his_emr_api_lab 1.1.1 → 1.1.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 7b74dc551624446991404886012f19260411d90f1aa12e092fc89418e607e81f
+  metadata.gz: 960dc05ef6fbcddc4538762d7c7f3369e77d2f24b879e14a110ffa4ab2141d22
+  data.tar.gz: 666ea51bb7ff2938b6d4fd733a619a49cf600aed37c330c8be3f9680bdc4e94e
 SHA512:
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-  data.tar.gz: 743cb12464310c16dfde6e37ce931253479d7394961a48bf86a9350e3254bfcb2ab608f2f84076c6739936c6b31642453997e6cf3b101d1607da01f17456b89e
+  metadata.gz: 3ba9d9cb6d59d656b8d72190d6ecb1bcf6c193fdeb22121608ec39fb2fbb77e1b11e2b53d45d8937f6969cb1212e1adb045bb4a53e76f1eefa825731c2abcb98
+  data.tar.gz: 6e27abac8e38b86238adecf6eec31e3cad2503b5d46e534b498b47cad563cf15ebacf74fdc66c552338ebc584e3f08c331480cb57be14df5951c297ce642a44a

data/app/jobs/lab/update_patient_orders_job.rb

@@ -12,9 +12,22 @@ module Lab
       User.current = Lab::Lims::Utils.lab_user
       Location.current = Location.find_by_name('ART clinic')
 
-      lims_api = Lab::Lims::Api::RestApi.new(Lab::Lims::Config.rest_api)
-      worker = Lab::Lims::PullWorker.new(lims_api)
-      worker.pull_orders(patient_id: patient_id)
+      lockfile = Rails.root.join('tmp', "update-patient-orders-#{patient_id}.lock")
+
+      done = File.open(lockfile, File::RDWR | File::CREAT) do |lock|
+        unless lock.flock(File::LOCK_NB | File::LOCK_EX)
+          Rails.logger.info('Another update patient job is already running...')
+          break false
+        end
+
+        lims_api = Lab::Lims::Api::RestApi.new(Lab::Lims::Config.rest_api)
+        worker = Lab::Lims::PullWorker.new(lims_api)
+        worker.pull_orders(patient_id: patient_id)
+
+        true
+      end
+
+      File.unlink(lockfile) if done
     end
   end
 end

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

@@ -38,6 +38,9 @@ module Lab
         end
 
         def create_order(order)
+          order = order.dup
+          order.delete('_id')
+
           bum.couch_rest :post, '/', order
         end
 

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

@@ -22,14 +22,13 @@ class Lab::Lims::Api::RestApi
       end
     end
 
-    update_order_results(order_dto)
-
-    data = JSON.parse(response.body)['data']
+    data = JSON.parse(response.body)
+    update_order_results(order_dto) unless data['message'].casecmp?('Order already available')
 
     ActiveSupport::HashWithIndifferentAccess.new(
-      id: data['tracking_number'],
+      id: order_dto.fetch(:_id, order_dto[:tracking_number]),
       rev: 0,
-      tracking_number: data['tracking_number']
+      tracking_number: order_dto[:tracking_number]
     )
   end
 
@@ -44,21 +43,25 @@ class Lab::Lims::Api::RestApi
   end
 
   def consume_orders(*_args, patient_id: nil, **_kwargs)
-    Rails.logger.info('Looking for orders without results...')
-    orders = Lab::OrdersSearchService.find_orders_without_results(patient_id: patient_id)
+    orders_pending_updates(patient_id).each do |order|
+      order_dto = Lab::Lims::OrderSerializer.serialize_order(order)
 
-    orders.each do |order|
-      response = in_authenticated_session do |headers|
-        Rails.logger.info("Fetching results for order ##{order.accession_number}")
-        RestClient.get(expand_uri("query_results_by_tracking_number/#{order.accession_number}"), headers)
+      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
 
-      Rails.logger.info("Result for order ##{order.accession_number} found... Parsing...")
-      results = JSON.parse(response).fetch('data').fetch('results')
-      order_dto = Lab::Lims::OrderSerializer.serialize_order(order)
-      yield lims_results_to_order_dto(results, order_dto), OpenStruct.new(last_seq: 0)
-    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}")
+      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
 
@@ -105,8 +108,8 @@ class Lab::Lims::Api::RestApi
     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
+    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?
@@ -117,7 +120,8 @@ class Lab::Lims::Api::RestApi
     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 = RestClient.get(expand_uri("re_authenticate/#{username}/#{password}"),
+                              headers: { 'Content-type' => 'application/json' })
     response_body = JSON.parse(response.body)
 
     if response_body['status'] == 401
@@ -153,9 +157,7 @@ class Lab::Lims::Api::RestApi
 
