his_emr_api_lab 2.1.7.pre.beta.0 → 2.1.7.pre.gamma

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 159e9321795329ae186bf7d4a88aa492f63634ed5b5a236fb6a634da0dbd8342
+  metadata.gz: 593219b282a6f5cbe26cdd80a8324412650f3242d6ab48d622d1572699033c82
+  data.tar.gz: fb5bf82bc4569423c1e8b3ac5ff5d076e7734c565736e51ab0d453a61269d027
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+  metadata.gz: 1a941f7c1be9866e55bdbc035e23566b9e185f6131ab52f5fb17b3dd362cbfeb2d2b630929aea6904121232247edcb69ff451a1bc5a3d4528a1373e8db79f907
+  data.tar.gz: 60e00f01de37eb379b7f1a816baa793452f0b4b05cdda4596c495f5049a2431d69946aa33c3cae26c23847a69e1a99a9903b25a6dcf48b73c4cd237896653671

data/app/jobs/lab/process_lab_result_job.rb

@@ -7,7 +7,7 @@ module Lab
     queue_as :default
     def perform(results_obs_id, serializer, result_enter_by)
       Rails.logger.info("Lab::ProcessLabResultJob: Processing result completion for #{serializer}")
-      results_obs = Lab::LabResult.find(results_obs_id)
+      results_obs = Lab::LabResult.unscoped.find(results_obs_id)
       Lab::ResultsService.process_result_completion(results_obs, serializer, result_enter_by)
     end
   end

data/app/services/lab/acknowledgement_service.rb

@@ -14,9 +14,12 @@ module Lab
                                         date_received: params[:date_received])
       end
 
-      def acknowledgements_pending_sync(batch_size)
-        Lab::LabAcknowledgement.where(pushed: false)
-                               .limit(batch_size)
+      def acknowledgements_pending_sync(batch_size, start_date: nil)
+        query = Lab::LabAcknowledgement.joins(:order).where(pushed: false)
+
+        query = query.where('orders.date_created >= ?', start_date) if start_date
+
+        query.limit(batch_size)
       end
 
       def push_acknowledgement(acknowledgement, lims_api)
@@ -30,7 +33,8 @@ module Lab
             Rails.logger.info("Updating acknowledgement ##{acknowledgement_dto[:tracking_number]} in LIMS")
             response = lims_api.acknowledge(acknowledgement_dto)
             Rails.logger.info("Info #{response}")
-            if ['results already delivered for test name given', 'test result acknowledged successfully', 'test result already acknowledged electronically at facility'].include?(response['message'])
+            if ['results already delivered for test name given', 'test result acknowledged successfully',
+                'test result already acknowledged electronically at facility'].include?(response['message'])
               acknowledgement.pushed = true
               acknowledgement.date_pushed = Time.now
               acknowledgement.save!

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

@@ -4,20 +4,22 @@ module Lab
   module Lims
     # This class is responsible for handling the acknowledgement of lab orders
     class AcknowledgementWorker
-      attr_reader :lims_api
+      attr_reader :lims_api, :start_date
 
       include Utils # for logger
 
       SECONDS_TO_WAIT_FOR_ORDERS = 30
 
-      def initialize(lims_api)
+      def initialize(lims_api, start_date: nil)
         @lims_api = lims_api
+        @start_date = start_date
       end
 
       def push_acknowledgement(batch_size: 1000, wait: false)
         loop do
           logger.info('Looking for new acknowledgements to push to LIMS...')
-          acknowledgements = Lab::AcknowledgementService.acknowledgements_pending_sync(batch_size).all
+          acknowledgements = Lab::AcknowledgementService.acknowledgements_pending_sync(batch_size,
+                                                                                       start_date: start_date).all
 
           logger.debug("Found #{acknowledgements.size} acknowledgements...")
           acknowledgements.each do |acknowledgement|

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

@@ -74,8 +74,8 @@ module Lab
           { tracking_number: order_dto[:tracking_number] }
         end
 
