his_emr_api_lab 2.1.0 → 2.1.2

data/app/services/lab/lims/api/rest_api.rb

@@ -1,15 +1,17 @@
 # frozen_string_literal: true
 
+require 'rest-client'
+
 module Lab
   module Lims
     module Api
       class RestApi
-        class LimsApiError < GatewayError; end
-
+        class LimsApiError < StandardError; end
         class AuthenticationTokenExpired < LimsApiError; end
-
         class InvalidParameters < LimsApiError; end
 
+        START_DATE = Time.parse('2024-09-03').freeze
+
         def initialize(config)
           @config = config
         end
@@ -17,11 +19,11 @@ module Lab
         def create_order(order_dto)
           response = in_authenticated_session do |headers|
             Rails.logger.info("Pushing order ##{order_dto[:tracking_number]} to LIMS")
-
             if order_dto['sample_type'].casecmp?('not_specified')
-              RestClient.post(expand_uri('request_order', api_version: 'v2'), make_create_params(order_dto), headers)
+              RestClient.post(expand_uri('orders/requests', api_version: 'v2'), make_create_params(order_dto),
+                              headers)
             else
-              RestClient.post(expand_uri('create_order'), make_create_params(order_dto), headers)
+              RestClient.post(expand_uri('orders', api_version: 'v2'), make_create_params(order_dto), headers)
             end
           end
 
@@ -37,16 +39,34 @@ module Lab
 
         def acknowledge(acknowledgement_dto)
           Rails.logger.info("Acknowledging order ##{acknowledgement_dto} in LIMS")
+          test_concept = ::ConceptName.find_by_name(acknowledgement_dto.fetch(:test))&.concept
+          if test_concept.nil?
+            return { 'status' => 400,
+                     'message' => "Test concept not found for '#{acknowledgement_dto.fetch(:test)}'" }
+          end
+
           response = in_authenticated_session do |headers|
-            RestClient.post(expand_uri('/acknowledge/test/results/recipient'), acknowledgement_dto, headers)
+            RestClient.post(expand_uri("tests/#{acknowledgement_dto[:tracking_number]}/acknowledge_test_results_receipt", api_version: 'v2'), {
+                              test_type: {
+                                name: test_concept.test_catalogue_name,
+                                nlims_code: test_concept.nlims_code
+                              },
+                              date_acknowledged: acknowledgement_dto[:date_acknowledged],
+                              recipient_type: acknowledgement_dto[:recipient_type],
+                              acknowledged_by: 'emr_at_facility'
+                            }, headers)
           end
           Rails.logger.info("Acknowledged order ##{acknowledgement_dto} in LIMS. Response: #{response}")
           JSON.parse(response)
+        rescue StandardError => e
+          Rails.logger.error("Failed to acknowledge order ##{acknowledgement_dto} in LIMS: #{e.class}")
+          { 'status' => 500, 'message' => e.message }
         end
 
         def update_order(_id, order_dto)
           in_authenticated_session do |headers|
-            RestClient.post(expand_uri('update_order'), make_update_params(order_dto), headers)
+            RestClient.put(expand_uri("orders/#{order_dto[:tracking_number]}", api_version: 'v2'),
+                           make_update_params(order_dto), headers)
           end
 
           update_order_results(order_dto)
@@ -57,35 +77,39 @@ module Lab
         def consume_orders(*_args, patient_id: nil, **_kwargs)
           orders_pending_updates(patient_id).each do |order|
             order_dto = Lab::Lims::OrderSerializer.serialize_order(order)
-
             if order_dto['priority'].nil? || order_dto['sample_type'].casecmp?('not_specified')
               patch_order_dto_with_lims_order!(order_dto, find_lims_order(order.accession_number))
             end
-
             if order_dto['test_results'].empty?
               begin
                 patch_order_dto_with_lims_results!(order_dto, find_lims_results(order.accession_number))
               rescue InvalidParameters => e # LIMS responds with a 401 when a result is not found :(
                 Rails.logger.error("Failed to fetch results for ##{order.accession_number}: #{e.message}")
+                next
               end
             end
 
