his_emr_api_lab 2.1.9.pre.alpha → 2.2.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: cfef9418fc9d94d233f24d04883623d67e0c59c2aacea66bc15d3cca61192f78
-  data.tar.gz: 2d6324bf11f30c87398819042e3a0835275596961bfd838d088a63ae7a4f93c2
+  metadata.gz: c59744a50921b0f2244c94e052d4d66cbf39096485f99755e84f9cb66c311a0b
+  data.tar.gz: 989cc056aa59acbcd9d24977d3fc34b330cd1793db5d35908ccce44ca08dab34
 SHA512:
-  metadata.gz: c7eaa989ae6027aaba3bcd29e90136d1f93eda66854f7ee5bf84453420e0c66a40a928e460e00ee48bdee3fac8e2de05b7c030a7c71c8d4a6bf9457704dc7c6f
-  data.tar.gz: 16048c52a25d2876d79d6b3526b13625c67de47c44717de48910f905a75bb02dbd1cd48d7ce22e8b58947e61a1cb603340ea3bbdb1cce7536bb1774f41a72d65
+  metadata.gz: 22429cb56bfb9c5af91e5b44e2da11b66551ac89d084eeea45f5b16bb06daf5cc4f99d41cb5f2e4f3d5a38443fb62c15e5a30a14c5e5fff85006a3233d8f71de
+  data.tar.gz: 622a040596dc790f1d5a3c05469f7afe131badeca6313eb2412f8da378e632b7b28643c6a12eba6f02c618b9bed680722a635ce6e2e57ea6863872eb5e9b0966

data/app/controllers/lab/orders_controller.rb

@@ -2,6 +2,7 @@
 
 module Lab
   class OrdersController < ApplicationController
+    skip_before_action :authenticate, only: %i[order_status order_result summary]
     before_action :authenticate_request, only: %i[order_status order_result summary]
 
     def create
@@ -77,8 +78,26 @@ module Lab
     private
 
     def authenticate_request
-      decoded_user = authorize_request
-      user(decoded_user)
+      header = request.headers['Authorization']
+      content = header.split(' ')
+      auth_scheme = content.first
+      unless header
+        errors = ['Authorization token required']
+        render json: { errors: errors }, status: :unauthorized
+        return false
+      end
+      unless auth_scheme == 'Bearer'
+        errors = ['Authorization token bearer scheme required']
+        render json: { errors: errors }, status: :unauthorized
+        return false
+      end
+      process_token(content.last)
+    end
+
+    def process_token(token)
+      browser = Browser.new(request.user_agent)
+      decoded = Lab::JsonWebTokenService.decode(token, request.remote_ip + browser.name + browser.version)
+      user(decoded)
     end
 
     def user(decoded)

data/app/serializers/lab/lab_order_serializer.rb

@@ -10,7 +10,7 @@ module Lab
       target_lab = target_lab&.value_text || order.target_lab&.value_text || Location.current_health_center&.name
 
       encounter = Encounter.find_by_encounter_id(order.encounter_id)
-      program = Program.find_by_program_id(encounter.program_id)
+      program = Program.find_by_program_id(encounter&.program_id)
 
       ActiveSupport::HashWithIndifferentAccess.new(
         {
@@ -19,8 +19,8 @@ module Lab
           order_id: order.order_id, # Deprecated: Link to :id
           encounter_id: order.encounter_id,
           order_date: order.start_date,
-          location_id: encounter.location_id,
-          program_id: encounter.program_id,
+          location_id: encounter&.location_id,
+          program_id: encounter&.program_id,
           program_name: program&.name,
           patient_id: order.patient_id,
           accession_number: order.accession_number,

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)
 
             # Always fetch the full order from NLIMS to get status trails
@@ -577,43 +577,47 @@ 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

@@ -300,6 +300,7 @@ module Lab
 
         concept = params.dig(:specimen, :concept)
         concept ||= params.dig(:specimen, :concept_id)
+        concept ||= unknown_concept_id
 
         order_type = nil
         order_type = OrderType.find_by_order_type_id!(params[:order_type_id])&.id if params[:order_type_id].present?
@@ -401,7 +402,7 @@ module Lab
       end
 
       def unknown_concept_id
-        ConceptName.find_by_name!('Unknown').concept
+        ConceptName.find_by_name!('Unknown').concept_id
       end
 
       def update_reason_for_test(order, concept_id, force_update: false)

data/lib/lab/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Lab
-  VERSION = '2.1.9-alpha'
+  VERSION = '2.2.1'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: his_emr_api_lab
 version: !ruby/object:Gem::Version
-  version: 2.1.9.pre.alpha
+  version: 2.2.1
 platform: ruby
 authors:
 - Elizabeth Glaser Pediatric Foundation Malawi
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2026-03-04 00:00:00.000000000 Z
+date: 2026-03-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: couchrest
@@ -341,9 +341,9 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">"
+  - - ">="
     - !ruby/object:Gem::Version
-      version: 1.3.1
+      version: '0'
 requirements: []
 rubygems_version: 3.4.1
 signing_key: