his_emr_api_lab 1.1.9 → 1.1.15

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 9b0a9cfb4676982b299600078fa0421133af14a0b8d15dd49ac9ca1933fad7e0
+  metadata.gz: a0345aafa5a183730006a41e0451a129eea8b201622af42c9ae9b13fb23e410d
+  data.tar.gz: d2003b6e1872c4d3c16b1bc80edea36d4ac353d62b37aad71932119085c5aecb
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+  metadata.gz: afb1c33968cb197c30b9f702b04188e93c886982a2304dc21aefcfd46add7aeb62df2307d53c6f2794dba8895a049f131b82835046280de920996d70eb6f1b84
+  data.tar.gz: ad3514949b17d623983acd6c8f7c4af305da52e4eda81e2345d94d7390e2d35aa7796d91397d819f0f64efa73803a011b4e9bd46baa574b265b04346da30b1d2

data/app/jobs/lab/push_order_job.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Lab
+  ##
+  # Push an order to LIMS.
+  class PushOrderJob < ApplicationJob
+    def perform(order_id)
+      push_worker = Lab::Lims::PushWorker.new(Lab::Lims::ApiFactory.create_api)
+      push_worker.push_order_by_id(order_id)
+    end
+  end
+end

data/app/jobs/lab/update_patient_orders_job.rb

@@ -20,8 +20,7 @@ module Lab
           break false
         end
 
-        lims_api = Lab::Lims::Api::RestApi.new(Lab::Lims::Config.rest_api)
-        worker = Lab::Lims::PullWorker.new(lims_api)
+        worker = Lab::Lims::PullWorker.new(Lab::Lims::ApiFactory.create_api)
         worker.pull_orders(patient_id: patient_id)
 
         true

data/app/jobs/lab/void_order_job.rb

@@ -10,8 +10,7 @@ module Lab
       User.current = Lab::Lims::Utils.lab_user
       Location.current = Location.find_by_name('ART clinic')
 
-      lims_api = Lab::Lims::Api::RestApi.new
-      worker = Lab::Lims::Worker.new(lims_api)
+      worker = Lab::Lims::PushWorker.new(Lab::Lims::ApiFactory.create_api)
       worker.push_order(Lab::LabOrder.unscoped.find(order_id))
     end
   end

data/app/models/lab/lab_order.rb

@@ -42,14 +42,21 @@ module Lab
     end
 
     scope :drawn, -> { where.not(concept_id: ConceptName.where(name: 'Unknown').select(:concept_id)) }
-
     scope :not_drawn, -> { where(concept_id: ConceptName.where(name: 'Unknown').select(:concept_id)) }
 
+    after_commit :queue_lims_push
+
     def self.prefetch_relationships
       includes(:reason_for_test,
                :requesting_clinician,
                :target_lab,
                tests: [:result])
     end
+
+    private
+
+    def queue_lims_push
+      Lab::PushOrderJob.perform_later(order_id)
+    end
   end
 end

data/app/serializers/lab/lab_order_serializer.rb

@@ -6,7 +6,7 @@ module Lab
       tests ||= order.voided == 1 ? voided_tests(order) : order.tests
       requesting_clinician ||= order.requesting_clinician
       reason_for_test ||= order.reason_for_test
-      target_lab ||= order.target_lab
+      target_lab = target_lab&.value_text || order.target_lab&.value_text || Location.current_health_center&.name
 
       ActiveSupport::HashWithIndifferentAccess.new(
         {
@@ -21,7 +21,7 @@ module Lab
             name: concept_name(order.concept_id)
           },
           requesting_clinician: requesting_clinician&.value_text,
-          target_lab: target_lab&.value_text,
+          target_lab: target_lab,
           reason_for_test: {
             concept_id: reason_for_test&.value_coded,
             name: concept_name(reason_for_test&.value_coded)

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

@@ -0,0 +1,21 @@
+# frozen_string_literal: true
+
+module Lab
+  module Lims
+    module Api
+      ##
+      # A LIMS Api wrappper that does nothing really.
+      #
+      # Primarily meant as a dummy for testing environments.
+      class BlackholeApi
+        def create_order(order_dto); end
+
+        def update_order(order_dto); end
+
+        def void_order(order_dto); end
+
+        def consume_orders(&_block); end
+      end
+    end
+  end
+end

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

@@ -44,9 +44,6 @@ class Lab::Lims::Api::RestApi
 
   def consume_orders(*_args, patient_id: nil, **_kwargs)
     orders_pending_updates(patient_id).each do |order|
-      mapping = Lab::LimsOrderMapping.find_by(order_id: order.order_id)
-      next if mapping.nil? || check_and_fix_duplicate!(mapping, order)
-
       order_dto = Lab::Lims::OrderSerializer.serialize_order(order)
 
       if order_dto['priority'].nil? || order_dto['sample_type'].casecmp?('not_specified')
@@ -389,6 +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
@@ -397,6 +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)
@@ -404,28 +403,9 @@ 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
   end
-
-  # Checks for duplicates previously created due to this proving orders that have
-  # not been pushed to LIMS as orders awaiting updates.
-  def check_and_fix_duplicate!(mapping, order)
-    duplicate_orders = Lab::LabOrder.where(accession_number: mapping.lims_id)
-                                    .where.not(order_id: mapping.order_id)
-    return false if duplicate_orders.size.zero?
-
-    unless order.discontinued
-      order.void('Duplicate created due to bug in HIS-EMR-API-Lab v1.1.7')
-      mapping.destroy
-      return true
-    end
-
-    duplicate_orders.each do |duplicate_order|
-      duplicate_order.void("Has duplicate that contains updates ##{order.order_id}: Duplicate was created by bug in HIS-EMR-API-Lab v1.1.7")
-    end
-
-    true
-  end
 end

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

@@ -0,0 +1,19 @@
+# frozen_string_literal: true
+
+module Lab
+  module Lims
+    ##
+    # Creates LIMS Apis based on current configuration
+    module ApiFactory
+      def self.create_api
+        return Lab::Lims::Api::BlackholeApi.new if Rails.env.casecmp?('test')
+
+        case Lab::Lims::Config.preferred_api
+        when /rest/i then Lab::Lims::Api::RestApi.new(Lab::Lims::Config.rest_api)
+        when /couchdb/ then Lab::Lims::Api::CouchDbApi.new(config: Lab::Lims::Config.couchdb_api)
+        else raise "Invalid lims_api configuration: #{Lab::Lims::Config.preferred_api}"
+        end
+      end
+    end
+  end
+end

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

@@ -46,9 +46,20 @@ require_relative 'utils'
 
 module Lab
   module Lims
+    ##
+    # Tools for performing a bulk import of data from LIMS' databases to local OpenMRS database.
+    #
+    # Migration sources supported:
+    #   - MySQL
+    #   - CouchDB
+    #
+    # The sources above can be changed by setting the environment various MIGRATION_SOURCE to
+    # either mysql or couchdb.
     module Migrator
       MAX_THREADS = ENV.fetch('MIGRATION_WORKERS', 6).to_i
 
+      ##
+      # A Lab::Lims::Api object that supports crawling of a LIMS CouchDB instance.
       class CouchDbMigratorApi < Lab::Lims::Api::CouchDbApi
         def initialize(*args, processes: 1, on_merge_processes: nil, **kwargs)
           super(*args, **kwargs)
@@ -91,6 +102,12 @@ module Lab
         end
       end
 
+      ##
+      # Extends the PullWorker to provide pause/resume capabilities.
+      #
+      # Migrations can be take a long time to complete, in cases where something
+      # went wrong you wouldn't to start all over. This worker thus saves
+      # progress and allows for the process to continue from whether it stopped.
       class MigrationWorker < PullWorker
         LOG_FILE_PATH = Utils::LIMS_LOG_PATH.join('migration-last-id.dat')
 

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

@@ -2,6 +2,8 @@
 
 module Lab
   module Lims
+    ##
+    # Pulls orders from a Lims API object and saves them to the local database.
     class PullWorker
       attr_reader :lims_api
 
@@ -100,9 +102,7 @@ module Lab
                           .distinct(:patient_id)
                           .all
 
-        if patients.size > 1
-          raise DuplicateNHID, "Duplicate National Health ID: #{nhid}"
-        end
+        raise DuplicateNHID, "Duplicate National Health ID: #{nhid}" if patients.size > 1
 
         patients.first
       end
@@ -166,9 +166,7 @@ module Lab
       def create_order(patient, order_dto)
         logger.debug("Creating order ##{order_dto['_id']}")
         order = OrdersService.order_test(order_dto.to_order_service_params(patient_id: patient.patient_id))
-        unless order_dto['test_results'].empty?
-          update_results(order, order_dto['test_results'])
-        end
+        update_results(order, order_dto['test_results']) unless order_dto['test_results'].empty?
 