-        def consume_orders(*_args, patient_id: nil, **_kwargs)
-          orders_pending_updates(patient_id).each do |order|
+        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)
             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))
@@ -510,43 +510,47 @@ module Lab
           }
         end
 
-        def orders_pending_updates(patient_id = nil)
+        def orders_pending_updates(patient_id = nil, start_date: 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_without_specimen(patient_id, start_date: start_date).each { |order| orders[order.order_id] = order }
+          orders_without_results(patient_id, start_date: start_date).each { |order| orders[order.order_id] = order }
+          orders_without_reason(patient_id, start_date: start_date).each { |order| orders[order.order_id] = order }
 
           orders.values
         end
 
-        def orders_without_specimen(patient_id = nil)
+        def orders_without_specimen(patient_id = nil, start_date: 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:) if patient_id
+          orders = orders.where('orders.date_created >= ?', start_date) if start_date
 
           orders
         end
 
-        def orders_without_results(patient_id = nil)
+        def orders_without_results(patient_id = nil, start_date: 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:)
-                                  .where(order_id: Lab::LimsOrderMapping.select(:order_id))
+          orders = Lab::OrdersSearchService.find_orders_without_results(patient_id:)
+                                           .where(order_id: Lab::LimsOrderMapping.select(:order_id))
+          orders = orders.where('orders.date_created >= ?', start_date) if start_date
+          orders
         end
 
-        def orders_without_reason(patient_id = nil)
+        def orders_without_reason(patient_id = nil, start_date: 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:) if patient_id
+          orders = orders.where('orders.date_created >= ?', start_date) if start_date
 
           orders
         end

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

@@ -5,14 +5,15 @@ module Lab
     ##
     # Pulls orders from a Lims API object and saves them to the local database.
     class PullWorker
-      attr_reader :lims_api
+      attr_reader :lims_api, :start_date
 
       include Utils # for logger
 
       LIMS_LOG_PATH = Rails.root.join('log', 'lims')
 
-      def initialize(lims_api)
+      def initialize(lims_api, start_date: nil)
         @lims_api = lims_api
+        @start_date = start_date
       end
 
       ##
@@ -20,7 +21,7 @@ module Lab
       def pull_orders(batch_size: 10_000, **)
         logger.info("Retrieving LIMS orders starting from #{last_seq}")
 
-        lims_api.consume_orders(from: last_seq, limit: batch_size, **) do |order_dto, context|
+        lims_api.consume_orders(from: last_seq, limit: batch_size, start_date: start_date, **) do |order_dto, context|
           logger.debug("Retrieved order ##{order_dto[:tracking_number]}: #{order_dto}")
 
           patient = find_patient_by_nhid(order_dto[:patient][:id], order_dto[:tracking_number])

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

@@ -5,15 +5,16 @@ module Lab
     ##
     # Pushes all local orders to a LIMS Api object.
     class PushWorker
-      attr_reader :lims_api
+      attr_reader :lims_api, :start_date
 
       include Utils # for logger
 
       SECONDS_TO_WAIT_FOR_ORDERS = 30
       START_DATE = Time.parse('2024-09-03').freeze
 
-      def initialize(lims_api)
+      def initialize(lims_api, start_date: nil)
         @lims_api = lims_api
+        @start_date = start_date
       end
 
       def push_orders(batch_size: 1000, wait: false)
@@ -81,8 +82,8 @@ module Lab
 
       def void_order_in_lims(order_id)
         order = Lab::LabOrder.joins(order_type: { name: 'Lab' })
-        .unscoped
-        .find(order_id)
+                             .unscoped
+                             .find(order_id)
         order_dto = Lab::Lims::OrderSerializer.serialize_order(order)
         Rails.logger.info("Deleting order ##{order_dto[:accession_number]} from LIMS")
         lims_api.delete_order('', order_dto)
@@ -100,10 +101,16 @@ module Lab
 
