %label{ :for => "visual_check"} Visual check performed
+        = check_box_tag "visual_check"
 
-   %li.hidden#witness_barcode_input
-    %label{ :for => "witness_barcode"} Witness barcode
-    = text_field_tag "witness_barcode"
+      %li.hidden#witness_barcode_input
+        %label{ :for => "witness_barcode"} Witness barcode
+        = text_field_tag "witness_barcode"
 
-   %li
-    %input{ :id => "btnSubmit", :type => "submit", :value => 'Submit' }
+      %li
+        %input{ :id => "btnSubmit", :type => "submit", :value => 'Submit' }
 
 - content_for :page_javascript do
- :javascript
+  :javascript
 
     (function($) {
 
diff --git a/app/views/process_plates/results.html.haml b/app/views/process_plates/results.html.haml
new file mode 100644
index 00000000..c1e7cb9b
--- /dev/null
+++ b/app/views/process_plates/results.html.haml
@@ -0,0 +1,20 @@
+#service_responses
+  %table
+    %tr
+      %th.th Barcode
+      %th Success?
+      %th Purpose
+      %th Study
+    - for row in @results
+      %tr
+        %td
+          = row[:barcode]
+        %td
+          = row[:success]
+        %td
+          = row[:purpose]
+        %td
+          = row[:study]
+
+%br
+= link_to 'Scan more labware', new_process_plate_path
\ No newline at end of file
diff --git a/config/environments/development.rb b/config/environments/development.rb
index f0cefa58..902bbbb8 100644
--- a/config/environments/development.rb
+++ b/config/environments/development.rb
@@ -30,7 +30,7 @@
   config.admin_email = 'example@example.com'
 
   # https://github.com/sanger/wrangler
-  config.wrangler_url = 'http://127.0.0.1:5001/tube_rack'
+  config.wrangler_url = 'http://127.0.0.1:5000/wrangle'
 
   # https://github.com/sanger/lighthouse
   config.lighthouse_host = 'http://127.0.0.1:5000'

From 646642c6b39160c2671850fbd04d6c3457fe37a8 Mon Sep 17 00:00:00 2001
From: Katy Taylor <kt17@sanger.ac.uk>
Date: Tue, 16 Jun 2020 14:46:17 +0100
Subject: [PATCH 02/21] refactor create method, adding more error handling

---
 app/controllers/process_plates_controller.rb | 84 ++++++++++----------
 1 file changed, 42 insertions(+), 42 deletions(-)

diff --git a/app/controllers/process_plates_controller.rb b/app/controllers/process_plates_controller.rb
index bdaadbfe..c03183ea 100644
--- a/app/controllers/process_plates_controller.rb
+++ b/app/controllers/process_plates_controller.rb
@@ -16,48 +16,48 @@ def new
   end
 
   def create
-    # respond_to do |format|
-      bed_verification_model = InstrumentProcessesInstrument.get_bed_verification_type(params[:instrument_barcode], params[:instrument_process])
-      if bed_verification_model.nil?
-        flash[:error] = 'Invalid instrument or process'
-      else
-        bed_layout_verification = bed_verification_model.new(
-          instrument_barcode: params[:instrument_barcode],
-          scanned_values: params[:robot],
-          api: api
-        )
-        if bed_layout_verification.validate_and_create_audits?(params)
-          # the param is called 'source_plates' but we could be working with tube racks or plates etc.
-          barcodes = sanitize_barcodes(params[:source_plates])
-
-          # find out if the 'receive_plates' process was executed
-          receive_plates_process = InstrumentProcess.find_by(id: params[:instrument_process]).key.eql?('slf_receive_plates')
-
-          message = ''
-          if barcodes && receive_plates_process
-            call_external_services(barcodes)
-
-            message = @lighthouse_responses.concat(@wrangler_responses)
-          end
-
-          # TODO: display the responses from the services in a partial, not a flash
-          # TODO: sort out original flash code below
-          flash[:notice] = message
-
-          # add a flash on the page for the number of unique barcodes scanned in
-          # num_unique_barcodes = bed_layout_verification.process_plate&.barcodes.uniq.length
-          # if num_unique_barcodes
-          #   flash[:notice] = "Success - #{num_unique_barcodes} unique plate(s) scanned"
-          # else
-          #   flash[:notice] = "Success"
-          # end
-        else
-          flash[:error] = bed_layout_verification.errors.values.flatten.join("\n")
-        end
-      end
-      @results = parse_responses
-      render :results
-    # end
+    bed_verification_model = InstrumentProcessesInstrument.get_bed_verification_type(
+      params[:instrument_barcode],
+      params[:instrument_process]
+    )
+    back_to_new_with_error('Invalid instrument or process') and return if bed_verification_model.nil?
+
+    bed_layout_verification = bed_verification_model.new(
+      instrument_barcode: params[:instrument_barcode],
+      scanned_values: params[:robot],
+      api: api
+    )
+    unless bed_layout_verification.validate_and_create_audits?(params)
+      errors = bed_layout_verification.errors.values.flatten.join("\n")
+      back_to_new_with_error(errors) and return
+    end
+
+    back_to_new_with_message('Success') and return unless receive_plates_process?(params)
+
+    # the param is called 'source_plates' but we could be working with tube racks or plates etc.
+    barcodes = sanitize_barcodes(params[:source_plates])
+    unless barcodes && !barcodes.empty?
+      back_to_new_with_error('No barcodes were provided') and return
+    end
+
+    call_external_services(barcodes)
+
+    @results = parse_responses
+    render :results
+  end
+
+  def back_to_new_with_message(message, flash_type=:notice)
+    flash[flash_type] = message
+    redirect_to(new_process_plate_path)
+  end
+
+  def back_to_new_with_error(message)
+    back_to_new_with_message(message, :error)
+  end
+
+  # find out if the 'receive_plates' process was executed
+  def receive_plates_process?(params)
+    @is_receive_plates_process ||= InstrumentProcess.find_by(id: params[:instrument_process]).key.eql?('slf_receive_plates')
   end
 
   # Call any external services - currently lighthouse service for plates from Lighthouse Labs and

From 3d0d967082815b6b9bc39e79977a73707d4752c7 Mon Sep 17 00:00:00 2001
From: Katy Taylor <kt17@sanger.ac.uk>
Date: Wed, 17 Jun 2020 16:38:20 +0100
Subject: [PATCH 03/21] results table now displays correctly for successful
 wrangler responses - integrating with Andrew's Sequencescape branch
 gpl442_feedback_for_sm

---
 app/controllers/process_plates_controller.rb |  4 +--
 app/views/process_plates/results.html.haml   | 30 +++++++++++---------
 lib/wrangler.rb                              |  5 ++--
 3 files changed, 21 insertions(+), 18 deletions(-)

diff --git a/app/controllers/process_plates_controller.rb b/app/controllers/process_plates_controller.rb
index c03183ea..5e5e04d9 100644
--- a/app/controllers/process_plates_controller.rb
+++ b/app/controllers/process_plates_controller.rb
@@ -117,8 +117,8 @@ def parse_responses
                 else
                   'No'
                 end
-      purpose = r[:purpose]
-      study = r[:study]
+      purpose = r[:json]['data']['attributes']['purpose_name']
+      study = r[:json]['data']['attributes']['study_names'].join(', ')
 
       output << {
         :barcode => barcode,
diff --git a/app/views/process_plates/results.html.haml b/app/views/process_plates/results.html.haml
index c1e7cb9b..e24ced34 100644
--- a/app/views/process_plates/results.html.haml
+++ b/app/views/process_plates/results.html.haml
@@ -1,20 +1,22 @@
 #service_responses
   %table
-    %tr
-      %th.th Barcode
-      %th Success?
-      %th Purpose
-      %th Study
-    - for row in @results
+    %thead
       %tr
-        %td
-          = row[:barcode]
-        %td
-          = row[:success]
-        %td
-          = row[:purpose]
-        %td
-          = row[:study]
+        %th.th Barcode
+        %th Success?
+        %th Purpose
+        %th Study
+    %tbody
+      - for row in @results
+        %tr
+          %td
+            = row[:barcode]
+          %td
+            = row[:success]
+          %td
+            = row[:purpose]
+          %td
+            = row[:study]
 
