his_emr_api_lab 1.2.0 → 2.0.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 9b30e492def430c355c0ac0a80c1c0af05d5fede383fa50f5664e3b9340b2180
-  data.tar.gz: 948693f89c85c6a2111c8b10c1accd91fdbb2d9bea3ad8ef41157d7421af7fd1
+  metadata.gz: d8ec4677af7163c2d90687ca46d2ebdfa5e438abe0d705a621545d26d2889b7e
+  data.tar.gz: 8a071aaef1ce28cae2b57253e739f406f60fe0724a8379414c667d20e756efa6
 SHA512:
-  metadata.gz: 69ec800aefa4f198dc16f392500723c47a6b1e24dd1b600b6646bf552c7c9a63533a7257810d7605128eab5f54c0c8ab76fe06ff60621f010209109675b7ba3e
-  data.tar.gz: ae17044c979b38e3f6182d23b29d36aeb90845e9238d9c85f63c7d7971cc2ae99bb87a64d4684b33b2dbc16a871ebf0615e3ec92b589ea9040dcd3d6eefedd91
+  metadata.gz: cddefdce79e09c49a190fc3c31d92eb15d5394b1fe1a5187d2a54c614d48da06b75d7863e24cf5196c076adc2c3400119d8a108ffdb62a72bdc85cf3523c7b55
+  data.tar.gz: caf9c33fc7480884576e83f07335d768705255a2586508c2e616cca9f0667cc422cde28267e3234f9995deb99727f5b2d482db4019fdfba6d83fdd699536c6e4

data/Rakefile

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 begin
   require 'bundler/setup'
 rescue LoadError
@@ -14,7 +16,7 @@ RDoc::Task.new(:rdoc) do |rdoc|
   rdoc.rdoc_files.include('lib/**/*.rb')
 end
 
-APP_RAKEFILE = File.expand_path("spec/dummy/Rakefile", __dir__)
+APP_RAKEFILE = File.expand_path('spec/dummy/Rakefile', __dir__)
 load 'rails/tasks/engine.rake'
 
 load 'rails/tasks/statistics.rake'

data/app/controllers/lab/application_controller.rb

@@ -2,5 +2,10 @@
 
 module Lab
   class ApplicationController < ::ApplicationController
+    before_action :permit_parameters
+
+    def permit_parameters
+      params.permit!
+    end
   end
 end

data/app/controllers/lab/orders_controller.rb

@@ -17,15 +17,15 @@ module Lab
     end
 
     def update
-      specimen = params.require(:specimen).permit(:concept_id)
-      order = OrdersService.update_order(params[:id], specimen: specimen, force_update: params[:force_update])
+      specimen = params.require(:specimen).slice(:concept_id)
+      order = OrdersService.update_order(params[:id], specimen:, force_update: params[:force_update])
       Lab::PushOrderJob.perform_later(order.fetch(:order_id))
 
       render json: order
     end
 
     def index
-      filters = params.permit(%i[patient_id accession_number date status])
+      filters = params.slice(:patient_id, :accession_number, :date, :status)
 
       Lab::UpdatePatientOrdersJob.perform_later(filters[:patient_id]) if filters[:patient_id]
       render json: OrdersSearchService.find_orders(filters)

data/app/controllers/lab/specimen_types_controller.rb

@@ -3,7 +3,7 @@
 module Lab
   class SpecimenTypesController < ApplicationController
     def index
-      filters = params.permit(%w[name test_type])
+      filters = params.slice(:name, :test_type)
 
       specimen_types = ConceptsService.specimen_types(name: filters['name'],
                                                       test_type: filters['test_type'])

data/app/controllers/lab/test_result_indicators_controller.rb

@@ -1,9 +1,11 @@
 # frozen_string_literal: true
 
-class Lab::TestResultIndicatorsController < ApplicationController
-  def index
-    test_type_id = params.require(:test_type_id)
+module Lab
+  class TestResultIndicatorsController < ApplicationController
+    def index
+      test_type_id = params.require(:test_type_id)
 