             yield order_dto, OpenStruct.new(last_seq: 0)
+          rescue RestClient::NotFound
+            Rails.logger.error("Order ##{order.accession_number} not found in LIMS")
+            next
           rescue LimsApiError => e
             Rails.logger.error("Failed to fetch updates for ##{order.accession_number}: #{e.class} - #{e.message}")
             sleep(1)
+          rescue StandardError => e
+            Rails.logger.error("Failed to fetch updates for ##{order.accession_number}: #{e.class} - #{e.message}")
+            next
           end
         end
 
         def delete_order(_id, order_dto)
           tracking_number = order_dto.fetch('tracking_number')
-
-          order_dto['tests'].each do |test|
-            Rails.logger.info("Voiding test '#{test}' (#{tracking_number}) in LIMS")
+          order_dto['tests_map'].each do |test|
+            Rails.logger.info("Voiding test '#{test.name}' (#{tracking_number}) in LIMS")
             in_authenticated_session do |headers|
-              date_voided, voided_status = find_test_status(order_dto, test, 'Voided')
+              date_voided, voided_status = find_test_status(order_dto, test.name, 'Voided')
               params = make_void_test_params(tracking_number, test, voided_status['updated_by'], date_voided)
-              RestClient.post(expand_uri('update_test'), params, headers)
+              RestClient.put(expand_uri("tests/#{tracking_number}", api_version: 'v2'), params.to_json, headers)
             end
           end
         end
@@ -172,7 +196,8 @@ module Lab
         #   Lims::ApiError - Thrown when we couldn't make sense of the error
         def check_response!(response)
           body = JSON.parse(response.body)
-          return response if body['status'] == 200
+
+          return response if [200, 201].include?(response.code)
 
           Rails.logger.error("Lims Api Error: #{response.body}")
 
@@ -200,28 +225,51 @@ module Lab
         # Converts an OrderDto to parameters for POST /create_order
         def make_create_params(order_dto)
           {
-            tracking_number: order_dto.fetch(:tracking_number),
-            district: current_district,
-            health_facility_name: order_dto.fetch(:sending_facility),
-            first_name: order_dto.fetch(:patient).fetch(:first_name),
-            last_name: order_dto.fetch(:patient).fetch(:last_name),
-            phone_number: order_dto.fetch(:patient).fetch(:phone_number),
-            gender: order_dto.fetch(:patient).fetch(:gender),
-            arv_number: order_dto.fetch(:patient).fetch(:arv_number),
-            art_regimen: order_dto.fetch(:patient).fetch(:art_regimen),
-            art_start_date: order_dto.fetch(:patient).fetch(:art_start_date),
-            date_of_birth: order_dto.fetch(:patient).fetch(:dob),
-            national_patient_id: order_dto.fetch(:patient).fetch(:id),
-            requesting_clinician: requesting_clinician(order_dto),
-            sample_type: order_dto.fetch(:sample_type),
-            tests: order_dto.fetch(:tests),
-            date_sample_drawn: sample_drawn_date(order_dto),
-            sample_priority: order_dto.fetch(:priority) || 'Routine',
-            sample_status: order_dto.fetch(:sample_status),
-            target_lab: order_dto.fetch(:receiving_facility),
-            order_location: order_dto.fetch(:order_location) || 'Unknown',
-            who_order_test_first_name: order_dto.fetch(:who_order_test).fetch(:first_name),
-            who_order_test_last_name: order_dto.fetch(:who_order_test).fetch(:last_name)
+            order: {
+              tracking_number: order_dto.fetch(:tracking_number),
+              district: current_district,
+              health_facility_name: order_dto.fetch(:sending_facility),
+              sending_facility: order_dto.fetch(:sending_facility),
+              arv_number: order_dto.fetch(:patient).fetch(:arv_number),
+              art_regimen: order_dto.fetch(:patient).fetch(:art_regimen),
+              art_start_date: order_dto.fetch(:patient).fetch(:art_start_date),
+              requesting_clinician: requesting_clinician(order_dto),
+              sample_type: order_dto.fetch(:sample_type_map),
+              date_sample_drawn: sample_drawn_date(order_dto),
+              date_created: sample_drawn_date(order_dto),
+              priority: order_dto.fetch(:priority) || 'Routine',
+              sample_status: {
+                name: order_dto.fetch(:sample_status)
+              },
+              target_lab: order_dto.fetch(:receiving_facility),
+              order_location: order_dto.fetch(:order_location) || 'Unknown',
+              who_order_test_first_name: order_dto.fetch(:who_order_test).fetch(:first_name),
+              who_order_test_last_name: order_dto.fetch(:who_order_test).fetch(:last_name),
+              requested_by: "#{order_dto.fetch(:who_order_test).fetch(:first_name)} #{order_dto.fetch(:who_order_test).fetch(:last_name)}",
+              drawn_by: {
+                id: order_dto.fetch(:who_order_test).fetch(:id),
+                name: "#{order_dto.fetch(:who_order_test).fetch(:first_name)} #{order_dto.fetch(:who_order_test).fetch(:last_name)}"
+              },
+              clinical_history: order_dto.fetch(:clinical_history)
+            },
+            patient: {
+              national_patient_id: order_dto.fetch(:patient).fetch(:id),
+              first_name: order_dto.fetch(:patient).fetch(:first_name),
+              last_name: order_dto.fetch(:patient).fetch(:last_name),
+              phone_number: order_dto.fetch(:patient).fetch(:phone_number),
+              gender: order_dto.fetch(:patient).fetch(:gender),
+              date_of_birth: order_dto.fetch(:patient).fetch(:dob)
+            },
+            tests: order_dto.fetch(:tests_map).map do |test|
+              concept = ::Concept.find(test.concept_id)
+              {
+                test_type: {
+                  name: concept.test_catalogue_name,
+                  nlims_code: concept.nlims_code,
+                  method_of_testing: test&.test_method&.name
+                }
+              }
+            end
           }
         end
 