 %br
 = link_to 'Scan more labware', new_process_plate_path
\ No newline at end of file
diff --git a/lib/wrangler.rb b/lib/wrangler.rb
index d813060e..b4468528 100644
--- a/lib/wrangler.rb
+++ b/lib/wrangler.rb
@@ -1,5 +1,7 @@
 # frozen_string_literal: true
 
+require 'json'
+
 class Wrangler
   require 'net/http'
 
@@ -17,8 +19,7 @@ def self.call_api(barcodes)
         res = Net::HTTP.start(url.host, url.port) do |http|
           http.request(req)
         end
-
-        responses << { barcode: barcode, code: res.code }
+        responses << { barcode: barcode, code: res.code, json: JSON.parse(res.body)}
       end
     rescue StandardError => e
       Rails.logger.error(e)

From ac10e0f50573266c6fda135bae9d4d4644766e3e Mon Sep 17 00:00:00 2001
From: Katy Taylor <kt17@sanger.ac.uk>
Date: Wed, 17 Jun 2020 17:25:46 +0100
Subject: [PATCH 04/21] add some more error handling and detail to the table -
 TO DO: don't show an error from the lighthouse service for a barcode, if the
 wrangler was subsequently successful for the same barcode

---
 app/controllers/process_plates_controller.rb | 19 ++++++++++++++-----
 app/views/process_plates/results.html.haml   |  5 +++++
 lib/lighthouse.rb                            |  2 +-
 lib/wrangler.rb                              |  2 +-
 4 files changed, 21 insertions(+), 7 deletions(-)

diff --git a/app/controllers/process_plates_controller.rb b/app/controllers/process_plates_controller.rb
index 5e5e04d9..867a7f5f 100644
--- a/app/controllers/process_plates_controller.rb
+++ b/app/controllers/process_plates_controller.rb
@@ -43,6 +43,8 @@ def create
     call_external_services(barcodes)
 
     @results = parse_responses
+    back_to_new_with_error('No response from services') and return if @results.empty?
+
     render :results
   end
 
@@ -63,7 +65,6 @@ def receive_plates_process?(params)
   # Call any external services - currently lighthouse service for plates from Lighthouse Labs and
   #   wrangler for tube racks. If no samples are found in the lighthouse service, try the wrangler
   def call_external_services(barcodes)
-    puts "DEBUG: call_external_services"
     # call the lighthouse service first as we are assuming that most labware scanned will be
     #   plates from Lighthouse Labs
     @lighthouse_responses = Lighthouse.call_api(barcodes)
@@ -98,12 +99,16 @@ def parse_responses
                 else
                   'No'
                 end
-      purpose = r[:purpose]
-      study = r[:study]
+      if r[:body].is_a? Hash
+        error = r.dig(:body, 'error')
+        purpose = r.dig(:body, 'data', 'attributes', 'purpose_name')
+        study = r.dig(:body, 'data', 'attributes', 'study_names')&.join(', ')
+      end
 
       output << {
         :barcode => barcode,
         :success => success,
+        :error => error,
         :purpose => purpose,
         :study => study
       }
@@ -117,12 +122,16 @@ def parse_responses
                 else
                   'No'
                 end
-      purpose = r[:json]['data']['attributes']['purpose_name']
-      study = r[:json]['data']['attributes']['study_names'].join(', ')
+      if r[:body].is_a? Hash
+        error = r.dig(:body, 'error')
+        purpose = r.dig(:body, 'data', 'attributes', 'purpose_name')
+        study = r.dig(:body, 'data', 'attributes', 'study_names')&.join(', ')
+      end
 
       output << {
         :barcode => barcode,
         :success => success,
+        :error => error,
         :purpose => purpose,
         :study => study
       }
diff --git a/app/views/process_plates/results.html.haml b/app/views/process_plates/results.html.haml
index e24ced34..5090505e 100644
--- a/app/views/process_plates/results.html.haml
+++ b/app/views/process_plates/results.html.haml
@@ -1,9 +1,12 @@
+%h2 Activity Logging
+
 #service_responses
   %table
     %thead
       %tr
         %th.th Barcode
         %th Success?
+        %th Error
         %th Purpose
         %th Study
     %tbody
@@ -13,6 +16,8 @@
             = row[:barcode]
           %td
             = row[:success]
+          %td
+            = row[:error]
           %td
             = row[:purpose]
           %td
diff --git a/lib/lighthouse.rb b/lib/lighthouse.rb
index 69842740..528360f1 100644
--- a/lib/lighthouse.rb
+++ b/lib/lighthouse.rb
@@ -20,7 +20,7 @@ def self.call_api(barcodes)
           http.request(req)
         end
 
-        responses << { code: res.code, body: res.body }
+        responses << { barcode: barcode, code: res.code, body: res.body }
       end
     rescue StandardError => e
       Rails.logger.error(e)
diff --git a/lib/wrangler.rb b/lib/wrangler.rb
index b4468528..2cdfd066 100644
--- a/lib/wrangler.rb
+++ b/lib/wrangler.rb
@@ -19,7 +19,7 @@ def self.call_api(barcodes)
         res = Net::HTTP.start(url.host, url.port) do |http|
           http.request(req)
         end
-        responses << { barcode: barcode, code: res.code, json: JSON.parse(res.body)}
+        responses << { barcode: barcode, code: res.code, body: JSON.parse(res.body)}
       end
     rescue StandardError => e
       Rails.logger.error(e)

From 0faefaa69b429f1f41707791a5c365e3ba697de2 Mon Sep 17 00:00:00 2001
From: Katy Taylor <kt17@sanger.ac.uk>
Date: Thu, 18 Jun 2020 10:22:39 +0100
Subject: [PATCH 05/21] re-structure results table by looping through scanned
 barcodes and looking for successful responses for them - solves issue of
 having a failed response from one service and successful from the other -
 error detail will still be in the logs - refactor controller code to reduce
 code duplication

---
 app/controllers/process_plates_controller.rb | 80 ++++++++------------
 app/views/process_plates/results.html.haml   | 41 +++++-----
 2 files changed, 51 insertions(+), 70 deletions(-)

diff --git a/app/controllers/process_plates_controller.rb b/app/controllers/process_plates_controller.rb
index 867a7f5f..47649f19 100644
--- a/app/controllers/process_plates_controller.rb
+++ b/app/controllers/process_plates_controller.rb
@@ -42,9 +42,14 @@ def create
 
     call_external_services(barcodes)
 
-    @results = parse_responses
+    @results = generate_results(barcodes)
     back_to_new_with_error('No response from services') and return if @results.empty?
 
