his_emr_api_lab 2.1.7.pre.gamma → 2.1.8

checksums.yaml

@@ -1,7 +1,7 @@
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data/README.md

@@ -22,25 +22,25 @@ For details on how to perform these operations please see the
 Add this line to your application's Gemfile:
 
 ```ruby
-gem 'lab', git: 'https://github.com/EGPAFMalawiHIS/HIS-EMR-API-Lab', branch: 'development'
+gem 'his_emr_api_lab', git: 'https://github.com/EGPAFMalawiHIS/HIS-EMR-API-Lab', branch: 'development'
 ```
 
 And then execute:
 
 ```bash
-$ bundle install lab
+$ bundle install 
 ```
 
 Or install it yourself as:
 
 ```bash
-$ gem install lab
+$ gem install his_emr_api_lab
 ```
 
 Finally run:
 
 ```bash
-$ bundle exec rails lab:install
+$ bundle exec rails his_emr_api_lab:install
 ```
 
 ## Configuration
@@ -66,6 +66,19 @@ but too much a departure from it is frowned upon. For example, you will be forgi
 for writing a method with 15 to 20 lines if you clearly justify why you couldn't
 break that method into multiple smaller methods.
 
+## Publishing
+
+To publish a new version of the gem, first update the version number in
+`lib/lab/version.rb` and then run the following command:
+
+```bash
+$ gem build his_emr_api_lab.gemspec
+$ gem push his_emr_api_lab-<version>.gem  
+```
+Make sure to replace `<version>` with the version number you set in `lib/lab/version.rb`.
+
+NB: You need to have an account on [rubygems.org](https://rubygems.org/) and permission to publish gems.
+
 ## License
 
 The gem is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).

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.unscoped.find(results_obs_id)
+      results_obs = Lab::LabResult.find(results_obs_id)
       Lab::ResultsService.process_result_completion(results_obs, serializer, result_enter_by)
     end
   end

data/app/services/lab/acknowledgement_service.rb

@@ -14,12 +14,9 @@ module Lab
                                         date_received: params[:date_received])
       end
 
-      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)
+      def acknowledgements_pending_sync(batch_size)
+        Lab::LabAcknowledgement.where(pushed: false)
+                               .limit(batch_size)
       end
 
       def push_acknowledgement(acknowledgement, lims_api)
@@ -33,8 +30,7 @@ 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/concepts_service.rb

@@ -34,11 +34,10 @@ module Lab
 
       unless specimen_type
         return ActiveRecord::Base.connection.select_all <<~SQL
-          SELECT ca.concept_id, ca.value_reference as name, ca2.value_reference as nlims_code, c.uuid
+          SELECT ca.concept_id, ca.value_reference as name, ca2.value_reference as nlims_code
             FROM concept_attribute ca
           INNER JOIN concept_attribute ca2 ON ca.concept_id = ca2.concept_id
             AND ca2.attribute_type_id = #{ConceptAttributeType.nlims_code.concept_attribute_type_id}
-          INNER JOIN concept c ON c.concept_id = ca.concept_id
           WHERE ca.attribute_type_id = #{ConceptAttributeType.test_catalogue_name.concept_attribute_type_id}
           AND ca.concept_id IN (#{test_types.select(:concept_id).to_sql})
           GROUP BY ca.concept_id
@@ -57,11 +56,10 @@ module Lab
       )
 
       return ActiveRecord::Base.connection.select_all <<~SQL
-        SELECT ca.concept_id, ca.value_reference as name, ca2.value_reference as nlims_code, c.uuid
+        SELECT ca.concept_id, ca.value_reference as name, ca2.value_reference as nlims_code
           FROM concept_attribute ca
         INNER JOIN concept_attribute ca2 ON ca.concept_id = ca2.concept_id
           AND ca2.attribute_type_id = #{ConceptAttributeType.nlims_code.concept_attribute_type_id}
-        INNER JOIN concept c ON c.concept_id = ca.concept_id
         WHERE ca.attribute_type_id = #{ConceptAttributeType.test_catalogue_name.concept_attribute_type_id}
         AND ca.concept_id IN (#{concept_set.select(:concept_set).to_sql})
         GROUP BY ca.concept_id
@@ -74,11 +72,10 @@ module Lab
 