@@ -229,13 +277,11 @@ module Lab
         # Converts an OrderDto to parameters for POST /update_order
         def make_update_params(order_dto)
           date_updated, status = sample_drawn_status(order_dto)
-
           {
-            tracking_number: order_dto.fetch(:tracking_number),
-            who_updated: status.fetch(:updated_by),
-            date_updated:,
-            specimen_type: order_dto.fetch(:sample_type),
-            status: 'specimen_collected'
+            status: 'specimen_collected',
+            time_updated: date_updated,
+            sample_type: order_dto.fetch(:sample_type_map),
+            updated_by: status.fetch(:updated_by)
           }
         end
 
@@ -283,17 +329,19 @@ module Lab
         def find_lims_order(tracking_number)
           response = in_authenticated_session do |headers|
             Rails.logger.info("Fetching order ##{tracking_number}")
-            RestClient.get(expand_uri("query_order_by_tracking_number/#{tracking_number}"), headers)
+            RestClient.get(expand_uri("orders/#{tracking_number}", api_version: 'v2'), headers)
           end
 
           Rails.logger.info("Order ##{tracking_number} found... Parsing...")
           JSON.parse(response).fetch('data')
+        rescue RestClient::NotFound
+          raise RestClient::NotFound, "Order ##{tracking_number} not found in LIMS"
         end
 
         def nlims_order_exists?(tracking_number)
           response = in_authenticated_session do |headers|
             Rails.logger.info("Verifying order ##{tracking_number}")
-            RestClient.get(expand_uri("verify_order_tracking_number_exist/#{tracking_number}"), headers)
+            RestClient.get(expand_uri("orders/#{tracking_number}", api_version: 'v2'), headers)
           end
 