+    if all_labware_created?(@results)
+      flash[:notice] = 'All labware were successfully created.'
+    else
+      flash[:error] = 'Some labware were not able to be created.'
+    end
     render :results
   end
 
@@ -68,12 +73,10 @@ def call_external_services(barcodes)
     # call the lighthouse service first as we are assuming that most labware scanned will be
     #   plates from Lighthouse Labs
     @lighthouse_responses = Lighthouse.call_api(barcodes)
-    puts "DEBUG: lighthouse_responses: #{@lighthouse_responses}"
 
     # keeping it simple for now, if all the responses are not CREATED, send ALL the barcodes
     #   to the wrangler
     @wrangler_responses = Wrangler.call_api(barcodes) unless all_created?(@lighthouse_responses)
-    puts "DEBUG: wrangler_responses: #{@wrangler_responses}"
   end
 
   # Returns a list of unique barcodes by removing blanks and duplicates
@@ -88,55 +91,34 @@ def all_created?(responses)
     responses.all? { |response| response[:code] == "201" }
   end
 
-  def parse_responses
-    output = []
-
-    @lighthouse_responses.each do |r|
-
-      barcode = r[:barcode]
-      success = if r[:code] == '201'
-                  'Yes'
-                else
-                  'No'
-                end
-      if r[:body].is_a? Hash
-        error = r.dig(:body, 'error')
-        purpose = r.dig(:body, 'data', 'attributes', 'purpose_name')
-        study = r.dig(:body, 'data', 'attributes', 'study_names')&.join(', ')
-      end
-
-      output << {
-        :barcode => barcode,
-        :success => success,
-        :error => error,
-        :purpose => purpose,
-        :study => study
-      }
-    end
+  def generate_results(barcodes)
+    output = {}
+    # default 'success' for each barcode to 'No'
+    barcodes.each { |b| output[b] = { success: 'No' } }
 
-    @wrangler_responses.each do |r|
-
-      barcode = r[:barcode]
-      success = if r[:code] == '201'
-                  'Yes'
-                else
-                  'No'
-                end
-      if r[:body].is_a? Hash
-        error = r.dig(:body, 'error')
-        purpose = r.dig(:body, 'data', 'attributes', 'purpose_name')
-        study = r.dig(:body, 'data', 'attributes', 'study_names')&.join(', ')
-      end
-
-      output << {
-        :barcode => barcode,
-        :success => success,
-        :error => error,
-        :purpose => purpose,
-        :study => study
-      }
+    # loop through service responses to update 'output' with successes
+    @lighthouse_responses.select { |r| r[:code] == '201' }.each do |r|
+      output[r[:barcode]] = parse_response(r, :Lighthouse)
+    end
+    @wrangler_responses.select { |r| r[:code] == '201' }.each do |r|
+      output[r[:barcode]] = parse_response(r, :CGaP)
     end
 
     output
   end
+
+  def parse_response(response, service)
+    {
+      success: 'Yes',
+      source: service,
+      purpose: response.dig(:body, 'data', 'attributes', 'purpose_name'),
+      study: response.dig(:body, 'data', 'attributes', 'study_names')&.join(', ')
+    }
+  end
+
+  def all_labware_created?(results)
+    return false if results.any?{ |_barcode, details| details[:success] == 'No' }
+
+    true
+  end
 end
diff --git a/app/views/process_plates/results.html.haml b/app/views/process_plates/results.html.haml
index 5090505e..8b4e97fd 100644
--- a/app/views/process_plates/results.html.haml
+++ b/app/views/process_plates/results.html.haml
@@ -1,27 +1,26 @@
 %h2 Activity Logging
 
-#service_responses
-  %table
-    %thead
+%table
+  %thead
+    %tr
+      %th Barcode
+      %th Success?
+      %th Source
+      %th Purpose
+      %th Study
+  %tbody
+    - @results.each do |barcode, details|
       %tr
-        %th.th Barcode
-        %th Success?
-        %th Error
-        %th Purpose
-        %th Study
-    %tbody
-      - for row in @results
-        %tr
-          %td
-            = row[:barcode]
-          %td
-            = row[:success]
-          %td
-            = row[:error]
-          %td
-            = row[:purpose]
-          %td
-            = row[:study]
+        %td
+          = barcode
+        %td
+          = details[:success]
+        %td
+          = details[:source]
+        %td
+          = details[:purpose]
+        %td
+          = details[:study]
 
 %br
 = link_to 'Scan more labware', new_process_plate_path
\ No newline at end of file

From d607a521577ad51f3479291180fc5dd91fdc0220 Mon Sep 17 00:00:00 2001
From: Katy Taylor <kt17@sanger.ac.uk>
Date: Thu, 18 Jun 2020 10:52:31 +0100
Subject: [PATCH 06/21] Add some basic styling for the table - also improves
 tables in admin/processes and admin/instruments - also get rid of weird ""
 marks around titles on above two pages - move custom css into the app/assets
 folder and add a manifest application.css file as per Rails Asset Pipeline
 docs

---
 app/assets/stylesheets/application.css                |  1 +
 .../assets/stylesheets/form_custom.css                | 11 +++++++++++
 app/views/admin/instruments/index.html.haml           |  2 +-
 app/views/admin/processes/index.html.haml             |  2 +-
 app/views/layouts/application.html.erb                |  2 +-
 5 files changed, 15 insertions(+), 3 deletions(-)
 create mode 100644 app/assets/stylesheets/application.css
 rename public/stylesheets/form.css => app/assets/stylesheets/form_custom.css (83%)

diff --git a/app/assets/stylesheets/application.css b/app/assets/stylesheets/application.css
new file mode 100644
index 00000000..d3a82b1f
--- /dev/null
+++ b/app/assets/stylesheets/application.css
@@ -0,0 +1 @@
+@import "form_custom";
\ No newline at end of file
diff --git a/public/stylesheets/form.css b/app/assets/stylesheets/form_custom.css
similarity index 83%
rename from public/stylesheets/form.css
rename to app/assets/stylesheets/form_custom.css
index d2a54b8f..e3b13c8b 100644
--- a/public/stylesheets/form.css
+++ b/app/assets/stylesheets/form_custom.css
@@ -62,5 +62,16 @@ li#beds_and_plates ul{
  padding: 0px;
 }
 
+table, td, th {
+  border: 1px solid #ddd;
+  text-align: left;
+}
 
+table {
+  border-collapse: collapse;
+  /* width: 100%; */
+}
 
+th, td {
+  padding: 15px;
+}
diff --git a/app/views/admin/instruments/index.html.haml b/app/views/admin/instruments/index.html.haml
index 2871583f..4936ae14 100644
--- a/app/views/admin/instruments/index.html.haml
+++ b/app/views/admin/instruments/index.html.haml
@@ -1,4 +1,4 @@
-%h1 "Manage Instruments"
+%h1 Manage Instruments
 
 %table#instruments
  %thead
diff --git a/app/views/admin/processes/index.html.haml b/app/views/admin/processes/index.html.haml
index 9f6e3812..39560d41 100644
--- a/app/views/admin/processes/index.html.haml
+++ b/app/views/admin/processes/index.html.haml
@@ -1,4 +1,4 @@
-%h1 "Manage Processes"
+%h1 Manage Processes
 
 %table#processes
  %thead
diff --git a/app/views/layouts/application.html.erb b/app/views/layouts/application.html.erb
index 015d6758..9506e150 100644
--- a/app/views/layouts/application.html.erb
+++ b/app/views/layouts/application.html.erb
@@ -2,7 +2,7 @@
 <html lang='en'>
 <head>
   <title><%= ProcessTracking::Application.config.name %></title>
-  <%= stylesheet_link_tag(:flash,:form,:formtastic_static,:formtastic_changes) %>
+  <%= stylesheet_link_tag(:flash,:formtastic_static,:formtastic_changes,:application) %>
   <%= javascript_include_tag('jquery.min.js','rails.js','application.js') %>
 