         order
       end
@@ -177,9 +175,7 @@ module Lab
         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'))
-        unless order_dto['test_results'].empty?
-          update_results(order, order_dto['test_results'])
-        end
+        update_results(order, order_dto['test_results']) unless order_dto['test_results'].empty?
 
         order
       end
@@ -283,9 +279,7 @@ module Lab
         mapping = Lab::LimsOrderMapping.find_by(lims_id: lims_id)
         return nil unless mapping
 
-        if Lab::LabOrder.where(order_id: mapping.order_id).exists?
-          return mapping
-        end
+        return mapping if Lab::LabOrder.where(order_id: mapping.order_id).exists?
 
         mapping.destroy
         nil

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

@@ -2,6 +2,8 @@
 
 module Lab
   module Lims
+    ##
+    # Pushes all local orders to a LIMS Api object.
     class PushWorker
       attr_reader :lims_api
 
@@ -17,27 +19,25 @@ 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
 
       def push_order_by_id(order_id)
-        order = Lab::LabOrder.unscoped.find(order_id)
+        order = Lab::LabOrder.joins(order_type: { name: 'Lab' })
+                             .unscoped
+                             .find(order_id)
         push_order(order)
       end
 
@@ -51,18 +51,20 @@ 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...")
-            nil
+            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)
@@ -85,6 +87,7 @@ 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
@@ -98,6 +101,7 @@ 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
@@ -106,6 +110,34 @@ 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

@@ -43,9 +43,12 @@ 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)
-        # ActiveRecord::Base.logger = Rails.logger
+        Rails.logger = LoggerMultiplexor.new(file_logger(worker_name), $stdout)
+        ActiveRecord::Base.logger = Rails.logger
         Rails.logger.level = :debug
 
         File.open(log_path("#{worker_name}.lock"), File::RDWR | File::CREAT, 0o644) do |fout|
@@ -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
@@ -72,11 +79,7 @@ module Lab
       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
+        Lab::Lims::ApiFactory.create_api
       end
     end
   end

data/app/services/lab/orders_service.rb

@@ -169,6 +169,8 @@ module Lab
       ##
       # Attach the lab where the test is going to get carried out.
       def add_target_lab(order, params)
+        return nil unless params['target_lab']
+
         create_order_observation(
           order,
           Lab::Metadata::TARGET_LAB_CONCEPT_NAME,

data/lib/lab/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Lab
-  VERSION = '1.1.9'
+  VERSION = '1.1.15'
 end

data/lib/tasks/loaders/data/test-measures.csv

@@ -68,6 +68,7 @@
 "Hepatitis B Test","Hepatitis B"
 "Hepatitis C Test","Hepatitis C"
 "Rheumatoid Factor Test","Rheumatoid Factor"
+"CrAg","CrAg"
 "Cryptococcus Antigen Test","CrAg"
 "Anti Streptolysis O","ASO"
 "C-reactive protein","CRP"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: his_emr_api_lab
 version: !ruby/object:Gem::Version
-  version: 1.1.9
+  version: 1.1.15
 platform: ruby
 authors:
 - Elizabeth Glaser Pediatric Foundation Malawi
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-08-23 00:00:00.000000000 Z
+date: 2021-10-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: couchrest
@@ -248,6 +248,7 @@ files:
 - app/controllers/lab/test_types_controller.rb
 - app/controllers/lab/tests_controller.rb
 - app/jobs/lab/application_job.rb
+- app/jobs/lab/push_order_job.rb
 - app/jobs/lab/update_patient_orders_job.rb
 - app/jobs/lab/void_order_job.rb
 - app/mailers/lab/application_mailer.rb
@@ -265,10 +266,12 @@ files:
 - app/services/lab/accession_number_service.rb
 - app/services/lab/concepts_service.rb
 - app/services/lab/labelling_service/order_label.rb
+- app/services/lab/lims/api/blackhole_api.rb
 - app/services/lab/lims/api/couchdb_api.rb
 - app/services/lab/lims/api/mysql_api.rb
 - app/services/lab/lims/api/rest_api.rb
 - app/services/lab/lims/api/ws_api.rb
+- app/services/lab/lims/api_factory.rb
 - app/services/lab/lims/config.rb
 - app/services/lab/lims/exceptions.rb
 - app/services/lab/lims/migrator.rb
@@ -331,7 +334,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.1.4
+rubygems_version: 3.0.8
 signing_key: 
 specification_version: 4
 summary: Lab extension for the HIS-EMR-API