mahis_emr_api_lab 1.2.0

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

@@ -0,0 +1,434 @@
+# frozen_string_literal: true
+require 'rest-client'
+
+class Lab::Lims::Api::RestApi
+  class LimsApiError < StandardError; end
+
+  class AuthenticationTokenExpired < LimsApiError; end
+
+  class InvalidParameters < LimsApiError; end
+
+  def initialize(config)
+    @config = config
+  end
+
+  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)
+      else
+        RestClient.post(expand_uri('create_order'), 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
+
+  def acknowledge(acknowledgement_dto)
+    Rails.logger.info("Acknowledging order ##{acknowledgement_dto} in LIMS")
+    response = in_authenticated_session do |headers|
+      RestClient.post(expand_uri('/acknowledge/test/results/recipient'), acknowledgement_dto, headers)
+    end
+    Rails.logger.info("Acknowledged order ##{acknowledgement_dto} in LIMS. Response: #{response}")
+    JSON.parse(response)
+  end
+
+  def update_order(_id, order_dto)
+    in_authenticated_session do |headers|
+      RestClient.post(expand_uri('update_order'), make_update_params(order_dto), headers)
+    end
+
+    update_order_results(order_dto)
+
+    { tracking_number: order_dto[:tracking_number] }
+  end
+
+  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}")
+        end
+      end
+
+      yield order_dto, OpenStruct.new(last_seq: 0)
+    rescue LimsApiError => e
+      Rails.logger.error("Failed to fetch updates for ##{order.accession_number}: #{e.class} - #{e.message}")
+      sleep(1)
+    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)
+                          .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))
+  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))
+                          .limit(1000)
+                          .where.not(accession_number: Lab::LimsOrderMapping.select(:lims_id))
+    orders = orders.where(patient_id: patient_id) if patient_id
+
+    orders
+  end
+end

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

@@ -0,0 +1,121 @@
+# frozen_string_literal: true
+
+require 'socket.io-client-simple'
+
+module Lab
+  module Lims
+    module Api
+      ##
+      # Retrieve results from LIMS only through a websocket
+      class WsApi
+        def initialize(config)
+          @config = config
+          @results_queue = []
+          @socket = nil
+        end
+
+        def consume_orders(**_kwargs)
+          loop do
+            results = fetch_results
+            unless results
+              Rails.logger.debug('No results available... Waiting for results...')
+              sleep(Lab::Lims::Config.updates_poll_frequency)
+              next
+            end
+
+            Rails.logger.info("Received result for ##{results['tracking_number']}")
+            order = find_order(results['tracking_number'])
+            next unless order
+
+            Rails.logger.info("Updating result for order ##{order.order_id}")
+            yield make_order_dto(order, results), OpenStruct.new(last_seq: 1)
+          end
+        end
+
+        private
+
+        def initialize_socket
+          Rails.logger.debug('Establishing connection to socket...')
+          socket = SocketIO::Client::Simple.connect(socket_url)
+          socket.on(:connect, &method(:on_socket_connect))
+          socket.on(:disconnect, &method(:on_socket_disconnect))
+          socket.on(:results, &method(:on_results_received))
+        end
+
+        def socket_url
+          @config.fetch('url')
+        end
+
+        def on_socket_connect
+          Rails.logger.debug('Connection to LIMS results socket established...')
+        end
+
+        def on_socket_disconnect
+          Rails.logger.debug('Connection to LIMS results socket lost...')
+          @socket = nil
+        end
+
+        def on_results_received(result)
+          Rails.logger.debug("Received result from LIMS: #{result}")
+          tracking_number = result['tracking_number']
+
+          Rails.logger.debug("Queueing result for order ##{tracking_number}")
+          @results_queue.push(result)
+        end
+
+        def order_exists?(tracking_number)
+          Rails.logger.debug("Looking for order for result ##{tracking_number}")
+          orders = OrdersSearchService.find_orders_without_results
+                                      .where(accession_number: tracking_number)
+          # The following ensures that the order was previously pushed to LIMS
+          # or was received from LIMS
+          Lab::LimsOrderMapping.where.not(order: orders).exists?
+        end
+
+        def fetch_results
+          loop do
+            @socket ||= initialize_socket
+
+            results = @results_queue.shift
+            return nil unless results
+
+            unless order_exists?(results['tracking_number'])
+              Rails.logger.debug("Ignoring result for order ##{tracking_number}")
+              next
+            end
+
+            return results
+          end
+        end
+
+        def find_order(lims_id)
+          mapping = Lab::LimsOrderMapping.where(lims_id: lims_id).select(:order_id)
+          Lab::LabOrder.find_by(order_id: mapping)
+        end
+
+        def make_order_dto(order, results)
+          Lab::Lims::OrderSerializer
+            .serialize_order(order)
+            .merge(
+              id: order.accession_number,
+              test_results: {
+                results['test_name'] => {
+                  results: results['results'].each_with_object({}) do |measure, formatted_measures|
+                    measure_name, measure_value = measure
+
+                    formatted_measures[measure_name] = { result_value: measure_value }
+                  end,
+                  result_date: results['date_updated'],
+                  result_entered_by: {
+                    first_name: results['who_updated']['first_name'],
+                    last_name: results['who_updated']['last_name'],
+                    id: results['who_updated']['id_number']
+                  }
+                }
+              }
+            )
+        end
+      end
+    end
+  end
+end