   <%= csrf_meta_tag %>

From f5312ad1d6c59c9b55588c9d57d4e39c3c61fdcb Mon Sep 17 00:00:00 2001
From: Katy Taylor <kt17@sanger.ac.uk>
Date: Thu, 18 Jun 2020 10:54:38 +0100
Subject: [PATCH 07/21] Get rid of commented out width style - don't think full
 width tables look very good here

---
 app/assets/stylesheets/form_custom.css | 1 -
 1 file changed, 1 deletion(-)

diff --git a/app/assets/stylesheets/form_custom.css b/app/assets/stylesheets/form_custom.css
index e3b13c8b..c126266b 100644
--- a/app/assets/stylesheets/form_custom.css
+++ b/app/assets/stylesheets/form_custom.css
@@ -69,7 +69,6 @@ table, td, th {
 
 table {
   border-collapse: collapse;
-  /* width: 100%; */
 }
 
 th, td {

From f4bbbbab9a25f970fcdcc60b74d8b3480e11057f Mon Sep 17 00:00:00 2001
From: Katy Taylor <kt17@sanger.ac.uk>
Date: Thu, 18 Jun 2020 11:05:19 +0100
Subject: [PATCH 08/21] the easy rubocop fixes

---
 app/controllers/process_plates_controller.rb | 18 ++++++++----------
 lib/wrangler.rb                              |  2 +-
 2 files changed, 9 insertions(+), 11 deletions(-)

diff --git a/app/controllers/process_plates_controller.rb b/app/controllers/process_plates_controller.rb
index 47649f19..c2d65568 100644
--- a/app/controllers/process_plates_controller.rb
+++ b/app/controllers/process_plates_controller.rb
@@ -20,7 +20,7 @@ def create
       params[:instrument_barcode],
       params[:instrument_process]
     )
-    back_to_new_with_error('Invalid instrument or process') and return if bed_verification_model.nil?
+    back_to_new_with_error('Invalid instrument or process') && return if bed_verification_model.nil?
 
     bed_layout_verification = bed_verification_model.new(
       instrument_barcode: params[:instrument_barcode],
@@ -29,21 +29,19 @@ def create
     )
     unless bed_layout_verification.validate_and_create_audits?(params)
       errors = bed_layout_verification.errors.values.flatten.join("\n")
-      back_to_new_with_error(errors) and return
+      back_to_new_with_error(errors) && return
     end
 
-    back_to_new_with_message('Success') and return unless receive_plates_process?(params)
+    back_to_new_with_message('Success') && return unless receive_plates_process?(params)
 
     # the param is called 'source_plates' but we could be working with tube racks or plates etc.
     barcodes = sanitize_barcodes(params[:source_plates])
-    unless barcodes && !barcodes.empty?
-      back_to_new_with_error('No barcodes were provided') and return
-    end
+    back_to_new_with_error('No barcodes were provided') && return unless barcodes && !barcodes.empty?
 
     call_external_services(barcodes)
 
     @results = generate_results(barcodes)
-    back_to_new_with_error('No response from services') and return if @results.empty?
+    back_to_new_with_error('No response from services') && return if @results.empty?
 
     if all_labware_created?(@results)
       flash[:notice] = 'All labware were successfully created.'
@@ -53,7 +51,7 @@ def create
     render :results
   end
 
-  def back_to_new_with_message(message, flash_type=:notice)
+  def back_to_new_with_message(message, flash_type = :notice)
     flash[flash_type] = message
     redirect_to(new_process_plate_path)
   end
@@ -64,7 +62,7 @@ def back_to_new_with_error(message)
 
   # find out if the 'receive_plates' process was executed
   def receive_plates_process?(params)
-    @is_receive_plates_process ||= InstrumentProcess.find_by(id: params[:instrument_process]).key.eql?('slf_receive_plates')
+    @receive_plates_process ||= InstrumentProcess.find_by(id: params[:instrument_process]).key.eql?('slf_receive_plates')
   end
 
   # Call any external services - currently lighthouse service for plates from Lighthouse Labs and
@@ -117,7 +115,7 @@ def parse_response(response, service)
   end
 
   def all_labware_created?(results)
-    return false if results.any?{ |_barcode, details| details[:success] == 'No' }
+    return false if results.any? { |_barcode, details| details[:success] == 'No' }
 
     true
   end
diff --git a/lib/wrangler.rb b/lib/wrangler.rb
index 2cdfd066..c46b7087 100644
--- a/lib/wrangler.rb
+++ b/lib/wrangler.rb
@@ -19,7 +19,7 @@ def self.call_api(barcodes)
         res = Net::HTTP.start(url.host, url.port) do |http|
           http.request(req)
         end
-        responses << { barcode: barcode, code: res.code, body: JSON.parse(res.body)}
+        responses << { barcode: barcode, code: res.code, body: JSON.parse(res.body) }
       end
     rescue StandardError => e
       Rails.logger.error(e)

From 964c9622cc5c48054b3484c8233feba5d20a966f Mon Sep 17 00:00:00 2001
From: Katy Taylor <kt17@sanger.ac.uk>
Date: Thu, 18 Jun 2020 11:26:31 +0100
Subject: [PATCH 09/21] Pre-existing tests now pass

---
 config/environments/test.rb  |  2 +-
 lib/wrangler.rb              | 10 +++++++++-
 test/unit/lighthouse_test.rb | 14 +++++++-------
 test/unit/wrangler_test.rb   | 14 +++++++-------
 4 files changed, 24 insertions(+), 16 deletions(-)

diff --git a/config/environments/test.rb b/config/environments/test.rb
index 7818eaac..25b92514 100644
--- a/config/environments/test.rb
+++ b/config/environments/test.rb
@@ -43,7 +43,7 @@
   config.admin_email = 'example@example.com'
 
   # https://github.com/sanger/wrangler
-  config.wrangler_url = 'http://example.com/tube_rack'
+  config.wrangler_url = 'http://example.com/wrangle'
 
   # https://github.com/sanger/lighthouse
   config.lighthouse_host = 'http://127.0.0.1:5000'
diff --git a/lib/wrangler.rb b/lib/wrangler.rb
index c46b7087..f2034555 100644
--- a/lib/wrangler.rb
+++ b/lib/wrangler.rb
@@ -19,7 +19,8 @@ def self.call_api(barcodes)
         res = Net::HTTP.start(url.host, url.port) do |http|
           http.request(req)
         end
-        responses << { barcode: barcode, code: res.code, body: JSON.parse(res.body) }
+
+        responses << { barcode: barcode, code: res.code, body: Wrangler.parse_body(res.body) }
       end
     rescue StandardError => e
       Rails.logger.error(e)
@@ -30,4 +31,11 @@ def self.call_api(barcodes)
     end
     responses
   end
+
+  def self.parse_body(body)
+    JSON.parse(body)
+  rescue StandardError
+    # return the body as is if not valid JSON
+    return body
+  end
 end
diff --git a/test/unit/lighthouse_test.rb b/test/unit/lighthouse_test.rb
index d4fc638e..12247fab 100644
--- a/test/unit/lighthouse_test.rb
+++ b/test/unit/lighthouse_test.rb
@@ -30,8 +30,8 @@ class LighthouseTest < ActiveSupport::TestCase
         stub_request(:any, uri_template).to_return(status: 201)
 
         assert_equal(
-          Lighthouse.call_api([@input_params[:source_plates]]),
-          [{ code: '201', body: '' }]
+          [{ barcode: 'barcode_one', code: '201', body: '' }],
+          Lighthouse.call_api([@input_params[:source_plates]])
         )
       end
 