     Rails.logger.error("Lims Api Error: #{response.body}")
 
-    if body['status'] != 401
-      raise LimsApiError, "#{body['status']} - #{body['message']}"
-    end
+    raise LimsApiError, "#{body['status']} - #{body['message']}" if body['status'] != 401
 
     if body['message'].match?(/token expired/i)
       raise AuthenticationTokenExpired, "Authentication token expired: #{body['message']}"
@@ -255,11 +257,31 @@ class Lab::Lims::Api::RestApi
     "#{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 lims_results_to_order_dto(results, order_dto)
-    order_dto.merge(
+  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|
@@ -277,10 +299,16 @@ class Lab::Lims::Api::RestApi
     )
   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)
-    if order_dto['test_results'].nil? || order_dto['test_results'].empty?
-      return nil
-    end
+    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']}")
@@ -341,4 +369,40 @@ class Lab::Lims::Api::RestApi
       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)
+    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)
+  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)
+    orders = orders.where(patient_id: patient_id) if patient_id
+
+    orders
+  end
 end

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

@@ -11,15 +11,19 @@ module Lab
       class ConfigNotFound < RuntimeError; end
 
       class << self
+        def preferred_api
+          emr_api_application('lims_api', 'couchdb')
+        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
+            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}")
 
@@ -64,9 +68,7 @@ module Lab
           @emr_api_application ||= YAML.load_file(Rails.root.join('config', 'application.yml'))
 
           @emr_api_application.fetch(param) do
-            unless fallback
-              raise ConfigNotFound, "Missing config param: #{param}"
-            end
+            raise ConfigNotFound, "Missing config param: #{param}" unless fallback
 
             fallback
           end
@@ -83,9 +85,7 @@ module Lab
             Rails.root.parent.join("nlims_controller/config/#{filename}")
           ]
 
-          if filename == 'couchdb.yml'
-            paths = [Rails.root.join('config/lims-couchdb.yml'), *paths]
-          end
+          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}")

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

@@ -22,7 +22,7 @@ module Lab
           date: start_date,
           target_lab: facility_name(self['receiving_facility']),
           order_location: facility_name(self['sending_facility']),
-          reason_for_test: reason_for_test
+          reason_for_test_id: reason_for_test
         )
       end
 
@@ -83,9 +83,14 @@ module Lab
 
       # Translates a LIMS sample priority to a concept_id
       def reason_for_test
-        return unknown_concept.concept_id unless self['priority']
+        return nil unless self['priority']
 
-        ConceptName.find_by_name!(self['priority']).concept_id
+        name = case self['priority']
+               when %r{Reapet / Missing}i then 'Repeat / Missing'
+               else self['priority']
+               end
+
+        ConceptName.find_by_name!(name).concept_id
       end
 
       def lab_program

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

@@ -16,6 +16,7 @@ module Lab
           serialized_order = Lims::Utils.structify(Lab::LabOrderSerializer.serialize_order(order))
 
           Lims::OrderDTO.new(
+            _id: Lab::LimsOrderMapping.find_by(order: order)&.lims_id || serialized_order.accession_number,
             tracking_number: serialized_order.accession_number,
             sending_facility: current_facility_name,
             receiving_facility: serialized_order.target_lab,
@@ -63,7 +64,7 @@ module Lab
             first_name: name&.given_name,
             last_name: name&.family_name,
             id: national_id&.identifier,
-            phone_number: phone_number&.value,
+            phone_number: phone_number&.value || 'Unknown',
             gender: person.gender,
             email: nil
           }
@@ -82,9 +83,7 @@ module Lab
         end
 
         def format_sample_status_trail(order)
-          if order.concept_id == ConceptName.find_by_name!('Unknown').concept_id
-            return []
-          end
+          return [] if order.concept_id == ConceptName.find_by_name!('Unknown').concept_id
 
           user = User.find(order.discontinued_by || order.creator)
           drawn_by = PersonName.find_by_person_id(user.user_id)

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

@@ -176,7 +176,7 @@ module Lab
       def update_order(patient, order_id, order_dto)
         logger.debug("Updating order ##{order_dto['_id']}")
         order = OrdersService.update_order(order_id, order_dto.to_order_service_params(patient_id: patient.patient_id)
-                                                              .merge(force_update: true))
+                                                              .merge(force_update: 'true'))
         unless order_dto['test_results'].empty?
           update_results(order, order_dto['test_results'])
         end
@@ -194,7 +194,7 @@ module Lab
             next
           end
 
