his_emr_api_lab 0.0.2 → 0.0.3
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- checksums.yaml +4 -4
- data/app/controllers/lab/labels_controller.rb +15 -0
- data/app/controllers/lab/orders_controller.rb +2 -1
- data/app/models/lab/lab_order.rb +5 -1
- data/app/models/lab/lab_result.rb +10 -0
- data/app/models/lab/lab_test.rb +5 -0
- data/app/services/lab/labelling_service/order_label.rb +85 -0
- data/app/services/lab/lims/api.rb +7 -0
- data/app/services/lab/lims/exceptions.rb +11 -0
- data/app/services/lab/lims/migrator.rb +206 -0
- data/app/services/lab/lims/order_dto.rb +41 -122
- data/app/services/lab/lims/order_serializer.rb +28 -2
- data/app/services/lab/lims/utils.rb +45 -1
- data/app/services/lab/lims/worker.rb +227 -38
- data/app/services/lab/metadata.rb +1 -1
- data/app/services/lab/orders_service.rb +9 -8
- data/app/services/lab/results_service.rb +38 -6
- data/config/routes.rb +2 -0
- data/lib/auto12epl.rb +201 -0
- data/lib/couch_bum/couch_bum.rb +11 -1
- data/lib/lab/version.rb +1 -1
- data/lib/tasks/loaders/data/tests.csv +21 -0
- metadata +21 -2
@@ -1,5 +1,8 @@
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# frozen_string_literal: true
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2
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+
require_relative './order_dto'
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4
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require_relative './utils'
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5
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+
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6
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module Lab
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7
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module Lims
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8
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##
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@@ -9,7 +12,7 @@ module Lab
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include Utils
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def serialize_order(order)
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12
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-
serialized_order = structify(Lab::LabOrderSerializer.serialize_order(order))
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+
serialized_order = Utils.structify(Lab::LabOrderSerializer.serialize_order(order))
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16
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OrderDTO.new(
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tracking_number: serialized_order.accession_number,
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@@ -20,6 +23,7 @@ module Lab
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order_location: format_order_location(serialized_order.encounter_id),
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sample_type: format_sample_type(serialized_order.specimen.name),
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sample_status: format_sample_status(serialized_order.specimen.name),
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+
sample_statuses: format_sample_status_trail(order),
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districy: current_district, # yes districy [sic]...
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priority: serialized_order.reason_for_test.name,
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date_created: serialized_order.order_date,
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@@ -56,7 +60,7 @@ module Lab
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first_name: name&.given_name,
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last_name: name&.family_name,
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id: national_id&.identifier,
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-
phone_number: phone_number
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+
phone_number: phone_number&.value,
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gender: person.gender,
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65
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email: nil
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}
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@@ -70,6 +74,28 @@ module Lab
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name.casecmp?('Unknown') ? 'specimen_not_collected' : 'specimen_collected'
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end
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+
def format_sample_status_trail(order)
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if order.concept_id == ConceptName.find_by_name!('Unknown').concept_id
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return []
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end
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user = User.find(order.discontinued_by || order.creator)
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drawn_by = PersonName.find_by_person_id(user.user_id)
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drawn_date = order.discontinued_date || order.start_date
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[
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drawn_date.strftime('%Y%m%d%H%M%S') => {
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'status' => 'Drawn',
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'updated_by' => {
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'first_name' => drawn_by&.given_name || user.username,
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'last_name' => drawn_by&.family_name,
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'phone_number' => nil,
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'id' => user.username
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}
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}
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]
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end
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+
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def format_test_results(order)
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order.tests.each_with_object({}) do |test, results|
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results[test.name] = {
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@@ -1,5 +1,7 @@
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# frozen_string_literal: true
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require 'cgi/util'
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module Lab
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module Lims
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##
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@@ -9,7 +11,21 @@ module Lab
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Rails.logger
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end
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-
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TEST_NAME_MAPPINGS = {
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# For some weird reason(s) some tests have multiple names in LIMS,
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# this is used to sanitize those names.
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'hiv_viral_load' => 'HIV Viral Load',
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'viral laod' => 'HIV Viral Load',
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'viral load' => 'HIV Viral Load',
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'i/ink' => 'India ink',
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'indian ink' => 'India ink'
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}.freeze
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def self.translate_test_name(test_name)
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TEST_NAME_MAPPINGS.fetch(test_name.downcase, test_name)
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end
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def self.structify(object)
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if object.is_a?(Hash)
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object.each_with_object(OpenStruct.new) do |kv_pair, struct|
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key, value = kv_pair
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@@ -22,6 +38,34 @@ module Lab
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object
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end
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end
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def self.parse_date(str_date, fallback_date = nil)
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if str_date.blank? && fallback_date.blank?
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raise "Can't parse blank date"
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end
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return parse_date(fallback_date) if str_date.blank?