@@ -45,12 +45,12 @@ class LighthouseTest < ActiveSupport::TestCase
         stub_request(:any, uri_template).to_return(status: 201)
 
         assert_equal(
-          Lighthouse.call_api(barcodes),
           [
-            { code: '201', body: '' },
-            { code: '201', body: '' },
-            { code: '201', body: '' }
-          ]
+            { barcode: 'barcode_one', code: '201', body: '' },
+            { barcode: 'barcode_two', code: '201', body: '' },
+            { barcode: 'barcode_three', code: '201', body: '' }
+          ],
+          Lighthouse.call_api(barcodes)
         )
       end
     end
diff --git a/test/unit/wrangler_test.rb b/test/unit/wrangler_test.rb
index 24a377ba..0a5f487f 100644
--- a/test/unit/wrangler_test.rb
+++ b/test/unit/wrangler_test.rb
@@ -31,8 +31,8 @@ class WranglerTest < ActiveSupport::TestCase
         stub_request(:any, uri_template).to_return(status: 200)
 
         assert_equal(
-          Wrangler.call_api([@input_params[:source_plates]]),
-          [{ barcode: @barcode, code: '200' }]
+          [{ barcode: @barcode, code: '200', body: '' }],
+          Wrangler.call_api([@input_params[:source_plates]])
         )
       end
 
@@ -46,12 +46,12 @@ class WranglerTest < ActiveSupport::TestCase
         stub_request(:any, uri_template).to_return(status: 200)
 
         assert_equal(
-          Wrangler.call_api(barcodes),
           [
-            { barcode: 'barcode_one', code: '200' },
-            { barcode: 'barcode_two', code: '200' },
-            { barcode: 'barcode_three', code: '200' }
-          ]
+            { barcode: 'barcode_one', code: '200', body: '' },
+            { barcode: 'barcode_two', code: '200', body: '' },
+            { barcode: 'barcode_three', code: '200', body: '' }
+          ],
+          Wrangler.call_api(barcodes)
         )
       end
     end

From ae0ba1be67110f98adb40ae000c651f2d7b49997 Mon Sep 17 00:00:00 2001
From: Katy Taylor <kt17@sanger.ac.uk>
Date: Fri, 19 Jun 2020 11:29:51 +0100
Subject: [PATCH 10/21] Null check lighthouse_responses and wrangler_responses
 variables - if all scanned barcodes were found in lighthouse,
 wrangler_responses won't exist - if lighthouse is down, lighthouse_responses
 won't exist - also add JSON parsing to lighthouse responses, as per wrangler

---
 app/controllers/process_plates_controller.rb | 12 ++++++++----
 lib/lighthouse.rb                            |  9 ++++++++-
 2 files changed, 16 insertions(+), 5 deletions(-)

diff --git a/app/controllers/process_plates_controller.rb b/app/controllers/process_plates_controller.rb
index c2d65568..7765dd45 100644
--- a/app/controllers/process_plates_controller.rb
+++ b/app/controllers/process_plates_controller.rb
@@ -95,11 +95,15 @@ def generate_results(barcodes)
     barcodes.each { |b| output[b] = { success: 'No' } }
 
     # loop through service responses to update 'output' with successes
-    @lighthouse_responses.select { |r| r[:code] == '201' }.each do |r|
-      output[r[:barcode]] = parse_response(r, :Lighthouse)
+    if @lighthouse_responses
+      @lighthouse_responses.select { |r| r[:code] == '201' }.each do |r|
+        output[r[:barcode]] = parse_response(r, :Lighthouse)
+      end
     end
-    @wrangler_responses.select { |r| r[:code] == '201' }.each do |r|
-      output[r[:barcode]] = parse_response(r, :CGaP)
+    if @wrangler_responses
+      @wrangler_responses.select { |r| r[:code] == '201' }.each do |r|
+        output[r[:barcode]] = parse_response(r, :CGaP)
+      end
     end
 
     output
diff --git a/lib/lighthouse.rb b/lib/lighthouse.rb
index 528360f1..e62659c9 100644
--- a/lib/lighthouse.rb
+++ b/lib/lighthouse.rb
@@ -20,7 +20,7 @@ def self.call_api(barcodes)
           http.request(req)
         end
 
-        responses << { barcode: barcode, code: res.code, body: res.body }
+        responses << { barcode: barcode, code: res.code, body: Lighthouse.parse_body(res.body) }
       end
     rescue StandardError => e
       Rails.logger.error(e)
@@ -30,4 +30,11 @@ def self.call_api(barcodes)
     end
     responses
   end
+
+  def self.parse_body(body)
+    JSON.parse(body)
+  rescue StandardError
+    # return the body as is if not valid JSON
+    return body
+  end
 end

From 348f47a8a2eecea7f0d8b3243a133c18ae7c9f06 Mon Sep 17 00:00:00 2001
From: Katy Taylor <kt17@sanger.ac.uk>
Date: Fri, 19 Jun 2020 13:09:28 +0100
Subject: [PATCH 11/21] some rubocop fixes

---
 app/controllers/process_plates_controller.rb | 12 ++++--------
 lib/lighthouse.rb                            |  2 +-
 lib/wrangler.rb                              |  2 +-
 3 files changed, 6 insertions(+), 10 deletions(-)

diff --git a/app/controllers/process_plates_controller.rb b/app/controllers/process_plates_controller.rb
index 7765dd45..fce8e99f 100644
--- a/app/controllers/process_plates_controller.rb
+++ b/app/controllers/process_plates_controller.rb
@@ -95,15 +95,11 @@ def generate_results(barcodes)
     barcodes.each { |b| output[b] = { success: 'No' } }
 
     # loop through service responses to update 'output' with successes
-    if @lighthouse_responses
-      @lighthouse_responses.select { |r| r[:code] == '201' }.each do |r|
-        output[r[:barcode]] = parse_response(r, :Lighthouse)
-      end
+    @lighthouse_responses&.select { |r| r[:code] == '201' }.each do |r|
+      output[r[:barcode]] = parse_response(r, :Lighthouse)
     end
-    if @wrangler_responses
-      @wrangler_responses.select { |r| r[:code] == '201' }.each do |r|
-        output[r[:barcode]] = parse_response(r, :CGaP)
-      end
+    @wrangler_responses&.select { |r| r[:code] == '201' }.each do |r|
+      output[r[:barcode]] = parse_response(r, :CGaP)
     end
 
     output
diff --git a/lib/lighthouse.rb b/lib/lighthouse.rb
index e62659c9..cda71078 100644
--- a/lib/lighthouse.rb
+++ b/lib/lighthouse.rb
@@ -35,6 +35,6 @@ def self.parse_body(body)
     JSON.parse(body)
   rescue StandardError
     # return the body as is if not valid JSON
-    return body
+    body
   end
 end
diff --git a/lib/wrangler.rb b/lib/wrangler.rb
index f2034555..62359aa2 100644
--- a/lib/wrangler.rb
+++ b/lib/wrangler.rb
@@ -36,6 +36,6 @@ def self.parse_body(body)
     JSON.parse(body)
   rescue StandardError
     # return the body as is if not valid JSON
-    return body
+    body
   end
 end

From 5499b9231481f163ea9c5e3cc36da1df543dc6d5 Mon Sep 17 00:00:00 2001
From: Katy Taylor <kt17@sanger.ac.uk>
Date: Fri, 19 Jun 2020 15:15:01 +0100
Subject: [PATCH 12/21] write some new tests for this new functionality -
 refactor a little to make more testable

---
 app/controllers/process_plates_controller.rb  | 18 ++++---
 test/controllers/process_plates_controller.rb | 51 +++++++++++++++++++
 test/test_helper.rb                           | 26 ++++++++++
 3 files changed, 88 insertions(+), 7 deletions(-)

diff --git a/app/controllers/process_plates_controller.rb b/app/controllers/process_plates_controller.rb
index fce8e99f..c6de383f 100644
--- a/app/controllers/process_plates_controller.rb
+++ b/app/controllers/process_plates_controller.rb
@@ -38,9 +38,9 @@ def create
     barcodes = sanitize_barcodes(params[:source_plates])
     back_to_new_with_error('No barcodes were provided') && return unless barcodes && !barcodes.empty?
 