-          next unless test_results['results']
+          next if test.result || test_results['results'].blank?
 
           measures = test_results['results'].map do |indicator, value|
             measure = find_measure(order, indicator, value)

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

@@ -17,7 +17,12 @@ module Lab
         loop do
           logger.info('Looking for new orders to push to LIMS...')
           orders = orders_pending_sync(batch_size).all
-          orders.each { |order| push_order(order) }
+          orders.each do |order|
+            push_order(order)
+          rescue GatewayError => e
+            logger.error("Failed to push order ##{order.accession_number}: #{e.class} - #{e.message}")
+            sleep(Lab::Lims::Config.updates_poll_frequency)
+          end
 
           # Doing this after .each above to stop ActiveRecord from executing
           # an extra request to the database (ActiveRecord's lazy evaluation
@@ -56,7 +61,8 @@ module Lab
           else
             Rails.logger.info("Creating order ##{order_dto['accession_number']} in LIMS")
             update = lims_api.create_order(order_dto)
-            Lab::LimsOrderMapping.create!(order: order, lims_id: update['id'], revision: update['rev'], pushed_at: Time.now)
+            Lab::LimsOrderMapping.create!(order: order, lims_id: update['id'], revision: update['rev'],
+                                          pushed_at: Time.now)
           end
         end
 

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

@@ -2,6 +2,8 @@
 
 require 'logger_multiplexor'
 
+require_relative './api/couchdb_api'
+
 module Lab
   module Lims
     ##
@@ -19,8 +21,7 @@ module Lab
 
       def self.start_push_worker
         start_worker('push_worker') do
-          api = Lims::Api::RestApi.new(Lab::Lims::Config.rest_api)
-          worker = PushWorker.new(api)
+          worker = PushWorker.new(lims_api)
 
           worker.push_orders # (wait: true)
         end
@@ -28,8 +29,7 @@ module Lab
 
       def self.start_pull_worker
         start_worker('pull_worker') do
-          api = Lims::Api::RestApi.new(Lab::Lims::Config.rest_api)
-          worker = PullWorker.new(api)
+          worker = PullWorker.new(lims_api)
 
           worker.pull_orders
         end
@@ -37,8 +37,7 @@ module Lab
 
       def self.start_realtime_pull_worker
         start_worker('realtime_pull_worker') do
-          api = Lims::Api::WsApi.new(Lab::Lims::Config.updates_socket)
-          worker = PullWorker.new(api)
+          worker = PullWorker.new(Lims::Api::WsApi.new(Lab::Lims::Config.updates_socket))
 
           worker.pull_orders
         end
@@ -71,6 +70,14 @@ module Lab
         Rails.logger.warn("Check for realtime updates failed: #{e.message}")
         false
       end
+
+      def self.lims_api
+        case Lims::Config.preferred_api
+        when /couchdb/i then Api::CouchDbApi.new(config: Lab::Lims::Config.couchdb)
+        when /rest/i then Api::RestApi.new(Lab::Lims::Config.rest_api)
+        else raise "Invalid LIMS API in application.yml, expected 'rest' or 'couchdb'"
+        end
+      end
     end
   end
 end

data/app/services/lab/metadata.rb

@@ -10,6 +10,7 @@ module Lab
     TEST_RESULT_CONCEPT_NAME = 'Lab test result'
     TEST_RESULT_INDICATOR_CONCEPT_NAME = 'Lab test result indicator'
     TEST_TYPE_CONCEPT_NAME = 'Test type'
+    UNKNOWN_SPECIMEN = 'Unknown'
 
     # Encounter
     ENCOUNTER_TYPE_NAME = 'Lab'

data/app/services/lab/orders_search_service.rb

@@ -26,8 +26,10 @@ module Lab
       end
 
       def find_orders_without_results(patient_id: nil)
-        query = Lab::LabOrder.where
-                             .not(order_id: Lab::LabResult.all.select(:order_id))
+        results_query = Lab::LabResult.all
+        results_query = results_query.where(person_id: patient_id) if patient_id
+
+        query = Lab::LabOrder.where.not(order_id: results_query.select(:order_id))
         query = query.where(patient_id: patient_id) if patient_id
 