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str_date = str_date.gsub(/^00/, '20').gsub(/^180/, '20')
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if str_date.match?(/\d{4}-\d{2}-\d{2}/)
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str_date
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elsif str_date.match?(/\d{2}-\d{2}-\d{2}/)
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Date.strptime(str_date, '%d-%m-%Y').strftime('%Y-%m-%d')
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elsif str_date.match?(/(\d{4}\d{2}\d{2})\d+/)
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Date.strptime(str_date, '%Y%m%d').strftime('%Y-%m-%d')
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else
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Rails.logger.warn("Invalid date: #{str_date}")
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parse_date(fallback_date)
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end
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end
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63
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def self.find_concept_by_name(name)
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ConceptName.joins(:concept)
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.merge(Concept.all) # Filter out voided
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.where(name: CGI.unescapeHTML(name))
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.first
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end
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end
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end
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end
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@@ -1,5 +1,9 @@
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# frozen_string_literal: true
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require 'cgi/util'
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require_relative './exceptions'
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require_relative './order_serializer'
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require_relative './utils'
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module Lab
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@@ -7,14 +11,14 @@ module Lab
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##
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# Pull/Push orders from/to the LIMS queue (Oops meant CouchDB).
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class Worker
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def initialize(lims_api)
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@lims_api = lims_api
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-
end
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-
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include Utils
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attr_reader :lims_api
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def initialize(lims_api)
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@lims_api = lims_api
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end
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def push_orders(batch_size: 100)
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loop do
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logger.info('Fetching new orders...')
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@@ -40,15 +44,17 @@ module Lab
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def push_order(order)
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logger.info("Pushing order ##{order.order_id}")
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-
order_dto =
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47
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+
order_dto = OrderSerializer.serialize_order(order)
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48
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mapping = LimsOrderMapping.find_by(order_id: order.order_id)
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-
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-
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-
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-
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-
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-
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ActiveRecord::Base.transaction do
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if mapping
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lims_api.update_order(mapping.lims_id, order_dto)
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mapping.update(pushed_at: Time.now)
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else
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order_dto = lims_api.create_order(order_dto)
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LimsOrderMapping.create!(order: order, lims_id: order_dto['_id'], pushed_at: Time.now)
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end
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end
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order_dto
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@@ -57,64 +63,247 @@ module Lab
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##
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# Pulls orders from the LIMS queue and writes them to the local database
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def pull_orders
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logger.info("Retrieving LIMS orders starting from #{last_seq}")
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lims_api.consume_orders(from: last_seq) do |order_dto, context|
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logger.debug(
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logger.debug("Retrieved order ##{order_dto[:tracking_number]}: #{order_dto}")
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patient = find_patient_by_nhid(order_dto[:patient][:id])
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-
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unless patient
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logger.debug(
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-
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logger.debug("Discarding order: Non local patient ##{order_dto[:patient][:id]} on order ##{order_dto[:tracking_number]}")
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next [:rejected, "Patient NPID, '#{order_dto[:patient][:id]}', didn't match any local NPIDs"]
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end
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diff = match_patient_demographics(patient, order_dto['patient'])
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if diff.empty?
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save_order(patient, order_dto)
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else
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save_failed_import(order_dto, 'Demographics not matching', diff)
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end
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-
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[:accepted, "Patient NPID, '#{order_dto[:patient][:id]}', matched"]
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rescue DuplicateNHID
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logger.warn("Failed to import order due to duplicate patient NHID: #{order_dto[:patient][:id]}")
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save_failed_import(order_dto, "Duplicate local patient NHID: #{order_dto[:patient][:id]}")
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rescue MissingAccessionNumber
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logger.warn("Failed to import order due to missing accession number: #{order_dto[:_id]}")
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save_failed_import(order_dto, 'Order missing tracking number')
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rescue LimsException => e
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logger.warn("Failed to import order due to #{e.class} - #{e.message}")
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save_failed_import(order_dto, e.message)
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ensure
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update_last_seq(context.last_seq)
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end
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end
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protected
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def last_seq
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File.open(last_seq_path, File::RDONLY | File::CREAT, 0o644) do |fin|
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data = fin.read&.strip
|
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return nil if data.blank?