-    call_external_services(barcodes)
+    responses = call_external_services(barcodes)
 
-    @results = generate_results(barcodes)
+    @results = generate_results(barcodes, responses)
     back_to_new_with_error('No response from services') && return if @results.empty?
 
     if all_labware_created?(@results)
@@ -68,13 +68,16 @@ def receive_plates_process?(params)
   # Call any external services - currently lighthouse service for plates from Lighthouse Labs and
   #   wrangler for tube racks. If no samples are found in the lighthouse service, try the wrangler
   def call_external_services(barcodes)
+    output = { lighthouse: [], wrangler: [] }
     # call the lighthouse service first as we are assuming that most labware scanned will be
     #   plates from Lighthouse Labs
-    @lighthouse_responses = Lighthouse.call_api(barcodes)
+    output[:lighthouse] = Lighthouse.call_api(barcodes)
 
     # keeping it simple for now, if all the responses are not CREATED, send ALL the barcodes
     #   to the wrangler
-    @wrangler_responses = Wrangler.call_api(barcodes) unless all_created?(@lighthouse_responses)
+    output[:wrangler] = Wrangler.call_api(barcodes) unless all_created?(output[:lighthouse])
+
+    output
   end
 
   # Returns a list of unique barcodes by removing blanks and duplicates
@@ -89,16 +92,17 @@ def all_created?(responses)
     responses.all? { |response| response[:code] == "201" }
   end
 
-  def generate_results(barcodes)
+  def generate_results(barcodes, responses)
     output = {}
     # default 'success' for each barcode to 'No'
     barcodes.each { |b| output[b] = { success: 'No' } }
 
     # loop through service responses to update 'output' with successes
-    @lighthouse_responses&.select { |r| r[:code] == '201' }.each do |r|
+    # puts "DEBUG: responses: #{JSON.pretty_generate(responses)}"
+    responses[:lighthouse]&.select { |r| r[:code] == '201' }.each do |r|
       output[r[:barcode]] = parse_response(r, :Lighthouse)
     end
-    @wrangler_responses&.select { |r| r[:code] == '201' }.each do |r|
+    responses[:wrangler]&.select { |r| r[:code] == '201' }.each do |r|
       output[r[:barcode]] = parse_response(r, :CGaP)
     end
 
diff --git a/test/controllers/process_plates_controller.rb b/test/controllers/process_plates_controller.rb
index 26e81fbf..e78265a9 100644
--- a/test/controllers/process_plates_controller.rb
+++ b/test/controllers/process_plates_controller.rb
@@ -37,4 +37,55 @@ class ProcessPlatesControllerTest < ActiveSupport::TestCase
       ProcessPlatesController.new.call_external_services(%w[123 456])
     end
   end
+
+  context '#generate_results' do
+    should 'give failed results if no response' do
+      barcodes = ['AB1']
+
+      responses = { lighthouse: [], wrangler: [] }
+
+      expected_results = { 'AB1' => { success: 'No' } }
+
+      results = ProcessPlatesController.new.generate_results(barcodes, responses)
+      assert_equal(expected_results, results)
+    end
+
+
+    should 'give detailed results if success' do
+      barcodes = ['AB1', 'AB2', 'AB3']
+
+      responses = {
+        lighthouse: [
+          generate_success_response('AB1', 'Purpose 1', ['Study 1', 'Study 2']),
+          generate_success_response('AB2', 'Purpose 1', ['Study 1']),
+          generate_fail_response('AB3') ],
+        wrangler: [
+          generate_fail_response('AB1'),
+          generate_fail_response('AB2'),
+          generate_success_response('AB3', 'Purpose 1', ['Study 1', 'Study 2']) ]}
+
+      expected_results = {
+        'AB1' => {
+          success: 'Yes',
+          source: :Lighthouse,
+          purpose: 'Purpose 1',
+          study: 'Study 1, Study 2'
+        },
+        'AB2' => {
+          success: 'Yes',
+          source: :Lighthouse,
+          purpose: 'Purpose 1',
+          study: 'Study 1'
+        },
+        'AB3' => {
+          success: 'Yes',
+          source: :CGaP,
+          purpose: 'Purpose 1',
+          study: 'Study 1, Study 2'
+        }
+      }
+      results = ProcessPlatesController.new.generate_results(barcodes, responses)
+      assert_equal(expected_results, results)
+    end
+  end
 end
diff --git a/test/test_helper.rb b/test/test_helper.rb
index 9bae8e1a..94b76c02 100644
--- a/test/test_helper.rb
+++ b/test/test_helper.rb
@@ -14,4 +14,30 @@ class ActiveSupport::TestCase
   # fixtures :all
 
   # Add more helper methods to be used by all tests here...
+  def generate_success_response(barcode, purpose_name, study_names)
+    {
+      barcode: barcode,
+      code: '201',
+      body: {
+        'data' => {
+          'attributes'=> {
+            'purpose_name' => purpose_name,
+            'study_names' => study_names
+          }
+        }
+      }
+    }
+  end
+
+  def generate_fail_response(barcode)
+    {
+      barcode: barcode,
+      code: '400',
+      body: {
+        'errors': [
+          'No samples for this barcode'
+        ]
+      }
+    }
+  end
 end

From a72038ebfadc424f890bcba861f3678ca01f059c Mon Sep 17 00:00:00 2001
From: Katy Taylor <kt17@sanger.ac.uk>
Date: Fri, 19 Jun 2020 15:17:19 +0100
Subject: [PATCH 13/21] rubocop formatting

---
 test/controllers/process_plates_controller.rb | 10 ++++++----
 test/test_helper.rb                           |  2 +-
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/test/controllers/process_plates_controller.rb b/test/controllers/process_plates_controller.rb
index e78265a9..fcbfbd1d 100644
--- a/test/controllers/process_plates_controller.rb
+++ b/test/controllers/process_plates_controller.rb
@@ -50,19 +50,21 @@ class ProcessPlatesControllerTest < ActiveSupport::TestCase
       assert_equal(expected_results, results)
     end
 
-
     should 'give detailed results if success' do
-      barcodes = ['AB1', 'AB2', 'AB3']
+      barcodes = %w[AB1 AB2 AB3]
 
       responses = {
         lighthouse: [
           generate_success_response('AB1', 'Purpose 1', ['Study 1', 'Study 2']),
           generate_success_response('AB2', 'Purpose 1', ['Study 1']),
-          generate_fail_response('AB3') ],
+          generate_fail_response('AB3')
+        ],
         wrangler: [
           generate_fail_response('AB1'),
           generate_fail_response('AB2'),
-          generate_success_response('AB3', 'Purpose 1', ['Study 1', 'Study 2']) ]}
+          generate_success_response('AB3', 'Purpose 1', ['Study 1', 'Study 2'])
+        ]
+      }
 
       expected_results = {
         'AB1' => {
diff --git a/test/test_helper.rb b/test/test_helper.rb
index 94b76c02..5c0cb058 100644
--- a/test/test_helper.rb
+++ b/test/test_helper.rb
@@ -20,7 +20,7 @@ def generate_success_response(barcode, purpose_name, study_names)
       code: '201',
       body: {
         'data' => {
-          'attributes'=> {
+          'attributes' => {
             'purpose_name' => purpose_name,
             'study_names' => study_names
           }