           Rails.logger.info("Order ##{tracking_number} verified... Parsing...")
@@ -303,11 +351,21 @@ module Lab
         def find_lims_results(tracking_number)
           response = in_authenticated_session do |headers|
             Rails.logger.info("Fetching results for order ##{tracking_number}")
-            RestClient.get(expand_uri("query_results_by_tracking_number/#{tracking_number}"), headers)
+            RestClient.get(expand_uri("orders/#{tracking_number}", api_version: 'v2'), headers)
+          end
+
+          Rails.logger.info("Found order ##{tracking_number}")
+          data = JSON.parse(response)
+
+          if data.fetch('data').fetch('tests').all? do |test|
+            test.fetch('test_results').blank?
           end
+            raise InvalidParameters, "No results found for order ##{tracking_number}"
+          end
+
+          Rails.logger.info("Result for order ##{tracking_number} found...")
 
-          Rails.logger.info("Result for order ##{tracking_number} found... Parsing...")
-          JSON.parse(response).fetch('data').fetch('results')
+          data.fetch('data').fetch('tests')
         end
 
         ##
@@ -318,25 +376,65 @@ module Lab
             '_id' => order_dto[:tracking_number],
             '_rev' => 0,
             'test_results' => results.each_with_object({}) do |result, formatted_results|
-              test_name, measures = result
-              result_date = measures.delete('result_date')
+              test_type = result.delete('test_type')
+              if test_type.nil?
+                Rails.logger.error("ERROR: test_type is nil for result: #{result.inspect}")
+                next
+              end
+              results = result.delete('test_results')
+              if results.nil?
+                Rails.logger.error("ERROR: test_results is nil for result: #{result.inspect}")
+                next
+              end
+
+              test_name = test_type['name']
+              Rails.logger.debug("test_name: #{test_name}")
+
+              if test_name.nil?
+                Rails.logger.error("ERROR: test_name is nil, test_type was: #{test_type.inspect}")
+                next
+              end
 
               formatted_results[test_name] = {
-                results: measures.each_with_object({}) do |measure, processed_measures|
-                  processed_measures[measure[0]] = { 'result_value' => measure[1] }
+                results: results.each_with_object({}) do |result, processed_measures|
+                  measure = result['measure']
+                  if measure.nil?
+                    Rails.logger.error("  ERROR: measure is nil for result: #{result.inspect}")
+                    next
+                  end
+                  result_data = result['result']
+                  if result_data.nil?
+                    Rails.logger.error("  ERROR: result_data is nil for result: #{result.inspect}")
+                    next
+                  end
+
+                  measure_name = measure['name']
+                  result_value = result_data['value']
+
+                  if measure_name.nil?
+                    Rails.logger.error("  ERROR: measure_name is nil, measure was: #{measure.inspect}")
+                    next
+                  end
+
+                  processed_measures[measure_name] = { 'result_value' => result_value }
                 end,
-                result_date:,
+                result_date: results&.first&.dig('result', 'result_date'),
                 result_entered_by: {}
               }
             end
           )
+        rescue StandardError => e
+          Rails.logger.error("EXCEPTION in patch_order_dto_with_lims_results!: #{e.class} - #{e.message}")
+          Rails.logger.error("Backtrace: #{e.backtrace.first(10).join("\n")}")
+          raise
         end
 
         def patch_order_dto_with_lims_order!(order_dto, lims_order)
+          order = lims_order['order']
           order_dto.merge!(
-            'sample_type' => lims_order['other']['sample_type'],
-            'sample_status' => lims_order['other']['specimen_status'],
-            'priority' => lims_order['other']['priority']
+            'sample_type' => order['sample_type']['name'],
+            'sample_status' => order['sample_status']['name'],
+            'priority' => order['priority']
           )
         end
 
@@ -348,27 +446,32 @@ module Lab
             in_authenticated_session do |headers|
               params = make_update_test_params(order_dto['tracking_number'], test_name, results)
 
-              RestClient.post(expand_uri('update_test'), params, headers)
+              RestClient.post(expand_uri("tests/#{order_dto['tracking_number']}", api_version: 'v2'), params, headers)
             end
           end
         end
 
