his_emr_api_lab 1.1.13 → 1.1.17

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: f7b7bee82670948e0315bde7a3d0f9cab91476bcb27646ec7c234e0c96d11bc9
-  data.tar.gz: 127d70d6a044a8ddc5dcc25ed2460d1fcb463d8f27f3817b54fca7d5ada6d88a
+  metadata.gz: 9180f5367d311361a972c4ec15d72bbd6296731adf1bd71b4ae25a1ff58dc4b5
+  data.tar.gz: d6b399321648924e31cecda13c4348b53370796a89344947b0932f0720ed0b11
 SHA512:
-  metadata.gz: 421db4bdc5cb32b994d9329c87ebe8c79eae681765abe980bd87c6fab83c70de74961d78845d2602af31aea018b480ddcad9f97de4dfa01a8cd975c8c9a49db8
-  data.tar.gz: 4d1c1df19df7b297e66d44055bcbe88b410f25e744a56f0bb46a99f8fd06af9e25ad332499cbd34e8ea10f7879c14455f8b16d376e24c7a50bf7518156ce3646
+  metadata.gz: 284aab03e785c885b3e1a88f8fef8826c73c89b9f7436e17aa730d14c2f3fc5fe14cb65e2f29ce6171675a363c5945b73d547094f11a4187d67dbdfc9636c4dd
+  data.tar.gz: 0c849e47f58c86fd221f9c97111c0028f3fafdad3cf07393baf64928ebd462008895550fd4ab754e2708654cde5867fb81abb07dcbdd289454e4da14bbafd4d2

data/app/controllers/lab/orders_controller.rb

@@ -8,14 +8,15 @@ module Lab
         OrdersService.order_test(order_params)
       end
 
+      orders.each { |order| Lab::PushOrderJob.perform_later(order.fetch(:order_id)) }
+
       render json: orders, status: :created
     end
 
     def update
       specimen = params.require(:specimen).permit(:concept_id)
-
-      order = OrdersService.update_order(params[:id], specimen: specimen,
-                                                      force_update: params[:force_update])
+      order = OrdersService.update_order(params[:id], specimen: specimen, force_update: params[:force_update])
+      Lab::PushOrderJob.perform_later(order.fetch(:order_id))
 
       render json: order
     end
@@ -23,11 +24,13 @@ module Lab
     def index
       filters = params.permit(%i[patient_id accession_number date status])
 
+      Lab::UpdatePatientOrdersJob.perform_later(filters[:patient_id]) if filters[:patient_id]
       render json: OrdersSearchService.find_orders(filters)
     end
 
     def destroy
       OrdersService.void_order(params[:id], params[:reason])
+      Lab::VoidOrderJob.perform_later(params[:id])
 
       render status: :no_content
     end

data/app/controllers/lab/tests_controller.rb

@@ -14,7 +14,8 @@ class Lab::TestsController < ::ApplicationController
     order_id, test_concepts = test_params.require(%i[order_id tests])
     date = test_params[:date] || Date.today
 
-    tests = service.create_tests(Order.find(order_id), date, test_concepts)
+    tests = service.create_tests(Lab::LabOrder.find(order_id), date, test_concepts)
+    Lab::PushOrderJob.perform_later(order_id)
 
     render json: tests, status: :created
   end

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

@@ -42,7 +42,6 @@ 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)) }
 
     def self.prefetch_relationships

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 = target_lab || order.target_lab || Location.current_health_center.name
+      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

@@ -395,7 +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))
+                            .where.not(accession_number: Lab::LimsOrderMapping.select(:lims_id).where("pulled_at IS NULL"))
   end
 
   def orders_without_reason(patient_id = nil)

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
 
@@ -33,7 +35,9 @@ module Lab
       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
 

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

@@ -79,11 +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_search_service.rb

@@ -5,14 +5,6 @@ module Lab
   module OrdersSearchService
     class << self
       def find_orders(filters)
-        # A bit of hack-ish solution to have a patient's orders updated upon
-        # scanning of a patient. Done in this way to deal with LIMS' lack of
-        # a notification system for lab order updates. We are limited to polling
-        # for updates on a per order basis.
-        if filters[:patient_id]
-          Lab::UpdatePatientOrdersJob.perform_later(filters[:patient_id])
-        end
-
         extra_filters = pop_filters(filters, :date, :end_date, :status)
 
         orders = Lab::LabOrder.prefetch_relationships
@@ -39,13 +31,9 @@ module Lab
         date = date&.to_date
         end_date = end_date&.to_date
 
-        if date && end_date
-          return orders.where('start_date BETWEEN ? AND ?', date, end_date + 1.day)
-        end
+        return orders.where('start_date BETWEEN ? AND ?', date, end_date + 1.day) if date && end_date
 
-        if date
-          return orders.where('start_date BETWEEN ? AND ?', date, date + 1.day)
-        end
+        return orders.where('start_date BETWEEN ? AND ?', date, date + 1.day) if date
 
         return orders.where('start_date < ?', end_date + 1.day) if end_date
 

data/app/services/lab/orders_service.rb

@@ -100,7 +100,6 @@ module Lab
 
         order.tests.each { |test| test.void(reason) }
         voided = order.void(reason)
-        Lab::VoidOrderJob.perform_later(order_id)
 
         voided
       end

data/lib/lab/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Lab
-  VERSION = '1.1.13'
+  VERSION = '1.1.17'
 end

data/lib/logger_multiplexor.rb

@@ -23,10 +23,16 @@ class LoggerMultiplexor
   end
 
   def method_missing(method_name, *args)
-    @loggers.each { |logger| logger.method(method_name).call(*args) }
+    if respond_to_missing?(method_name)
+      @loggers.each { |logger| logger.send(method_name, *args) }
+    else
+      super
+    end
   end
 
   def respond_to_missing?(method_name)
-    @loggers.all? { |logger| logger.respond_to_missing?(method_name) }
+    @loggers.all? do |logger|
+      logger.respond_to?(method_name)
+    end
   end
 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: 1.1.13
+  version: 1.1.17
 platform: ruby
 authors:
 - Elizabeth Glaser Pediatric Foundation Malawi
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-09-06 00:00:00.000000000 Z
+date: 2021-11-02 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: 3.2.3
 signing_key: 
 specification_version: 4
 summary: Lab extension for the HIS-EMR-API