-    render json: Lab::ConceptsService.test_result_indicators(test_type_id)
+      render json: Lab::ConceptsService.test_result_indicators(test_type_id)
+    end
   end
 end

data/app/controllers/lab/test_types_controller.rb

@@ -3,7 +3,7 @@
 module Lab
   class TestTypesController < ApplicationController
     def index
-      filters = params.permit(%w[name specimen_type])
+      filters = params.slice(:name, :specimen_type)
 
       test_types = ConceptsService.test_types(name: filters['name'],
                                               specimen_type: filters['specimen_type'])

data/app/controllers/lab/tests_controller.rb

@@ -1,26 +1,29 @@
 # frozen_string_literal: true
 
-class Lab::TestsController < ::ApplicationController
-  def index
-    filters = params.permit(%i[order_date accession_number patient_id test_type_id specimen_type_id pending_results])
+module Lab
+  class TestsController < ApplicationController
+    def index
+      filters = params.slice(:order_date, :accession_number, :patient_id, :test_type_id, :specimen_type_id,
+                             :pending_results)
 
-    tests = service.find_tests(filters)
-    render json: tests
-  end
+      tests = service.find_tests(filters)
+      render json: tests
+    end
 
-  # Add a specimen to an existing order
-  def create
-    test_params = params.permit(:order_id, :date, tests: [:concept_id])
-    order_id, test_concepts = test_params.require(%i[order_id tests])
-    date = test_params[:date] || Date.today
+    # Add a specimen to an existing order
+    def create
+      test_params = params.slice(:order_id, :date, tests: [:concept_id])
+      order_id, test_concepts = test_params.require(%i[order_id tests])
+      date = test_params[:date] || Date.today
 
-    tests = service.create_tests(Lab::LabOrder.find(order_id), date, test_concepts)
-    Lab::PushOrderJob.perform_later(order_id)
+      tests = service.create_tests(Lab::LabOrder.find(order_id), date, test_concepts)
+      Lab::PushOrderJob.perform_later(order_id)
 
-    render json: tests, status: :created
-  end
+      render json: tests, status: :created
+    end
 
-  def service
-    Lab::TestsService
+    def service
+      Lab::TestsService
+    end
   end
 end

data/app/jobs/lab/application_job.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 module Lab
   class ApplicationJob < ActiveJob::Base
   end

data/app/jobs/lab/update_patient_orders_job.rb

@@ -21,7 +21,7 @@ module Lab
         end
 
         worker = Lab::Lims::PullWorker.new(Lab::Lims::ApiFactory.create_api)
-        worker.pull_orders(patient_id: patient_id)
+        worker.pull_orders(patient_id:)
 
         true
       end

data/app/mailers/lab/application_mailer.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 module Lab
   class ApplicationMailer < ActionMailer::Base
     default from: 'from@example.com'

data/app/models/lab/application_record.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 module Lab
   class ApplicationRecord < ActiveRecord::Base
     self.abstract_class = true

data/app/models/lab/lab_order.rb

@@ -6,7 +6,7 @@ module Lab
       def make_obs_concept_filter(concept_name)
         concept = ConceptName.where(name: concept_name).select(:concept_id)
 
-        -> { where(concept: concept) }
+        -> { where(concept:) }
       end
     end
 

data/app/models/lab/lims_failed_import.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 module Lab
   class LimsFailedImport < ApplicationRecord
   end

data/app/serializers/lab/lab_order_serializer.rb

@@ -21,7 +21,7 @@ module Lab
             name: concept_name(order.concept_id)
           },
           requesting_clinician: requesting_clinician&.value_text,
-          target_lab: target_lab,
+          target_lab:,
           reason_for_test: {
             concept_id: reason_for_test&.value_coded,
             name: concept_name(reason_for_test&.value_coded)
@@ -50,7 +50,7 @@ module Lab
     def self.voided_tests(order)
       concept = ConceptName.where(name: Lab::Metadata::TEST_TYPE_CONCEPT_NAME)
                            .select(:concept_id)
-      LabTest.unscoped.where(concept: concept, order: order, voided: true)
+      LabTest.unscoped.where(concept:, order:, voided: true)
     end
   end
 end

data/app/serializers/lab/result_serializer.rb

@@ -16,8 +16,8 @@ module Lab
             name: concept_name&.name
           },
           date: measure.obs_datetime,
-          value: value,
-          value_type: value_type,
+          value:,
+          value_type:,
           value_modifier: measure.value_modifier
         }
       end

data/app/services/lab/accession_number_service.rb

@@ -24,10 +24,10 @@ module Lab
       private
 
       def find_counter(date)
-        counter = Lab::LabAccessionNumberCounter.find_by(date: date)
+        counter = Lab::LabAccessionNumberCounter.find_by(date:)
         return counter if counter
 
-        Lab::LabAccessionNumberCounter.create(date: date, value: 1)
+        Lab::LabAccessionNumberCounter.create(date:, value: 1)
       end
 