-        def make_update_test_params(tracking_number, test_name, results, test_status = 'Drawn')
+        def make_update_test_params(_tracking_number, test, results, test_status = 'Drawn')
           {
-            tracking_number:,
-            test_name:,
-            result_date: results['result_date'],
+            test_status:,
             time_updated: results['result_date'],
-            who_updated: {
-              first_name: results[:result_entered_by][:first_name],
-              last_name: results[:result_entered_by][:last_name],
-              id_number: results[:result_entered_by][:id]
+            test_type: {
+              name: ::Concept.find(test.concept_id).test_catalogue_name,
+              nlims_code: ::Concept.find(test.concept_id).nlims_code
             },
-            test_status:,
-            results: results['results']&.each_with_object({}) do |measure, formatted_results|
+            test_results: results['results'].map do |measure, _value|
               measure_name, measure_value = measure
-
-              formatted_results[measure_name] = measure_value['result_value']
+              {
+                measure: {
+                  name: measure_name,
+                  nlims_code: ::ConceptAttribute.find_by(value_reference: measure_name,
+                                                         attribute_type: ConceptAttributeType.nlims_code)&.value_reference
+                },
+                result: {
+                  value: measure_value,
+                  result_date: results['result_date']
+                }
+              }
             end
           }
         end
@@ -387,19 +490,23 @@ module Lab
           nil
         end
 
-        def make_void_test_params(tracking_number, test_name, voided_by, void_date = nil)
+        def make_void_test_params(_tracking_number, test, voided_by, void_date = nil)
           void_date ||= Time.now
 
           {
-            tracking_number:,
-            test_name:,
+            test_status: 'voided',
             time_updated: void_date,
-            who_updated: {
-              first_name: voided_by[:first_name],
-              last_name: voided_by[:last_name],
-              id_number: voided_by[:id]
+            test_type: {
+              name: ::Concept.find(test.concept_id).test_catalogue_name,
+              nlims_code: ::Concept.find(test.concept_id).nlims_code
             },
-            test_status: 'voided'
+            status_trail: [
+              updated_by: {
+                first_name: voided_by[:first_name],
+                last_name: voided_by[:last_name],
+                id_number: voided_by[:id]
+              }
+            ]
           }
         end
 