data/app/services/lab/lims/api_factory.rb

@@ -0,0 +1,19 @@
+# frozen_string_literal: true
+
+module Lab
+  module Lims
+    ##
+    # Creates LIMS Apis based on current configuration
+    module ApiFactory
+      def self.create_api
+        return Lab::Lims::Api::BlackholeApi.new if Rails.env.casecmp?('test')
+
+        case Lab::Lims::Config.preferred_api
+        when /rest/i then Lab::Lims::Api::RestApi.new(Lab::Lims::Config.rest_api)
+        when /couchdb/ then Lab::Lims::Api::CouchDbApi.new(config: Lab::Lims::Config.couchdb_api)
+        else raise "Invalid lims_api configuration: #{Lab::Lims::Config.preferred_api}"
+        end
+      end
+    end
+  end
+end

data/app/services/lab/lims/config.rb

@@ -0,0 +1,105 @@
+# frozen_string_literal: true
+
+module Lab
+  module Lims
+    ##
+    # Load LIMS' configuration files
+    module Config
+      # TODO: Replace this maybe with `Rails.application.configuration.lab.lims`
+      # so that we do not have to directly mess with configuration files.
+
+      class ConfigNotFound < RuntimeError; end
+
+      class << self
+        def preferred_api
+          emr_api_application('lims_api')
+        end
+
+        ##
+        # Returns LIMS' couchdb configuration file for the current environment (Rails.env)
+        def couchdb
+          config_path = begin
+            find_config_path('couchdb.yml')
+          rescue ConfigNotFound => e
+            Rails.logger.error("Failed to find default LIMS couchdb config: #{e.message}")
+            find_config_path('couchdb-lims.yml') # This can be placed in HIS-EMR-API/config
+          end
+
+          Rails.logger.debug("Using LIMS couchdb config: #{config_path}")
+
+          YAML.load_file(config_path)[Rails.env]
+        end
+
+        def rest_api
+          @rest_api ||= {
+            protocol: emr_api_application('lims_protocol', 'http'),
+            host: emr_api_application('lims_host'),
+            port: emr_api_application('lims_port'),
+            username: emr_api_application('lims_username'),
+            password: emr_api_application('lims_password')
+          }
+        end
+
+        def updates_socket
+          @updates_socket ||= {
+            'url' => emr_api_application('lims_realtime_updates_url')
+          }
+        end
+
+        def updates_poll_frequency
+          30 # Seconds
+        end
+
+        def config_file_name
+          # if nlims.yml exists return it, else return application.yml
+          File.exist?(Rails.root.join('config', 'nlims.yml')) ? 'nlims.yml' : 'application.yml'
+        end
+
+        ##
+        # Returns LIMS' application.yml configuration file
+        def application
+          @application ||= YAML.load_file(find_config_path(config_file_name))
+        end
+
+        ##
+        # Returns LIMS' database.yml configuration file
+        def database
+          @database ||= YAML.load_file(find_config_path('database.yml'))
+        end
+
+        private
+
+        def emr_api_application(param, fallback = nil)
+          @emr_api_application ||= YAML.load_file(Rails.root.join('config', config_file_name))
+
+          @emr_api_application.fetch(param) do
+            raise ConfigNotFound, "Missing config param: #{param}" unless fallback
+
+            fallback
+          end
+        end
+
+        ##
+        # Looks for a config file in various LIMS installation directories
+        #
+        # Returns: a path to a file found
+        def find_config_path(filename)
+          paths = [
+            "#{Dir.home}/apps/nlims_controller/config/#{filename}",
+            "/var/www/nlims_controller/config/#{filename}",
+            Rails.root.parent.join("nlims_controller/config/#{filename}")
+          ]
+
+          paths = [Rails.root.join('config/lims-couchdb.yml'), *paths] if filename == 'couchdb.yml'
+
+          paths.each do |path|
+            Rails.logger.debug("Looking for LIMS couchdb config at: #{path}")
+            return path if File.exist?(path)
+          end
+
+          raise ConfigNotFound, "Could not find a configuration file, checked: #{paths.join(':')}"
+        end
+      end
+    end
+  end
+end

data/app/services/lab/lims/exceptions.rb

@@ -0,0 +1,11 @@
+# frozen_string_literal: true
+
+module Lab
+  module Lims
+    class LimsException < StandardError; end
+    class DuplicateNHID < LimsException; end
+    class MissingAccessionNumber < LimsException; end
+    class UnknownSpecimenType < LimsException; end
+    class UnknownTestType < LimsException; end
+  end
+end