       # Checks if date does not exceed system date

data/app/services/lab/concepts_service.rb

@@ -5,7 +5,7 @@ module Lab
   module ConceptsService
     def self.test_types(name: nil, specimen_type: nil)
       test_types = ConceptSet.find_members_by_name(Lab::Metadata::TEST_TYPE_CONCEPT_NAME)
-      test_types = test_types.filter_members(name: name) if name
+      test_types = test_types.filter_members(name:) if name
 
       unless specimen_type
         return test_types.joins('INNER JOIN concept_name ON concept_set.concept_id = concept_name.concept_id AND concept_name.voided = 0 AND concept_name.locale_preferred = 1')
@@ -31,7 +31,7 @@ module Lab
 
     def self.specimen_types(name: nil, test_type: nil)
       specimen_types = ConceptSet.find_members_by_name(Lab::Metadata::SPECIMEN_TYPE_CONCEPT_NAME)
-      specimen_types = specimen_types.filter_members(name: name) if name
+      specimen_types = specimen_types.filter_members(name:) if name
 
       unless test_type
         return specimen_types.select('concept_name.concept_id, concept_name.name')

data/app/services/lab/labelling_service/order_label.rb

@@ -1,6 +1,6 @@
 # frozen_string_literal: true
 
-require 'auto12epl'
+require_relative '../../../../lib/auto12epl'
 
 module Lab
   module LabellingService
@@ -89,7 +89,7 @@ module Lab
       end
 
       def short_concept_name(concept_id)
-        ConceptName.where(concept_id: concept_id)
+        ConceptName.where(concept_id:)
                    .min_by { |concept| concept.name.size }
                    &.name
       end

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

@@ -14,7 +14,7 @@ module Lab
 
         def void_order(order_dto); end
 
-        def consume_orders(&_block); end
+        def consume_orders(&); end
       end
     end
   end

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

@@ -9,7 +9,7 @@ module Lab
     module Api
       ##
       # Talk to LIMS like a boss
-      class CouchDbApi
+      class CouchdbApi
         attr_reader :bum
 
         def initialize(config: nil)
@@ -30,10 +30,10 @@ module Lab
         # given block until the queue is empty or connection is terminated
         # by calling method +choke+.
         def consume_orders(from: 0, limit: 30)
-          bum.binge_changes(since: from, limit: limit, include_docs: true) do |change|
+          bum.binge_changes(since: from, limit:, include_docs: true) do |change|
             next unless change['doc']['type']&.casecmp?('Order')
 
-            yield OrderDTO.new(change['doc']), self
+            yield OrderDto.new(change['doc']), self
           end
         end
 

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

@@ -28,7 +28,7 @@ module Lab
         def consume_orders(from: nil, limit: 1000)
           loop do
             specimens_to_process = specimens(from, limit)
-            break if specimens_to_process.size.zero?
+            break if specimens_to_process.empty?
 
             processes = multiprocessed? ? @processes : 0
             on_merge_processes = ->(_item, index, _result) { @on_merge_processes&.call(from + index) }
@@ -42,7 +42,7 @@ module Lab
               end
 
               dto = make_order_dto(
-                specimen: specimen,
+                specimen:,
                 patient: specimen_patient(specimen['specimen_id']),
                 test_results: results,
                 specimen_status_trail: specimen_status_trail(specimen['specimen_id']),
@@ -162,7 +162,7 @@ module Lab
           drawn_by_first_name, drawn_by_last_name = specimen['drawn_by_name']&.split
           patient_first_name, patient_last_name = patient['name'].split
 
-          OrderDTO.new(
+          OrderDto.new(
             _id: specimen['doc_id'].blank? ? SecureRandom.uuid : specimen['doc_id'],
             _rev: '0',
             tracking_number: specimen['tracking_number'],
@@ -197,8 +197,8 @@ module Lab
               object[format_date(trail_entry['date'])] = {
                 status: trail_entry['status_name'],
                 updated_by: {
-                  first_name: first_name,
-                  last_name: last_name,
+                  first_name:,
+                  last_name:,
                   phone_number: trail_entry['updated_by_phone_number'],
                   id: trail_entry['updated_by_id']
                 }
@@ -230,7 +230,7 @@ module Lab
         end
 
         def format_test_result_for_dto(test_name, specimen, results, test_status_trail)
-          return {} if results.size.zero?
+          return {} if results.empty?
 
           result_create_event = test_status_trail[test_name]&.find do |trail_entry|
             trail_entry['status_name'].casecmp?('drawn')