@@ -446,4 +553,362 @@ module Lab
       end
     end
   end
+
+  def delete_order(_id, order_dto)
+    tracking_number = order_dto.fetch('tracking_number')
+
+    order_dto['tests'].each do |test|
+      Rails.logger.info("Voiding test '#{test}' (#{tracking_number}) in LIMS")
+      in_authenticated_session do |headers|
+        date_voided, voided_status = find_test_status(order_dto, test, 'Voided')
+        params = make_void_test_params(tracking_number, test, voided_status['updated_by'], date_voided)
+        RestClient.post(expand_uri('update_test'), params, headers)
+      end
+    end
+  end
+
+  def verify_tracking_number(tracking_number)
+    find_lims_order(tracking_number)
+  rescue InvalidParameters => e
+    Rails.logger.error("Failed to verify tracking number #{tracking_number}: #{e.message}")
+    false
+  end
+
+  private
+
+  attr_reader :config
+
+  MAX_LIMS_RETRIES = 5 # LIMS API Calls can only fail this number of times before we give up on it
+
+  ##
+  # Execute LIMS API calls within an authenticated session.
+  #
+  # Method automatically checks authenticates with LIMS if necessary and passes
+  # down the necessary headers for authentication to the REST call being made.
+  #
+  # Example:
+  #
+  #   response = in_authenticated_session do |headers|
+  #     RestClient.get(expand_uri('query_results_by_tracking_number/XXXXXX'), headers)
+  #   end
+  #
+  #   pp JSON.parse(response.body) if response.code == 200
+  def in_authenticated_session
+    retries ||= MAX_LIMS_RETRIES
+
+    self.authentication_token = authenticate unless authentication_token
+
+    response = yield 'token' => authentication_token, 'Content-type' => 'application/json'
+    check_response!(response)
+  rescue AuthenticationTokenExpired => e
+    self.authentication_token = nil
+    retry if (retries -= 1).positive?
+  rescue RestClient::ExceptionWithResponse => e
+    Rails.logger.error("LIMS Error: #{e.response&.code} - #{e.response&.body}")
+    raise e unless e.response&.code == 401
+
+    self.authentication_token = nil
+    retry if (retries -= 1).positive?
+  end
+
+  def authenticate
+    username = config.fetch(:username)
+    password = config.fetch(:password)
+
+    Rails.logger.debug("Authenticating with LIMS as: #{username}")
+    response = RestClient.get(expand_uri("re_authenticate/#{username}/#{password}"),
+                              headers: { 'Content-type' => 'application/json' })
+    response_body = JSON.parse(response.body)
+
+    if response_body['status'] == 401
+      Rails.logger.error("Failed to authenticate with LIMS as #{config.fetch(:username)}: #{response_body['message']}")
+      raise LimsApiError, 'LIMS authentication failed'
+    end
+
+    response_body['data']['token']
+  end
+
+  def authentication_token=(token)
+    Thread.current[:lims_authentication_token] = token
+  end
+
+  def authentication_token
+    Thread.current[:lims_authentication_token]
+  end
+
+  ##
+  # Examines a response from LIMS to check if token has expired.
+  #
+  # LIMS' doesn't properly use HTTP status codes; the codes are embedded in the
+  # response body. 200 is used for success responses and 401 for everything else.
+  # We have this work around to examine the response body and
+  # throw errors accordingly. The following are the errors thrown:
+  #
+  #   Lims::AuthenticationTokenExpired
+  #   Lims::InvalidParameters
+  #   Lims::ApiError - Thrown when we couldn't make sense of the error
+  def check_response!(response)
+    body = JSON.parse(response.body)
+    return response if body['status'] == 200
+
+    Rails.logger.error("Lims Api Error: #{response.body}")
+
+    raise LimsApiError, "#{body['status']} - #{body['message']}" if body['status'] != 401
+
+    if body['message'].match?(/token expired/i)
+      raise AuthenticationTokenExpired, "Authentication token expired: #{body['message']}"
+    end
+
+    raise InvalidParameters, body['message']
+  end
+
+  ##
+  # Takes a LIMS API relative URI and converts it to a full URL.
+  def expand_uri(uri, api_version: 'v1')
+    protocol = config.fetch(:protocol)
+    host = config.fetch(:host)
+    port = config.fetch(:port)
+    uri = uri.gsub(%r{^/+}, '')
+
+    "#{protocol}://#{host}:#{port}/api/#{api_version}/#{uri}"
+  end
+
+  ##
+  # Converts an OrderDto to parameters for POST /create_order
+  def make_create_params(order_dto)
+    {
+      tracking_number: order_dto.fetch(:tracking_number),
+      district: current_district,