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+
|
105
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+
return data
|
106
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end
|
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end
|
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+
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def update_last_seq(last_seq)
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File.open(last_seq_path, File::WRONLY | File::CREAT, 0o644) do |fout|
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fout.flock(File::LOCK_EX)
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+
|
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fout.write(last_seq.to_s)
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end
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end
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+
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private
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118
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119
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def find_patient_by_nhid(nhid)
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-
national_id_type = PatientIdentifierType.where(name: 'National id')
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79
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-
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80
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-
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120
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+
national_id_type = PatientIdentifierType.where(name: ['National id', 'Old Identification Number'])
|
121
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+
identifiers = PatientIdentifier.where(type: national_id_type, identifier: nhid)
|
122
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+
if identifiers.count.zero?
|
123
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+
identifiers = PatientIdentifier.unscoped.where(voided: 1, type: national_id_type, identifier: nhid)
|
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+
end
|
125
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+
return nil if identifiers.count.zero?
|
81
126
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|
82
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-
|
127
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+
patients = Patient.where(patient_id: identifiers.select(:patient_id))
|
128
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+
.distinct(:patient_id)
|
129
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.all
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130
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+
|
131
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+
if patients.size > 1
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+
raise DuplicateNHID, "Duplicate National Health ID: #{nhid}"
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+
end
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134
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84
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patients.first
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136
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end
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-
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-
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-
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-
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-
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-
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-
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138
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+
##
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139
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+
# Matches a local patient's demographics to a LIMS patient's demographics
|
140
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+
def match_patient_demographics(local_patient, lims_patient)
|
141
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+
diff = {}
|
142
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+
person = Person.find(local_patient.id)
|
143
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+
person_name = PersonName.find_by_person_id(local_patient.id)
|
144
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+
|
145
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+
unless (person.gender.blank? && lims_patient['gender'].blank?)\
|
146
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+
|| person.gender&.first&.casecmp?(lims_patient['gender']&.first)
|
147
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+
diff[:gender] = { local: person.gender, lims: lims_patient['gender'] }
|
96
148
|
end
|
97
149
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|
98
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-
|
150
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+
unless names_match?(person_name&.given_name, lims_patient['first_name'])
|
151
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+
diff[:given_name] = { local: person_name&.given_name, lims: lims_patient['first_name'] }
|
152
|
+
end
|
153
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+
|
154
|
+
unless names_match?(person_name&.family_name, lims_patient['last_name'])
|
155
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+
diff[:family_name] = { local: person_name&.family_name, lims: lims_patient['last_name'] }
|
156
|
+
end
|
157
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+
|
158
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+
diff
|
159
|
+
end
|
160
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+
|
161
|
+
def names_match?(name1, name2)
|
162
|
+
name1 = name1&.gsub(/'/, '')&.strip
|
163
|
+
name2 = name2&.gsub(/'/, '')&.strip
|
164
|
+
|
165
|
+
return true if name1.blank? && name2.blank?
|
166
|
+
|
167
|
+
return false if name1.blank? || name2.blank?
|
168
|
+
|
169
|
+
name1.casecmp?(name2)
|
170
|
+
end
|
171
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+
|
172
|
+
def save_order(patient, order_dto)
|
173
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+
raise MissingAccessionNumber if order_dto[:tracking_number].blank?
|
174
|
+
|
175
|
+
logger.info("Importing LIMS order ##{order_dto[:tracking_number]}")
|
176
|
+
mapping = LimsOrderMapping.find_by(lims_id: order_dto[:_id])
|
177
|
+
|
178
|
+
ActiveRecord::Base.transaction do
|
179
|
+
if mapping
|
180
|
+
order = update_order(patient, mapping.order_id, order_dto)
|
181
|
+
mapping.update(pulled_at: Time.now)
|
182
|
+
else
|
183
|
+
order = create_order(patient, order_dto)
|
184
|
+
LimsOrderMapping.create!(lims_id: order_dto[:_id],
|
185
|
+
order_id: order['id'],
|
186
|
+
pulled_at: Time.now,
|
187
|
+
revision: order_dto['_rev'])
|
188
|
+
end
|
189
|
+
|
190
|
+
order
|
191
|
+
end
|
99
192
|
end
|
100
193
|
|
101
194
|
def create_order(patient, order_dto)
|
102
|
-
|
103
|
-
|
195
|
+
logger.debug("Creating order ##{order_dto['_id']}")
|
196
|
+
order = OrdersService.order_test(order_dto.to_order_service_params(patient_id: patient.patient_id))
|
197
|
+
unless order_dto['test_results'].empty?
|
198
|
+
update_results(order, order_dto['test_results'])
|
199
|
+
end
|
104
200
|
|
105
201
|
order
|
106
202
|
end
|
107
203
|
|
108
|
-
def update_order(
|
109
|
-
|
110
|
-
|
204
|
+
def update_order(patient, order_id, order_dto)
|
205
|
+
logger.debug("Updating order ##{order_dto['_id']}")
|
206
|
+
order = OrdersService.update_order(order_id, order_dto.to_order_service_params(patient_id: patient.patient_id)
|
207
|
+
.merge(force_update: true))
|
208
|
+
unless order_dto['test_results'].empty?
