Class: Lab::Lims::Api::RestApi

Inherits:
Object
  • Object
show all
Defined in:
app/services/lab/lims/api/rest_api.rb

Defined Under Namespace

Classes: AuthenticationTokenExpired, InvalidParameters, LimsApiError

Constant Summary collapse

START_DATE = 
Time.parse('2024-09-03').freeze

Instance Method Summary collapse

Constructor Details

#initialize(config) ⇒ RestApi

Returns a new instance of RestApi.



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# File 'app/services/lab/lims/api/rest_api.rb', line 15

def initialize(config)
  @config = config
end

Instance Method Details

#acknowledge(acknowledgement_dto) ⇒ Object 



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# File 'app/services/lab/lims/api/rest_api.rb', line 40

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("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

#consume_orders(*_args, patient_id: nil, start_date: nil, **_kwargs) ⇒ Object 



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# File 'app/services/lab/lims/api/rest_api.rb', line 77

def consume_orders(*_args, patient_id: nil, start_date: nil, **_kwargs)
  orders_pending_updates(patient_id, start_date: start_date).each do |order|
    order_dto = Lab::Lims::OrderSerializer.serialize_order(order)

    # Always fetch the full order from NLIMS to get status trails
    begin
      lims_order = find_lims_order(order.accession_number)
      patch_order_dto_with_lims_order!(order_dto, lims_order)

      Rails.logger.debug("NLIMS order structure for #{order.accession_number}:")
      Rails.logger.debug("  Has 'order' key: #{lims_order.key?('order')}")
      Rails.logger.debug("  Has 'data' key: #{lims_order.key?('data')}")
      Rails.logger.debug("  Top level keys: #{lims_order.keys.inspect}")

      # Also extract status trails from the NLIMS order
      # Note: NLIMS might return order data under 'order' or 'data.order'
      order_data = lims_order['order'] || lims_order.dig('data', 'order') || lims_order

      if order_data && order_data['status_trail']
        Rails.logger.info("Found #{order_data['status_trail'].size} order status trail entries from NLIMS")
        order_dto[:sample_statuses] ||= []
        # Convert NLIMS status trail to the format expected by PullWorker
        # Note: sample_statuses must be an array of single-key hashes
        order_data['status_trail'].each do |trail|
          # Convert ISO 8601 timestamp to YYYYMMDDHHmmss format
          timestamp_key = convert_timestamp_to_key(trail['timestamp'])
          order_dto[:sample_statuses] << {
            timestamp_key => {
              'status_id' => trail['status_id'],
              'status' => trail['status'],
              'updated_by' => trail['updated_by']
            }
          }
          Rails.logger.debug("  Added order status: #{trail['status']} at #{timestamp_key}")
        end
        Rails.logger.debug("Final sample_statuses: #{order_dto[:sample_statuses].inspect}")
      else
        Rails.logger.warn("No order status_trail found in NLIMS response for #{order.accession_number}")
        Rails.logger.debug("Order data keys: #{order_data&.keys&.inspect}")
      end

      # Extract test status trails from NLIMS tests
      tests_data = lims_order['tests'] || lims_order.dig('data', 'tests') || []
      if tests_data.is_a?(Array)
        Rails.logger.debug("Processing #{tests_data.size} tests from NLIMS")
        order_dto['test_statuses'] ||= {}
        tests_data.each do |test|
          next unless test['status_trail'].is_a?(Array)

          test_name = test.dig('test_type', 'name')
          next unless test_name

          Rails.logger.debug("  Found #{test['status_trail'].size} status trail entries for test #{test_name}")
          order_dto['test_statuses'][test_name] ||= {}
          test['status_trail'].each do |trail|
            # Convert ISO 8601 timestamp to YYYYMMDDHHmmss format
            timestamp_key = convert_timestamp_to_key(trail['timestamp'])
            order_dto['test_statuses'][test_name][timestamp_key] = {
              'status_id' => trail['status_id'],
              'status' => trail['status'],
              'updated_by' => trail['updated_by']
            }
          end
        end
      end
    rescue RestClient::NotFound
      Rails.logger.warn("Order ##{order.accession_number} not found in NLIMS, using local data only")
    end

    # Try to fetch results if available
    if order_dto['test_results'].empty?
      begin
        patch_order_dto_with_lims_results!(order_dto, find_lims_results(order.accession_number))
      rescue InvalidParameters => e
        Rails.logger.info("No results available for ##{order.accession_number}: #{e.message}")
        # Don't skip - continue processing to save status trails
      rescue RestClient::NotFound
        Rails.logger.info("No results found for ##{order.accession_number}")
        # Don't skip - continue processing to save status trails
      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

#create_order(order_dto) ⇒ Object 



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# File 'app/services/lab/lims/api/rest_api.rb', line 19

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('orders/requests', api_version: 'v2'), make_create_params(order_dto),
                      headers)
    else
      RestClient.post(expand_uri('orders', api_version: 'v2'), make_create_params(order_dto), headers)
    end
  end

  data = JSON.parse(response.body)
  update_order_results(order_dto) unless data['message'].casecmp?('Order already available')

  ActiveSupport::HashWithIndifferentAccess.new(
    id: order_dto.fetch(:_id, order_dto[:tracking_number]),
    rev: 0,
    tracking_number: order_dto[:tracking_number]
  )
end

#delete_order(_id, order_dto) ⇒ Object 



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# File 'app/services/lab/lims/api/rest_api.rb', line 172

def delete_order(_id, order_dto)
  tracking_number = order_dto.fetch('tracking_number')
  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.name, 'Voided')
      params = make_void_test_params(tracking_number, test, voided_status['updated_by'], date_voided)
      RestClient.put(expand_uri("tests/#{tracking_number}", api_version: 'v2'), params.to_json, headers)
    end
  end
end

#update_order(_id, order_dto) ⇒ Object 



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# File 'app/services/lab/lims/api/rest_api.rb', line 66

def update_order(_id, order_dto)
  in_authenticated_session do |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)

  { tracking_number: order_dto[:tracking_number] }
end

#verify_tracking_number(tracking_number) ⇒ Object 



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# File 'app/services/lab/lims/api/rest_api.rb', line 184

def verify_tracking_number(tracking_number)
  nlims_order_exists?(tracking_number)
rescue InvalidParameters => e
  Rails.logger.error("Failed to verify tracking number #{tracking_number}: #{e.message}")
  false
end