Merge pull request #170 from sanger/GPL-442-feedback-scanning-plates

Gpl 442 feedback scanning plates

app/controllers/process_plates_controller.rb

@@ -15,56 +15,61 @@ 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')
-
-          call_external_services(barcodes) if barcodes && receive_plates_process
-
-          # add a flash on the page for the number of unique barcodes scanned in
-          num_unique_barcodes = bed_layout_verification.process_plate&.num_unique_barcodes
-          flash[:notice] = if num_unique_barcodes
-                             "Success - #{num_unique_barcodes} unique plate(s) scanned"
-                           else
-                             'Success'
-                           end
-        else
-          flash[:error] = bed_layout_verification.errors.values.flatten.join("\n")
-        end
-      end
-      format.html { redirect_to(new_process_plate_path) }
-    end
+    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
+    )
+    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])
+    raise 'No barcodes were provided' if barcodes.empty?
+
+    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
+    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)
+    flash[flash_type] = message
+    redirect_to(new_process_plate_path)
+  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')
   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)
+    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
-  # rubocop:enable Lint/UselessAssignment
 
   # Returns a list of unique barcodes by removing blanks and duplicates
   def sanitize_barcodes(barcodes)
@@ -77,4 +82,36 @@ def all_created?(responses)
 
     responses.all? { |response| response[:code] == '201' }
   end
+
+  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
+    # 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
+    responses[:wrangler]&.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

app/views/admin/instruments/index.html.haml

@@ -1,4 +1,4 @@
-%h1 "Manage Instruments"
+%h1 Manage Instruments
 
 %table#instruments
  %thead

app/views/admin/processes/index.html.haml

@@ -1,4 +1,4 @@
-%h1 "Manage Processes"
+%h1 Manage Processes
 
 %table#processes
  %thead

app/views/layouts/application.html.erb

@@ -2,9 +2,9 @@
 <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 -->
-  <%= stylesheet_link_tag(:flash,:form,:formtastic_static,:formtastic_changes, skip_pipeline: true ) %>
-  <%= javascript_include_tag('jquery.min.js','rails.js','application.js', skip_pipeline: true ) %>
+  <!-- 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) %>
 
   <%= csrf_meta_tag %>
 

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($) {
 

app/views/process_plates/results.html.haml

@@ -0,0 +1,27 @@
+%h2 Activity Logging
+%h3 Labware import results
+
+%table
+  %thead
+    %tr
+      %th Barcode
+      %th Imported?
+      %th Source
+      %th Purpose
+      %th Study
+  %tbody
+    - @results.each do |barcode, details|
+      %tr
+        %td
+          = barcode
+        %td
+          = details[:success]
+        %td
+          = details[:source]
+        %td
+          = details[:purpose]
+        %td
+          = details[:study]
+
+%br
+= link_to 'Scan more labware', new_process_plate_path

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

config/environments/development.rb

@@ -47,7 +47,7 @@
   config.admin_email = '[email protected]'
 
   # 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'

config/environments/test.rb

@@ -45,7 +45,7 @@
   config.admin_email = '[email protected]'
 
   # 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'

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: 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
+    body
+  end
 end

lib/wrangler.rb

@@ -1,5 +1,7 @@
 # frozen_string_literal: true
 
+require 'json'
+
 class Wrangler
   require 'net/http'
 
@@ -18,7 +20,7 @@ def self.call_api(barcodes)
           http.request(req)
         end
 
-        responses << { barcode: barcode, code: res.code }
+        responses << { barcode: barcode, code: res.code, body: Wrangler.parse_body(res.body) }
       end
     rescue StandardError => e
       Rails.logger.error(e)
@@ -29,4 +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
+    body
+  end
 end

public/stylesheets/form.css → public/stylesheets/form_custom.css

@@ -62,5 +62,15 @@ li#beds_and_plates ul{
  padding: 0px;
 }
 
+table, td, th {
+  border: 1px solid #ddd;
+  text-align: left;
+}
 
+table {
+  border-collapse: collapse;
+}
 
+th, td {
+  padding: 15px;
+}