+      health_facility_name: order_dto.fetch(:sending_facility),
+      first_name: order_dto.fetch(:patient).fetch(:first_name),
+      last_name: order_dto.fetch(:patient).fetch(:last_name),
+      phone_number: order_dto.fetch(:patient).fetch(:phone_number),
+      gender: order_dto.fetch(:patient).fetch(:gender),
+      arv_number: order_dto.fetch(:patient).fetch(:arv_number),
+      art_regimen: order_dto.fetch(:patient).fetch(:art_regimen),
+      art_start_date: order_dto.fetch(:patient).fetch(:art_start_date),
+      date_of_birth: order_dto.fetch(:patient).fetch(:dob),
+      national_patient_id: order_dto.fetch(:patient).fetch(:id),
+      requesting_clinician: requesting_clinician(order_dto),
+      sample_type: order_dto.fetch(:sample_type),
+      tests: order_dto.fetch(:tests),
+      date_sample_drawn: sample_drawn_date(order_dto),
+      sample_priority: order_dto.fetch(:priority) || 'Routine',
+      sample_status: order_dto.fetch(:sample_status),
+      target_lab: order_dto.fetch(:receiving_facility),
+      order_location: order_dto.fetch(:order_location) || 'Unknown',
+      who_order_test_first_name: order_dto.fetch(:who_order_test).fetch(:first_name),
+      who_order_test_last_name: order_dto.fetch(:who_order_test).fetch(:last_name)
+    }
+  end
+
+  ##
+  # Converts an OrderDto to parameters for POST /update_order
+  def make_update_params(order_dto)
+    date_updated, status = sample_drawn_status(order_dto)
+
+    {
+      tracking_number: order_dto.fetch(:tracking_number),
+      who_updated: status.fetch(:updated_by),
+      date_updated: date_updated,
+      specimen_type: order_dto.fetch(:sample_type),
+      status: 'specimen_collected'
+    }
+  end
+
+  def current_district
+    health_centre = Location.current_health_center
+    raise 'Current health centre not set' unless health_centre
+
+    district = health_centre.district || Lab::Lims::Config.application['district']
+
+    unless district
+      health_centre_name = "##{health_centre.id} - #{health_centre.name}"
+      raise "Current health centre district not set: #{health_centre_name}"
+    end
+
+    district
+  end
+
+  ##
+  # Extracts sample drawn status from an OrderDto
+  def sample_drawn_status(order_dto)
+    order_dto[:sample_statuses].each do |trail_entry|
+      date, status = trail_entry.each_pair.find { |_date, status| status['status'].casecmp?('Drawn') }
+      next unless date
+
+      return Date.strptime(date, '%Y%m%d%H%M%S').strftime('%Y-%m-%d'), status
+    end
+
+    [order_dto['date_created'], nil]
+  end
+
+  ##
+  # Extracts a sample drawn date from a LIMS OrderDto.
+  def sample_drawn_date(order_dto)
+    sample_drawn_status(order_dto).first
+  end
+
+  ##
+  # Extracts the requesting clinician from a LIMS OrderDto
+  def requesting_clinician(order_dto)
+    orderer = order_dto[:who_order_test]
+
+    "#{orderer[:first_name]} #{orderer[:last_name]}"
+  end
+
+  def find_lims_order(tracking_number)
+    response = in_authenticated_session do |headers|
+      Rails.logger.info("Fetching order ##{tracking_number}")
+      RestClient.get(expand_uri("query_order_by_tracking_number/#{tracking_number}"), headers)
+    end
+
+    Rails.logger.info("Order ##{tracking_number} found... Parsing...")
+    JSON.parse(response).fetch('data')
+  end
+
+  def find_lims_results(tracking_number)
+    response = in_authenticated_session do |headers|
+      Rails.logger.info("Fetching results for order ##{tracking_number}")
+      RestClient.get(expand_uri("query_results_by_tracking_number/#{tracking_number}"), headers)
+    end
+
+    Rails.logger.info("Result for order ##{tracking_number} found... Parsing...")
+    JSON.parse(response).fetch('data').fetch('results')
+  end
+
+  ##
+  # Make a copy of the order_dto with the results from LIMS parsed
+  # and appended to it.
+  def patch_order_dto_with_lims_results!(order_dto, results)
+    order_dto.merge!(
+      '_id' => order_dto[:tracking_number],
+      '_rev' => 0,
+      'test_results' => results.each_with_object({}) do |result, formatted_results|
+        test_name, measures = result
+        result_date = measures.delete('result_date')
+
+        formatted_results[test_name] = {
+          results: measures.each_with_object({}) do |measure, processed_measures|
+            processed_measures[measure[0]] = { 'result_value' => measure[1] }
+          end,
+          result_date: result_date,
+          result_entered_by: {}
+        }
+      end