       unless test_type
         return ActiveRecord::Base.connection.select_all <<~SQL
-          SELECT ca.concept_id, ca.value_reference as name, ca2.value_reference as nlims_code, c.uuid
+          SELECT ca.concept_id, ca.value_reference as name, ca2.value_reference as nlims_code
             FROM concept_attribute ca
           INNER JOIN concept_attribute ca2 ON ca.concept_id = ca2.concept_id
             AND ca2.attribute_type_id = #{ConceptAttributeType.nlims_code.concept_attribute_type_id}
-          INNER JOIN concept c ON c.concept_id = ca.concept_id
           WHERE ca.attribute_type_id = #{ConceptAttributeType.test_catalogue_name.concept_attribute_type_id}
           AND ca.concept_id IN (#{specimen_types.select(:concept_id).to_sql})
           GROUP BY ca.concept_id
@@ -97,11 +94,10 @@ module Lab
       )
 
       return ActiveRecord::Base.connection.select_all <<~SQL
-        SELECT ca.concept_id, ca.value_reference as name, ca2.value_reference as nlims_code, c.uuid
+        SELECT ca.concept_id, ca.value_reference as name, ca2.value_reference as nlims_code
           FROM concept_attribute ca
         INNER JOIN concept_attribute ca2 ON ca.concept_id = ca2.concept_id
           AND ca2.attribute_type_id = #{ConceptAttributeType.nlims_code.concept_attribute_type_id}
-        INNER JOIN concept c ON c.concept_id = ca.concept_id
         WHERE ca.attribute_type_id = #{ConceptAttributeType.test_catalogue_name.concept_attribute_type_id}
         AND ca.concept_id IN (#{concept_set.pluck(:concept_id).push(0).join(',')})
         GROUP BY ca.concept_id
@@ -118,16 +114,15 @@ module Lab
       measures = ConceptSet.find_members_by_name(Lab::Metadata::TEST_RESULT_INDICATOR_CONCEPT_NAME)
                            .select(:concept_id)
 
-      sets = ConceptSet.where(concept_set: test, concept_id: measures)
+      sets = ConceptSet.where(concept_set: measures, concept_id: test)
 
       return ActiveRecord::Base.connection.select_all <<~SQL
-        SELECT ca.concept_id, ca.value_reference as name, ca2.value_reference as nlims_code, c.uuid
+        SELECT ca.concept_id, ca.value_reference as name, ca2.value_reference as nlims_code
           FROM concept_attribute ca
           INNER JOIN concept_attribute ca2 ON ca.concept_id = ca2.concept_id
             AND ca2.attribute_type_id = #{ConceptAttributeType.nlims_code.concept_attribute_type_id}
-          INNER JOIN concept c ON c.concept_id = ca.concept_id
           WHERE ca.attribute_type_id = #{ConceptAttributeType.test_catalogue_name.concept_attribute_type_id}
-          AND ca.concept_id IN (#{sets.pluck(:concept_id).push(0).join(',')})
+          AND ca.concept_id IN (#{sets.pluck(:concept_set).push(0).join(',')})
           GROUP BY ca.concept_id
       SQL
     end

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

@@ -4,22 +4,20 @@ module Lab
   module Lims
     # This class is responsible for handling the acknowledgement of lab orders
     class AcknowledgementWorker
-      attr_reader :lims_api, :start_date
+      attr_reader :lims_api
 
       include Utils # for logger
 
       SECONDS_TO_WAIT_FOR_ORDERS = 30
 
-      def initialize(lims_api, start_date: nil)
+      def initialize(lims_api)
         @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,
-                                                                                       start_date: start_date).all
+          acknowledgements = Lab::AcknowledgementService.acknowledgements_pending_sync(batch_size).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, start_date: nil, **_kwargs)
-          orders_pending_updates(patient_id, start_date: start_date).each do |order|
+        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))
@@ -510,47 +510,43 @@ module Lab
           }
         end
 
-        def orders_pending_updates(patient_id = nil, start_date: nil)
+        def orders_pending_updates(patient_id = nil)
           Rails.logger.info('Looking for orders that need to be updated...')
           orders = {}
 
-          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_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, start_date: nil)
+        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:) if patient_id
-          orders = orders.where('orders.date_created >= ?', start_date) if start_date
 
           orders
         end
 
-        def orders_without_results(patient_id = nil, start_date: nil)
+        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"))
-          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
+          Lab::OrdersSearchService.find_orders_without_results(patient_id:)
+                                  .where(order_id: Lab::LimsOrderMapping.select(:order_id))
         end
 
-        def orders_without_reason(patient_id = nil, start_date: nil)
+        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:) if patient_id
-          orders = orders.where('orders.date_created >= ?', start_date) if start_date
 
           orders
         end

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

@@ -5,15 +5,14 @@ module Lab
     ##
     # Pulls orders from a Lims API object and saves them to the local database.
     class PullWorker
-      attr_reader :lims_api, :start_date
+      attr_reader :lims_api
 
       include Utils # for logger
 
       LIMS_LOG_PATH = Rails.root.join('log', 'lims')
 
-      def initialize(lims_api, start_date: nil)
+      def initialize(lims_api)
         @lims_api = lims_api
-        @start_date = start_date
       end
 
       ##
@@ -21,7 +20,7 @@ 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, start_date: start_date, **) do |order_dto, context|
+        lims_api.consume_orders(from: last_seq, limit: batch_size, **) 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

@@ -5,16 +5,15 @@ module Lab
     ##
     # Pushes all local orders to a LIMS Api object.
     class PushWorker
-      attr_reader :lims_api, :start_date
+      attr_reader :lims_api
 
       include Utils # for logger
 
       SECONDS_TO_WAIT_FOR_ORDERS = 30
       START_DATE = Time.parse('2024-09-03').freeze
 
-      def initialize(lims_api, start_date: nil)
+      def initialize(lims_api)
         @lims_api = lims_api
-        @start_date = start_date
       end
 
       def push_orders(batch_size: 1000, wait: false)
@@ -82,8 +81,8 @@ 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)
@@ -101,16 +100,10 @@ module Lab
 
       def new_orders
         Rails.logger.debug('Looking for new orders that need to be created in LIMS...')
-        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)
+        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)
       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(start_date: nil)
+      def self.start
         User.current = Utils.lab_user
 
-        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?
+        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?
 
         Process.waitall
       end
 
-      def self.start_push_worker(start_date: nil)
+      def self.start_push_worker
         start_worker('push_worker') do
-          worker = PushWorker.new(lims_api, start_date: start_date)
+          worker = PushWorker.new(lims_api)
 
           worker.push_orders # (wait: true)
         end
       end
 
-      def self.start_acknowledgement_worker(start_date: nil)
+      def self.start_acknowledgement_worker
         start_worker('acknowledgement_worker') do
-          worker = AcknowledgementWorker.new(lims_api, start_date: start_date)
+          worker = AcknowledgementWorker.new(lims_api)
           worker.push_acknowledgement
         end
       end
 
-      def self.start_pull_worker(start_date: nil)
+      def self.start_pull_worker
         start_worker('pull_worker') do
-          worker = PullWorker.new(lims_api, start_date: start_date)
+          worker = PullWorker.new(lims_api)
 
           worker.pull_orders
         end
       end
 
-      def self.start_realtime_pull_worker(start_date: nil)
+      def self.start_realtime_pull_worker
         start_worker('realtime_pull_worker') do
-          worker = PullWorker.new(Lims::Api::WsApi.new(Lab::Lims::Config.updates_socket), start_date: start_date)
+          worker = PullWorker.new(Lims::Api::WsApi.new(Lab::Lims::Config.updates_socket))
 
           worker.pull_orders
         end

data/app/services/lab/orders_service.rb

@@ -247,6 +247,7 @@ 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?
@@ -259,8 +260,7 @@ 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
-        # It will be created via add_comment_to_fulfiller method
+        order.comment_to_fulfiller = params[:comment_to_fulfiller] if params[:comment_to_fulfiller]
         order.accession_number = access_number
         order.orderer = User.current&.user_id
 
@@ -348,7 +348,7 @@ 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 = '2.1.7-gamma'
+  VERSION = '2.1.8'
 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.gamma
+  version: 2.1.8
 platform: ruby
 authors:
 - Elizabeth Glaser Pediatric Foundation Malawi
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2026-02-26 00:00:00.000000000 Z
+date: 2026-02-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: couchrest
@@ -340,9 +340,9 @@ 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: