his_emr_api_lab 1.1.6 → 1.1.12

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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+  metadata.gz: a64e5dbfcbbeff8e1574ebab38f4af1d637849468056f0d764a0f9d2833747b3
+  data.tar.gz: c8714fea2237f63b31bb2b33fa2b2e6a52e4d228c2ea63a0ceeb4be350c251d4
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+  data.tar.gz: ab53beacd38b5c8ae75f5e93e63db7d57d56533565acfce963aa3df8464fbebdfb9170cb5740f97a4fd902a57861c0b65100c0dda81cb3572389a0222550148a

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

@@ -386,6 +386,7 @@ class Lab::Lims::Api::RestApi
     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: patient_id) if patient_id
 
     orders
@@ -394,6 +395,7 @@ class Lab::Lims::Api::RestApi
   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))
   end
 
   def orders_without_reason(patient_id = nil)
@@ -401,6 +403,7 @@ class Lab::Lims::Api::RestApi
     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: patient_id) if patient_id
 
     orders

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

@@ -12,7 +12,7 @@ module Lab
 
       class << self
         def preferred_api
-          emr_api_application('lims_api', 'couchdb')
+          emr_api_application('lims_api')
         end
 
         ##

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

@@ -32,7 +32,7 @@ module Lab
       def specimen_type_id
         lims_specimen_name = self['sample_type']&.strip&.downcase
 
-        if %w[specimen_not_collected not_assigned not_specified].include?(lims_specimen_name)
+        if lims_specimen_name.nil? || %w[specimen_not_collected not_assigned not_specified].include?(lims_specimen_name)
           return ConceptName.select(:concept_id).find_by_name!('Unknown').concept_id
         end
 

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

@@ -17,21 +17,17 @@ module Lab
         loop do
           logger.info('Looking for new orders to push to LIMS...')
           orders = orders_pending_sync(batch_size).all
+
+          logger.debug("Found #{orders.size} orders...")
           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
-          # sometimes leads to unnecessary database hits for checking counts).
-          if orders.empty? && !wait
-            logger.info('Finished processing orders; exiting...')
-            break
-          end
+          break unless wait
 
+          logger.info('Waiting for orders...')
           sleep(Lab::Lims::Config.updates_poll_frequency)
         end
       end
@@ -51,15 +47,20 @@ module Lab
 
         ActiveRecord::Base.transaction do
           if mapping && !order.voided.zero?
-            Rails.logger.info("Deleting order ##{order_dto['accession_number']} from LIMS")
+            Rails.logger.info("Deleting order ##{order_dto[:accession_number]} from LIMS")
             lims_api.delete_order(mapping.lims_id, order_dto)
             mapping.destroy
           elsif mapping
-            Rails.logger.info("Updating order ##{order_dto['accession_number']} in LIMS")
+            Rails.logger.info("Updating order ##{order_dto[:accession_number]} in LIMS")
             lims_api.update_order(mapping.lims_id, order_dto)
             mapping.update(pushed_at: Time.now)
+          elsif order_dto[:_id] && Lab::LimsOrderMapping.where(lims_id: order_dto[:_id]).exists?
+            # HACK: v1.1.7 had a bug where duplicates of recently created orders where being created by
+            # the pull worker. This here detects those duplicates and voids them.
+            Rails.logger.warn("Duplicate accession number found: #{order_dto[:_id]}, skipping order...")
+            fix_duplicates!(order)
           else
-            Rails.logger.info("Creating order ##{order_dto['accession_number']} in LIMS")
+            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)
@@ -82,6 +83,7 @@ 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))
+                     .order(date_created: :desc)
       end
 
       def updated_orders
@@ -95,6 +97,7 @@ module Lab
                              OR obs.date_created > :last_updated',
                             last_updated: last_updated)
                      .group('orders.order_id')
+                     .order(discontinued_date: :desc, date_created: :desc)
       end
 
       def voided_orders
@@ -103,6 +106,34 @@ module Lab
                      .where(order_type: OrderType.where(name: Lab::Metadata::ORDER_TYPE_NAME),
                             order_id: Lab::LimsOrderMapping.all.select(:order_id),
                             voided: 1)
+                     .order(date_voided: :desc)
+      end
+
+      ##
+      # HACK: Checks for duplicates previously created by version 1.1.7 pull worker bug due to this proving orders
+      # that have not been pushed to LIMS as orders awaiting updates.
+      def fix_duplicates!(order)
+        return order.void('Duplicate created by bug in HIS-EMR-API-Lab v1.1.7') unless order_has_specimen?(order)
+
+        duplicate_order = Lab::LabOrder.where(accession_number: order.accession_number)
+                                       .where.not(order_id: order.order_id)
+                                       .first
+        return unless duplicate_order
+
+        if !order_has_results?(order) && (order_has_results?(duplicate_order) || order_has_specimen?(duplicate_order))
+          order.void('DUplicate created by bug in HIS-EMR-API-Lab v1.1.7')
+        else
+          duplicate_order.void('Duplicate created by bug in HIS-EMR-API-Lab v1.1.7')
+          Lab::LimsOrderMapping.find_by_lims_id(order.accession_number)&.destroy
+        end
+      end
+
+      def order_has_results?(order)
+        order.results.exists?
+      end
+
+      def order_has_specimen?(order)
+        order.concept_id == ConceptName.find_by_name!('Unknown').concept_id
       end
     end
   end

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

@@ -43,8 +43,11 @@ module Lab
         end
       end
 
+      LOG_FILES_TO_KEEP = 5
+      LOG_FILE_SIZE = 500.megabytes
+
       def self.start_worker(worker_name)
-        Rails.logger = LoggerMultiplexor.new(log_path("#{worker_name}.log"), $stdout)
+        Rails.logger = LoggerMultiplexor.new(file_logger(worker_name), $stdout)
         ActiveRecord::Base.logger = Rails.logger
         Rails.logger.level = :debug
 
@@ -60,6 +63,10 @@ module Lab
         end
       end
 
+      def self.file_logger(worker_name)
+        Logger.new(log_path("#{worker_name}.log"), LOG_FILES_TO_KEEP, LOG_FILE_SIZE)
+      end
+
       def self.log_path(filename)
         Lab::Lims::Utils::LIMS_LOG_PATH.join(filename)
       end

data/db/migrate/20210807111531_add_default_to_lims_order_mapping.rb

@@ -1,6 +1,6 @@
 class AddDefaultToLimsOrderMapping < ActiveRecord::Migration[5.2]
   def up
-    ActiveRecord::Base.connection.execute('ALTER TABLE lab_lims_order_mappings MODIFY revision VARCHAR(256) DEFAULT NULL')
+    change_column :lab_lims_order_mappings, :revision, :string, limit: 256, default: nil, null: true
   end
 
   def down; end

data/lib/lab/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Lab
-  VERSION = '1.1.6'
+  VERSION = '1.1.12'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: his_emr_api_lab
 version: !ruby/object:Gem::Version
-  version: 1.1.6
+  version: 1.1.12
 platform: ruby
 authors:
 - Elizabeth Glaser Pediatric Foundation Malawi
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-08-07 00:00:00.000000000 Z
+date: 2021-08-24 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: couchrest
@@ -331,7 +331,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.8
+rubygems_version: 3.1.4
 signing_key: 
 specification_version: 4
 summary: Lab extension for the HIS-EMR-API