From 51befa35da35404428fed4f0e046a10460fc23dd Mon Sep 17 00:00:00 2001
From: Katy Taylor <kt17@sanger.ac.uk>
Date: Fri, 19 Jun 2020 15:53:47 +0100
Subject: [PATCH 14/21] refactor to reduce complexity of 'create' method for
 rubocop

---
 app/controllers/process_plates_controller.rb | 42 ++++++++++----------
 1 file changed, 21 insertions(+), 21 deletions(-)

diff --git a/app/controllers/process_plates_controller.rb b/app/controllers/process_plates_controller.rb
index c6de383f..47932312 100644
--- a/app/controllers/process_plates_controller.rb
+++ b/app/controllers/process_plates_controller.rb
@@ -16,39 +16,35 @@ def new
   end
 
   def create
-    bed_verification_model = InstrumentProcessesInstrument.get_bed_verification_type(
-      params[:instrument_barcode],
-      params[:instrument_process]
-    )
-    back_to_new_with_error('Invalid instrument or process') && return if bed_verification_model.nil?
+    bed_verification_model = InstrumentProcessesInstrument.get_bed_verification_type(params[:instrument_barcode], params[:instrument_process])
+    raise 'Invalid instrument or process' if bed_verification_model.nil?
 
     bed_layout_verification = bed_verification_model.new(
       instrument_barcode: params[:instrument_barcode],
       scanned_values: params[:robot],
       api: api
     )
-    unless bed_layout_verification.validate_and_create_audits?(params)
-      errors = bed_layout_verification.errors.values.flatten.join("\n")
-      back_to_new_with_error(errors) && return
-    end
+    raise format_errors(bed_layout_verification) unless bed_layout_verification.validate_and_create_audits?(params)
 
     back_to_new_with_message('Success') && return unless receive_plates_process?(params)
 
+    # here on is relevant to 'receiving plates' only
     # the param is called 'source_plates' but we could be working with tube racks or plates etc.
     barcodes = sanitize_barcodes(params[:source_plates])
-    back_to_new_with_error('No barcodes were provided') && return unless barcodes && !barcodes.empty?
+    raise 'No barcodes were provided' if barcodes.empty?
 
     responses = call_external_services(barcodes)
-
     @results = generate_results(barcodes, responses)
-    back_to_new_with_error('No response from services') && return if @results.empty?
 
-    if all_labware_created?(@results)
-      flash[:notice] = 'All labware were successfully created.'
-    else
-      flash[:error] = 'Some labware were not able to be created.'
-    end
+    display_flash_message(@results)
     render :results
+  rescue StandardError => e
+    flash[:error] = e.message
+    redirect_to(new_process_plate_path)
+  end
+
+  def format_errors(obj)
+    obj.errors.values.flatten.join("\n")
   end
 
   def back_to_new_with_message(message, flash_type = :notice)
@@ -56,10 +52,6 @@ def back_to_new_with_message(message, flash_type = :notice)
     redirect_to(new_process_plate_path)
   end
 
-  def back_to_new_with_error(message)
-    back_to_new_with_message(message, :error)
-  end
-
   # find out if the 'receive_plates' process was executed
   def receive_plates_process?(params)
     @receive_plates_process ||= InstrumentProcess.find_by(id: params[:instrument_process]).key.eql?('slf_receive_plates')
@@ -123,4 +115,12 @@ def all_labware_created?(results)
 
     true
   end
+
+  def display_flash_message(results)
+    if all_labware_created?(results)
+      flash[:notice] = 'All labware were successfully created.'
+    else
+      flash[:error] = 'Some labware were not able to be created.'
+    end
+  end
 end

From f97a98ec1bd03a5872cb9ae88d4f2d45ddca5a26 Mon Sep 17 00:00:00 2001
From: Katy Taylor <kt17@sanger.ac.uk>
Date: Fri, 19 Jun 2020 16:18:44 +0100
Subject: [PATCH 15/21] Change it so the results table is less weird if they
 are scanning plates in that already exist in Sequencescape - it will not show
 an error message, and the column heading is 'Imported?' rather than
 'Success?' - we forgot this is the 'usual' way of receiving plates, as
 opposed to the heron function which is an import

---
 app/controllers/process_plates_controller.rb | 9 ---------
 app/views/process_plates/results.html.haml   | 3 ++-
 2 files changed, 2 insertions(+), 10 deletions(-)

diff --git a/app/controllers/process_plates_controller.rb b/app/controllers/process_plates_controller.rb
index 47932312..d157149c 100644
--- a/app/controllers/process_plates_controller.rb
+++ b/app/controllers/process_plates_controller.rb
@@ -36,7 +36,6 @@ def create
     responses = call_external_services(barcodes)
     @results = generate_results(barcodes, responses)
 
-    display_flash_message(@results)
     render :results
   rescue StandardError => e
     flash[:error] = e.message
@@ -115,12 +114,4 @@ def all_labware_created?(results)
 
     true
   end
-
-  def display_flash_message(results)
-    if all_labware_created?(results)
-      flash[:notice] = 'All labware were successfully created.'
-    else
-      flash[:error] = 'Some labware were not able to be created.'
-    end
-  end
 end
diff --git a/app/views/process_plates/results.html.haml b/app/views/process_plates/results.html.haml
index 8b4e97fd..089b313b 100644
--- a/app/views/process_plates/results.html.haml
+++ b/app/views/process_plates/results.html.haml
@@ -1,10 +1,11 @@
 %h2 Activity Logging
+%h3 Labware import results
 
 %table
   %thead
     %tr
       %th Barcode
-      %th Success?
+      %th Imported?
       %th Source
       %th Purpose
       %th Study

From e05e58fc7566472bf2519e520058707716187e53 Mon Sep 17 00:00:00 2001
From: Katy Taylor <kt17@sanger.ac.uk>
Date: Mon, 22 Jun 2020 10:13:04 +0100
Subject: [PATCH 16/21] rubocop

---
 app/controllers/process_plates_controller.rb | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/app/controllers/process_plates_controller.rb b/app/controllers/process_plates_controller.rb
index b5c19220..6c4f9efe 100644
--- a/app/controllers/process_plates_controller.rb
+++ b/app/controllers/process_plates_controller.rb
@@ -55,9 +55,6 @@ def receive_plates_process?(params)
     @receive_plates_process ||= InstrumentProcess.find_by(id: params[:instrument_process]).key.eql?('slf_receive_plates')
   end
 
-  # rubocop:todo Lint/UselessAssignment
-  # Disabling Lint/UselessAssignment here as I know KT and AS are both actively working on
-  # displaying some of this information to the user. So don't want to create merge issues by removing it.
   # Call any external services - currently lighthouse service for plates from Lighthouse Labs and
   # wrangler for tube racks. If no samples are found in the lighthouse service, try the wrangler
   def call_external_services(barcodes)
@@ -72,7 +69,6 @@ def call_external_services(barcodes)
 
     output
   end
-  # rubocop:enable Lint/UselessAssignment
 
   # Returns a list of unique barcodes by removing blanks and duplicates
   def sanitize_barcodes(barcodes)
@@ -93,10 +89,10 @@ def generate_results(barcodes, responses)
 
     # loop through service responses to update 'output' with successes
     # puts "DEBUG: responses: #{JSON.pretty_generate(responses)}"
-    responses[:lighthouse]&.select { |r| r[:code] == '201' }.each do |r|
+    responses[:lighthouse]&.select { |r| r[:code] == '201' }&.each do |r|
       output[r[:barcode]] = parse_response(r, :Lighthouse)
     end
-    responses[:wrangler]&.select { |r| r[:code] == '201' }.each do |r|
+    responses[:wrangler]&.select { |r| r[:code] == '201' }&.each do |r|
       output[r[:barcode]] = parse_response(r, :CGaP)
     end
 

From 73c12b32ec1d3e1435156c110a64dc2d1e7b9bdb Mon Sep 17 00:00:00 2001
From: Katy Taylor <kt17@sanger.ac.uk>
Date: Mon, 22 Jun 2020 10:17:15 +0100
Subject: [PATCH 17/21] Put barcode count message back in - shouldn't really
 lose this feature.

---
 app/controllers/process_plates_controller.rb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/app/controllers/process_plates_controller.rb b/app/controllers/process_plates_controller.rb
index 6c4f9efe..811faa30 100644
--- a/app/controllers/process_plates_controller.rb
+++ b/app/controllers/process_plates_controller.rb
@@ -35,6 +35,7 @@ def create
     responses = call_external_services(barcodes)
     @results = generate_results(barcodes, responses)
 
+    flash[:notice] = "Scanned #{bed_layout_verification.process_plate&.num_unique_barcodes} barcodes."
     render :results
   rescue StandardError => e
     flash[:error] = e.message

From 78e149b9339bfe45c4a17f3480b8a668827e3798 Mon Sep 17 00:00:00 2001
From: Katy Taylor <kt17@sanger.ac.uk>
Date: Mon, 22 Jun 2020 10:19:46 +0100
Subject: [PATCH 18/21] Got this error when trying to start the server:
 "DEPRECATION WARNING: Using `Rails::Application` subclass to start the server
 is deprecated and will be removed in Rails 6.0. Please change `run
 ProcessTracking::Application` to `run Rails.application` in config.ru.
 (called from require at bin/rails:5) (ActiveSupport::DeprecationException)"

---
 config.ru | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config.ru b/config.ru
index 93277a0e..3476455e 100644
--- a/config.ru
+++ b/config.ru
@@ -2,4 +2,4 @@
 # This file is used by Rack-based servers to start the application.
 
 require ::File.expand_path('../config/environment', __FILE__)
-run ProcessTracking::Application
+run Rails.application

From 39e5cee45fbc901782d14ba9561fa4fc64bcbc53 Mon Sep 17 00:00:00 2001
From: Katy Taylor <kt17@sanger.ac.uk>
Date: Mon, 22 Jun 2020 10:22:23 +0100
Subject: [PATCH 19/21] need to include 'skip_pipeline' for the static assets
 in the public folder

---
 app/views/layouts/application.html.erb | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/app/views/layouts/application.html.erb b/app/views/layouts/application.html.erb
index 7732a292..887281ec 100644
--- a/app/views/layouts/application.html.erb
+++ b/app/views/layouts/application.html.erb
@@ -2,9 +2,10 @@
 <html lang='en'>
 <head>
   <title><%= ProcessTracking::Application.config.name %></title>
-  <%= stylesheet_link_tag(:flash,:formtastic_static,:formtastic_changes,:application) %>
+  <%= stylesheet_link_tag(:application) %>
   <!-- The following are all unmanaged static assets. skip_pipeline: true  Tells rails to jump straight to public -->
-  <%= javascript_include_tag('jquery.min.js','rails.js','application.js', skip_pipeline: true ) %>
+  <%= stylesheet_link_tag(:flash,:formtastic_static,:formtastic_changes, skip_pipeline: true) %>
+  <%= javascript_include_tag('jquery.min.js','rails.js','application.js', skip_pipeline: true) %>
 
   <%= csrf_meta_tag %>
 

From 1f5894bd51cae9d25d125786aace5dff9c6d1ff2 Mon Sep 17 00:00:00 2001
From: Katy Taylor <kt17@sanger.ac.uk>
Date: Mon, 22 Jun 2020 10:37:58 +0100
Subject: [PATCH 20/21] put all the css back in the static folder, because I
 couldn't get it to work using the asset pipeline

---
 app/assets/stylesheets/application.css             | 1 -
 app/views/layouts/application.html.erb             | 5 ++---
 {app/assets => public}/stylesheets/form_custom.css | 0
 3 files changed, 2 insertions(+), 4 deletions(-)
 delete mode 100644 app/assets/stylesheets/application.css
 rename {app/assets => public}/stylesheets/form_custom.css (100%)

diff --git a/app/assets/stylesheets/application.css b/app/assets/stylesheets/application.css
deleted file mode 100644
index d3a82b1f..00000000
--- a/app/assets/stylesheets/application.css
+++ /dev/null
@@ -1 +0,0 @@
-@import "form_custom";
\ No newline at end of file
diff --git a/app/views/layouts/application.html.erb b/app/views/layouts/application.html.erb
index 887281ec..52ff6ca1 100644
--- a/app/views/layouts/application.html.erb
+++ b/app/views/layouts/application.html.erb
@@ -2,9 +2,8 @@
 <html lang='en'>
 <head>
   <title><%= ProcessTracking::Application.config.name %></title>
-  <%= stylesheet_link_tag(:application) %>
-  <!-- The following are all unmanaged static assets. skip_pipeline: true  Tells rails to jump straight to public -->
-  <%= stylesheet_link_tag(:flash,:formtastic_static,:formtastic_changes, skip_pipeline: true) %>
+  <!-- The following are all unmanaged static assets. skip_pipeline: true  Tells raisl to jump straight to public -->
+  <%= stylesheet_link_tag(:flash, :form_custom, :formtastic_static, :formtastic_changes, skip_pipeline: true) %>
   <%= javascript_include_tag('jquery.min.js','rails.js','application.js', skip_pipeline: true) %>
 
   <%= csrf_meta_tag %>
diff --git a/app/assets/stylesheets/form_custom.css b/public/stylesheets/form_custom.css
similarity index 100%
rename from app/assets/stylesheets/form_custom.css
rename to public/stylesheets/form_custom.css

From 4539f0e24d006aec1b66db47e736ac12f6c61136 Mon Sep 17 00:00:00 2001
From: Katy Taylor <kt17@sanger.ac.uk>
Date: Mon, 22 Jun 2020 10:38:26 +0100
Subject: [PATCH 21/21] fix typo

---
 app/views/layouts/application.html.erb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/views/layouts/application.html.erb b/app/views/layouts/application.html.erb
index 52ff6ca1..e27974e7 100644
--- a/app/views/layouts/application.html.erb
+++ b/app/views/layouts/application.html.erb
@@ -2,7 +2,7 @@
 <html lang='en'>
 <head>
   <title><%= ProcessTracking::Application.config.name %></title>
-  <!-- The following are all unmanaged static assets. skip_pipeline: true  Tells raisl to jump straight to public -->
+  <!-- The following are all unmanaged static assets. skip_pipeline: true  Tells rails to jump straight to public -->
   <%= stylesheet_link_tag(:flash, :form_custom, :formtastic_static, :formtastic_changes, skip_pipeline: true) %>
   <%= javascript_include_tag('jquery.min.js','rails.js','application.js', skip_pipeline: true) %>