+    )
+  end
+
+  def patch_order_dto_with_lims_order!(order_dto, lims_order)
+    order_dto.merge!(
+      'sample_type' => lims_order['other']['sample_type'],
+      'sample_status' => lims_order['other']['specimen_status'],
+      'priority' => lims_order['other']['priority']
+    )
+  end
+
+  def update_order_results(order_dto)
+    return nil if order_dto['test_results'].nil? || order_dto['test_results'].empty?
+
+    order_dto['test_results'].each do |test_name, results|
+      Rails.logger.info("Pushing result for order ##{order_dto['tracking_number']}")
+      in_authenticated_session do |headers|
+        params = make_update_test_params(order_dto['tracking_number'], test_name, results)
+
+        RestClient.post(expand_uri('update_test'), params, headers)
+      end
+    end
+  end
+
+  def make_update_test_params(tracking_number, test_name, results, test_status = 'Drawn')
+    {
+      tracking_number: tracking_number,
+      test_name: test_name,
+      result_date: results['result_date'],
+      time_updated: results['result_date'],
+      who_updated: {
+        first_name: results[:result_entered_by][:first_name],
+        last_name: results[:result_entered_by][:last_name],
+        id_number: results[:result_entered_by][:id]
+      },
+      test_status: test_status,
+      results: results['results']&.each_with_object({}) do |measure, formatted_results|
+        measure_name, measure_value = measure
+
+        formatted_results[measure_name] = measure_value['result_value']
+      end
+    }
+  end
+
+  def find_test_status(order_dto, target_test, target_status)
+    order_dto['test_statuses'].each do |test, statuses|
+      next unless test.casecmp?(target_test)
+
+      statuses.each do |date, status|
+        next unless status['status'].casecmp?(target_status)
+
+        return [Date.strptime(date, '%Y%m%d%H%M%S'), status]
+      end
+    end
+
+    nil
+  end
+
+  def make_void_test_params(tracking_number, test_name, voided_by, void_date = nil)
+    void_date ||= Time.now
+
+    {
+      tracking_number: tracking_number,
+      test_name: test_name,
+      time_updated: void_date,
+      who_updated: {
+        first_name: voided_by[:first_name],
+        last_name: voided_by[:last_name],
+        id_number: voided_by[:id]
+      },
+      test_status: 'voided'
+    }
+  end
+
+  def orders_pending_updates(patient_id = nil)
+    Rails.logger.info('Looking for orders that need to be updated...')
+    orders = {}
+
+    orders_without_specimen(patient_id).each { |order| orders[order.order_id] = order }
+    orders_without_results(patient_id).each { |order| orders[order.order_id] = order }
+    orders_without_reason(patient_id).each { |order| orders[order.order_id] = order }
+
+    orders.values
+  end
+
+  def orders_without_specimen(patient_id = nil)
+    Rails.logger.debug('Looking for orders without a specimen')
+    unknown_specimen = ConceptName.where(name: Lab::Metadata::UNKNOWN_SPECIMEN)
+                                  .select(:concept_id)
+    orders = Lab::LabOrder.where(concept_id: unknown_specimen, date_created: START_DATE..(Date.today + 1.day))
+                          .where.not(accession_number: Lab::LimsOrderMapping.select(:lims_id))
+    orders = orders.where(patient_id: patient_id) if patient_id
+
+    orders
+  end
+
+  def orders_without_results(patient_id = nil)
+    Rails.logger.debug('Looking for orders without a result')
+    # Lab::OrdersSearchService.find_orders_without_results(patient_id: patient_id)
+    #                         .where.not(accession_number: Lab::LimsOrderMapping.select(:lims_id).where("pulled_at IS NULL"))
+    Lab::OrdersSearchService.find_orders_without_results(patient_id: patient_id)
+                            .where(order_id: Lab::LimsOrderMapping.select(:order_id), date_created: START_DATE..(Date.today + 1.day))
+  end
+
+  def orders_without_reason(patient_id = nil)
+    Rails.logger.debug('Looking for orders without a reason for test')
+    orders = Lab::LabOrder.joins(:reason_for_test)
+                          .merge(Observation.where(value_coded: nil, value_text: nil))
+                          .where(date_created: START_DATE..(Date.today + 1.day))
+                          .limit(1000)
+                          .where.not(accession_number: Lab::LimsOrderMapping.select(:lims_id))
+    orders = orders.where(patient_id: patient_id, date_created: START_DATE..(Date.today + 1.day)) if patient_id
+
+    orders
+  end
 end