       def new_orders
         Rails.logger.debug('Looking for new orders that need to be created in LIMS...')
-        Lab::LabOrder.where.not(order_id: Lab::LimsOrderMapping.all.select(:order_id))
-                     .where("accession_number IS NOT NULL AND accession_number !=''")
-                     .where(date_created: START_DATE..(Date.today + 1.day))
-                     .order(date_created: :desc)
+        query = Lab::LabOrder.where.not(order_id: Lab::LimsOrderMapping.all.select(:order_id))
+                             .where("accession_number IS NOT NULL AND accession_number !=''")
+
+        query = if start_date
+                  query.where('orders.date_created >= ?', start_date)
+                else
+                  query.where('orders.date_created >= ? AND orders.date_created <= ?', START_DATE, Date.today + 1.day)
+                end
+
+        query.order(date_created: :desc)
       end
 
       def updated_orders

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

@@ -9,43 +9,43 @@ module Lab
     ##
     # Pull/Push orders from/to the LIMS queue (Oops meant CouchDB).
     module Worker
-      def self.start
+      def self.start(start_date: nil)
         User.current = Utils.lab_user
 
-        fork(&method(:start_push_worker))
-        fork(&method(:start_pull_worker))
-        fork(&method(:start_acknowledgement_worker))
-        fork(&method(:start_realtime_pull_worker)) if realtime_updates_enabled?
+        fork { start_push_worker(start_date: start_date) }
+        fork { start_pull_worker(start_date: start_date) }
+        fork { start_acknowledgement_worker(start_date: start_date) }
+        fork { start_realtime_pull_worker(start_date: start_date) } if realtime_updates_enabled?
 
         Process.waitall
       end
 
-      def self.start_push_worker
+      def self.start_push_worker(start_date: nil)
         start_worker('push_worker') do
-          worker = PushWorker.new(lims_api)
+          worker = PushWorker.new(lims_api, start_date: start_date)
 
           worker.push_orders # (wait: true)
         end
       end
 
-      def self.start_acknowledgement_worker
+      def self.start_acknowledgement_worker(start_date: nil)
         start_worker('acknowledgement_worker') do
-          worker = AcknowledgementWorker.new(lims_api)
+          worker = AcknowledgementWorker.new(lims_api, start_date: start_date)
           worker.push_acknowledgement
         end
       end
 
-      def self.start_pull_worker
+      def self.start_pull_worker(start_date: nil)
         start_worker('pull_worker') do
-          worker = PullWorker.new(lims_api)
+          worker = PullWorker.new(lims_api, start_date: start_date)
 
           worker.pull_orders
         end
       end
 
-      def self.start_realtime_pull_worker
+      def self.start_realtime_pull_worker(start_date: nil)
         start_worker('realtime_pull_worker') do
-          worker = PullWorker.new(Lims::Api::WsApi.new(Lab::Lims::Config.updates_socket))
+          worker = PullWorker.new(Lims::Api::WsApi.new(Lab::Lims::Config.updates_socket), start_date: start_date)
 
           worker.pull_orders
         end

data/app/services/lab/orders_service.rb

@@ -102,16 +102,14 @@ module Lab
 
         if reason_for_test
           Rails.logger.debug("Updating reason for test on order ##{order.order_id}")
-          update_reason_for_test(order, Concept.find(reason_for_test)&.id,
-                                 force_update: params.fetch('force_update', false))
+          update_reason_for_test(order, Concept.find(reason_for_test)&.id, force_update: params.fetch('force_update', false))
         end
 
         Lab::LabOrderSerializer.serialize_order(order)
       end
 
       def void_order(order_id, reason)
-        order = Lab::LabOrder.includes(%i[requesting_clinician reason_for_test target_lab comment_to_fulfiller],
-                                       tests: [:result])
+        order = Lab::LabOrder.includes(%i[requesting_clinician reason_for_test target_lab comment_to_fulfiller], tests: [:result])
                              .find(order_id)
 
         order.requesting_clinician&.void(reason)
@@ -162,15 +160,13 @@ module Lab
           last_order_date: Lab::LabOrder.last&.start_date&.to_date,
           lab_orders: []
         }
-        if include_data
-          data[:lab_orders] = orders.map do |order|
-            Lab::LabOrderSerializer.serialize_order(
-              order, requesting_clinician: order.requesting_clinician,
-                     reason_for_test: order.reason_for_test,
-                     target_lab: order.target_lab
-            )
-          end
-        end
+        data[:lab_orders] = orders.map do |order|
+          Lab::LabOrderSerializer.serialize_order(
+            order, requesting_clinician: order.requesting_clinician,
+                   reason_for_test: order.reason_for_test,
+                   target_lab: order.target_lab
+          )
+        end if include_data
         data
       end
 
@@ -178,14 +174,14 @@ module Lab
 
       def create_rejection_notification(order_params)
         order = find_order order_params['tracking_number']
-        data = { type: 'LIMS',
-                 specimen: ConceptName.find_by(concept_id: order.concept_id)&.name,
-                 accession_number: order&.accession_number,
-                 order_date: order&.start_date,
-                 arv_number: find_arv_number(order.patient_id),
-                 patient_id: result.person_id,
-                 ordered_by: order&.provider&.person&.name,
-                 rejection_reason: order_params['comments'] }.as_json
+        data = { 'type': 'LIMS',
+                 'specimen': ConceptName.find_by(concept_id: order.concept_id)&.name,
+                 'accession_number': order&.accession_number,
+                 'order_date': order&.start_date,
+                 'arv_number': find_arv_number(order.patient_id),
+                 'patient_id': result.person_id,
+                 'ordered_by': order&.provider&.person&.name,
+                 'rejection_reason': order_params['comments'] }.as_json
         NotificationService.new.create_notification('LIMS', data)
       end
 
@@ -239,9 +235,7 @@ module Lab
         encounter.encounter_datetime = order_params[:date] || Date.today
         encounter.visit = Visit.find_by_uuid(visit) if Encounter.column_names.include?('visit_id')
         encounter.provider_id = User.current&.person&.id if Encounter.column_names.include?('provider_id')
-        if Encounter.column_names.include?('program_id') && order_params[:program_id].present?
-          encounter.program_id = order_params[:program_id]
-        end
+        encounter.program_id = order_params[:program_id] if Encounter.column_names.include?('program_id') && order_params[:program_id].present?
         encounter.save!
         encounter.reload
       end
@@ -265,7 +259,7 @@ module Lab
         order.date_created = params[:date]&.to_date || Date.today if order.respond_to?(:date_created)
         order.start_date = params[:date]&.to_date || Date.today if order.respond_to?(:start_date)
         order.auto_expire_date = params[:end_date]
-        # NOTE: comment_to_fulfiller is a has_one association, not a field
+        # Note: comment_to_fulfiller is a has_one association, not a field
         # It will be created via add_comment_to_fulfiller method
         order.accession_number = access_number
         order.orderer = User.current&.user_id
@@ -362,10 +356,7 @@ module Lab
 
         return if order.reason_for_test&.value_coded == concept_id
 
-        if order.reason_for_test&.value_coded && !force_update
-          raise InvalidParameterError,
-                "Can't change reason for test once set"
-        end
+        raise InvalidParameterError, "Can't change reason for test once set" if order.reason_for_test&.value_coded && !force_update
 
         order.reason_for_test&.delete
         date = order.start_date if order.respond_to?(:start_date)

data/lib/lab/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Lab
-  VERSION = '2.1.7-beta.0'
+  VERSION = '2.1.7-gamma'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: his_emr_api_lab
 version: !ruby/object:Gem::Version
-  version: 2.1.7.pre.beta.0
+  version: 2.1.7.pre.gamma
 platform: ruby
 authors:
 - Elizabeth Glaser Pediatric Foundation Malawi
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2026-02-19 00:00:00.000000000 Z
+date: 2026-02-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: couchrest