         query

data/app/services/lab/orders_service.rb

@@ -66,20 +66,27 @@ module Lab
 
       def update_order(order_id, params)
         specimen_id = params.dig(:specimen, :concept_id)
-        unless specimen_id
-          raise ::InvalidParameterError, 'Specimen concept_id is required'
-        end
+        raise ::InvalidParameterError, 'Specimen concept_id is required' unless specimen_id
 
         order = Lab::LabOrder.find(order_id)
-        unless order.concept_id == unknown_concept_id || params[:force_update]&.to_s&.casecmp?('true')
-          raise ::UnprocessableEntityError
+        if order.concept_id != unknown_concept_id && !params[:force_update]&.casecmp?('true')
+          raise ::UnprocessableEntityError, "Can't change order specimen once set"
+        end
+
+        if specimen_id.to_i != order.concept_id
+          Rails.logger.debug("Updating order ##{order.order_id}")
+          order.update!(concept_id: specimen_id,
+                        discontinued: true,
+                        discontinued_by: User.current.user_id,
+                        discontinued_date: params[:date]&.to_date || Time.now,
+                        discontinued_reason_non_coded: 'Sample drawn/updated')
+        end
+
+        if params[:reason_for_test_id]
+          Rails.logger.debug("Updating reason for test on order ##{order.order_id}")
+          update_reason_for_test(order, params[:reason_for_test_id])
         end
 
-        order.update!(concept_id: specimen_id,
-                      discontinued: true,
-                      discontinued_by: User.current.user_id,
-                      discontinued_date: params[:date]&.to_date || Time.now,
-                      discontinued_reason_non_coded: 'Sample drawn/updated')
         Lab::LabOrderSerializer.serialize_order(order)
       end
 
@@ -107,13 +114,9 @@ module Lab
       # a 'Lab' encounter is created using the provided program_id and
       # patient_id.
       def find_encounter(order_params)
-        if order_params[:encounter_id]
-          return Encounter.find(order_params[:encounter_id])
-        end
+        return Encounter.find(order_params[:encounter_id]) if order_params[:encounter_id]
 
-        unless order_params[:patient_id]
-          raise InvalidParameterError, 'encounter_id or patient_id required'
-        end
+        raise InvalidParameterError, 'encounter_id or patient_id required' unless order_params[:patient_id]
 
         program_id = order_params[:program_id] || Program.find_by_name!(Lab::Metadata::LAB_PROGRAM_NAME).program_id
 
@@ -159,7 +162,7 @@ module Lab
           order,
           Lab::Metadata::REASON_FOR_TEST_CONCEPT_NAME,
           params[:date],
-          value_coded: params['reason_for_test_id']
+          value_coded: params[:reason_for_test_id]
         )
       end
 
@@ -192,6 +195,17 @@ module Lab
       def unknown_concept_id
         ConceptName.find_by_name!('Unknown').concept_id
       end
+
+      def update_reason_for_test(order, concept_id)
+        raise InvalidParameterError, "Reason for test can't be blank" if concept_id.blank?
+
+        return if order.reason_for_test&.value_coded == concept_id
+
+        raise InvalidParameterError, "Can't change reason for test once set" if order.reason_for_test&.value_coded
+
+        order.reason_for_test&.delete
+        add_reason_for_test(order, date: order.start_date, reason_for_test_id: concept_id)
+      end
     end
   end
 end

data/lib/lab/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Lab
-  VERSION = '1.1.1'
+  VERSION = '1.1.5'
 end

data/lib/tasks/loaders/data/reasons-for-test.csv

@@ -3,4 +3,5 @@
 "Repeat / Missing"
 "Targeted"
 "Confirmatory"
+"Stat"
 "Other"

data/lib/tasks/loaders/data/tests.csv

@@ -86,8 +86,6 @@ Blood,HbA1c,"2019-11-19 14:05:31"
 Blood,Microalbumin,"2019-11-19 14:05:31"
 Blood,Microprotein,"2019-11-19 14:05:31"
 Blood,"Von Willebrand Factor","2019-11-19 14:05:31"
-Blood,"HIV_viral_load","2021-04-13 00:00:00"
-Blood,"Viral laod","2021-04-11 00:00:00"
 Blood,"Viral Load","2019-11-19 14:05:31"
 Blood,"Urine Lam","2019-11-19 14:05:31"
 Blood,"Protein and Sugar","2021-04-16"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: his_emr_api_lab
 version: !ruby/object:Gem::Version
-  version: 1.1.1
+  version: 1.1.5
 platform: ruby
 authors:
 - Elizabeth Glaser Pediatric Foundation Malawi
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-07-12 00:00:00.000000000 Z
+date: 2021-07-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: couchrest