|
209
|
+
update_results(order, order_dto['test_results'])
|
210
|
+
end
|
111
211
|
|
112
212
|
order
|
113
213
|
end
|
114
214
|
|
115
|
-
def update_results(
|
116
|
-
|
117
|
-
|
215
|
+
def update_results(order, lims_results)
|
216
|
+
logger.debug("Updating results for order ##{order[:accession_number]}: #{lims_results}")
|
217
|
+
|
218
|
+
lims_results.each do |test_name, test_results|
|
219
|
+
test = find_test(order['id'], test_name)
|
220
|
+
unless test
|
221
|
+
logger.warn("Couldn't find test, #{test_name}, in order ##{order[:id]}")
|
222
|
+
next
|
223
|
+
end
|
224
|
+
|
225
|
+
measures = test_results['results'].map do |indicator, value|
|
226
|
+
measure = find_measure(order, indicator, value)
|
227
|
+
next nil unless measure
|
228
|
+
|
229
|
+
measure
|
230
|
+
end
|
231
|
+
|
232
|
+
measures = measures.compact
|
233
|
+
|
234
|
+
next if measures.empty?
|
235
|
+
|
236
|
+
creator = format_result_entered_by(test_results['result_entered_by'])
|
237
|
+
|
238
|
+
ResultsService.create_results(test.id, provider_id: User.current.person_id,
|
239
|
+
date: Utils.parse_date(test_results['date_result_entered'], order[:order_date].to_s),
|
240
|
+
comments: "LIMS import: Entered by: #{creator}",
|
241
|
+
measures: measures)
|
242
|
+
end
|
243
|
+
end
|
244
|
+
|
245
|
+
def find_test(order_id, test_name)
|
246
|
+
test_name = Utils.translate_test_name(test_name)
|
247
|
+
test_concept = Utils.find_concept_by_name(test_name)
|
248
|
+
raise "Unknown test name, #{test_name}!" unless test_concept
|
249
|
+
|
250
|
+
LabTest.find_by(order_id: order_id, value_coded: test_concept.concept_id)
|
251
|
+
end
|
252
|
+
|
253
|
+
def find_measure(_order, indicator_name, value)
|
254
|
+
indicator = Utils.find_concept_by_name(indicator_name)
|
255
|
+
unless indicator
|
256
|
+
logger.warn("Result indicator #{indicator_name} not found in concepts list")
|
257
|
+
return nil
|
258
|
+
end
|
259
|
+
|
260
|
+
value_modifier, value, value_type = parse_lims_result_value(value)
|
261
|
+
return nil if value.blank?
|
262
|
+
|
263
|
+
ActiveSupport::HashWithIndifferentAccess.new(
|
264
|
+
indicator: { concept_id: indicator.concept_id },
|
265
|
+
value_type: value_type,
|
266
|
+
value: value_type == 'numeric' ? value.to_f : value,
|
267
|
+
value_modifier: value_modifier
|
268
|
+
)
|
269
|
+
end
|
270
|
+
|
271
|
+
def parse_lims_result_value(value)
|
272
|
+
value = value['result_value']
|
273
|
+
return nil, nil, nil if value.blank?
|
274
|
+
|
275
|
+
match = value&.match(/^(>|=|<|<=|>=)(.*)$/)
|
276
|
+
return nil, value, guess_result_datatype(value) unless match
|
277
|
+
|
278
|
+
[match[1], match[2], guess_result_datatype(match[2])]
|
279
|
+
end
|
280
|
+
|
281
|
+
def guess_result_datatype(result)
|
282
|
+
return 'numeric' if result.match?(/^[+-]?(\d+(\.\d+)|\.\d+)?$/)
|
283
|
+
|
284
|
+
'text'
|
285
|
+
end
|
286
|
+
|
287
|
+
def format_result_entered_by(result_entered_by)
|
288
|
+
first_name = result_entered_by['first_name']
|
289
|
+
last_name = result_entered_by['last_name']
|
290
|
+
phone_number = result_entered_by['phone_number']
|
291
|
+
id = result_entered_by['id'] # Looks like a user_id of some sort
|
292
|
+
|
293
|
+
"#{id}:#{first_name} #{last_name}:#{phone_number}"
|
294
|
+
end
|
295
|
+
|
296
|
+
def save_failed_import(order_dto, reason, diff = nil)
|
297
|
+
logger.info("Failed to import LIMS order ##{order_dto[:tracking_number]} due to '#{reason}'")
|
298
|
+
LimsFailedImport.create!(lims_id: order_dto[:_id],
|
299
|
+
tracking_number: order_dto[:tracking_number],
|
300
|
+
patient_nhid: order_dto[:patient][:id],
|
301
|
+
reason: reason,
|
302
|
+
diff: diff&.to_json)
|
303
|
+
end
|
304
|
+
|
305
|
+
def last_seq_path
|
306
|
+
Rails.root.join('log/lims/last-seq.dat')
|
118
307
|
end
|
119
308
|
end
|
120
309
|
end
|