his_emr_api_lab 1.2.0 → 2.0.0

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

@@ -89,7 +89,7 @@ module Lab
         end
 
         def find_order(lims_id)
-          mapping = Lab::LimsOrderMapping.where(lims_id: lims_id).select(:order_id)
+          mapping = Lab::LimsOrderMapping.where(lims_id:).select(:order_id)
           Lab::LabOrder.find_by(order_id: mapping)
         end
 

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

@@ -10,7 +10,7 @@ module Lab
 
         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)
+        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

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

@@ -80,7 +80,7 @@ module Lab
         # Returns: a path to a file found
         def find_config_path(filename)
           paths = [
-            "#{ENV['HOME']}/apps/nlims_controller/config/#{filename}",
+            "#{Dir.home}/apps/nlims_controller/config/#{filename}",
             "/var/www/nlims_controller/config/#{filename}",
             Rails.root.parent.join("nlims_controller/config/#{filename}")
           ]

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

@@ -2,6 +2,7 @@
 
 module Lab
   module Lims
+    class Exceptions < StandardError; end
     class LimsException < StandardError; end
     class DuplicateNHID < LimsException; end
     class MissingAccessionNumber < LimsException; end

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

@@ -29,10 +29,10 @@ require 'lab/lab_test'
 require 'lab/lims_order_mapping'
 require 'lab/lims_failed_import'
 
-require_relative './api/couchdb_api'
-require_relative './config'
-require_relative './pull_worker'
-require_relative './utils'
+require_relative 'api/couchdb_api'
+require_relative 'config'
+require_relative 'pull_worker'
+require_relative 'utils'
 
 require_relative '../orders_service'
 require_relative '../results_service'
@@ -42,7 +42,6 @@ require_relative '../../../serializers/lab/result_serializer'
 require_relative '../../../serializers/lab/test_serializer'
 
 require_relative 'order_dto'
-require_relative 'utils'
 
 module Lab
   module Lims
@@ -60,7 +59,7 @@ module Lab
 
       ##
       # A Lab::Lims::Api object that supports crawling of a LIMS CouchDB instance.
-      class CouchDbMigratorApi < Lab::Lims::Api::CouchDbApi
+      class CouchDbMigratorApi < Lab::Lims::Api::CouchdbApi
         def initialize(*args, processes: 1, on_merge_processes: nil, **kwargs)
           super(*args, **kwargs)
 
@@ -82,7 +81,7 @@ module Lab
               next unless row['doc']['type']&.casecmp?('Order')
 
               User.current = Utils.lab_user
-              yield OrderDTO.new(row['doc']), OpenStruct.new(last_seq: (from || 0) + limit, current_seq: from)
+              yield OrderDto.new(row['doc']), OpenStruct.new(last_seq: (from || 0) + limit, current_seq: from)
             end
 
             from += orders.size
@@ -141,7 +140,7 @@ module Lab
         def order_rejected(order_dto, reason)
           @rejections ||= []
 
-          @rejections << OpenStruct.new(order: order_dto, reason: reason)
+          @rejections << OpenStruct.new(order: order_dto, reason:)
         end
       end
 
@@ -168,7 +167,7 @@ module Lab
           ]
         end
 
-        save_csv(MIGRATION_REJECTIONS_CSV_PATH, headers: headers, rows: rows)
+        save_csv(MIGRATION_REJECTIONS_CSV_PATH, headers:, rows:)
       end
 
       MIGRATION_FAILURES_CSV_PATH = Utils::LIMS_LOG_PATH.join('migration-failures.csv')
@@ -185,13 +184,13 @@ module Lab
           ]
         end
 
-        save_csv(MIGRATION_FAILURES_CSV_PATH, headers: headers, rows: rows)
+        save_csv(MIGRATION_FAILURES_CSV_PATH, headers:, rows:)
       end
 
       MIGRATION_LOG_PATH = Utils::LIMS_LOG_PATH.join('migration.log')
 
       def self.start_migration
-        Dir.mkdir(Utils::LIMS_LOG_PATH) unless File.exist?(Utils::LIMS_LOG_PATH)
+        FileUtils.mkdir_p(Utils::LIMS_LOG_PATH)
 
         logger = LoggerMultiplexor.new(Logger.new($stdout), MIGRATION_LOG_PATH)
         logger.level = :debug
@@ -202,7 +201,7 @@ module Lab
         api_class = case ENV.fetch('MIGRATION_SOURCE', 'couchdb').downcase
                     when 'couchdb' then CouchDbMigratorApi
                     when 'mysql' then Api::MysqlApi
-                    else raise "Invalid MIGRATION_SOURCE: #{ENV['MIGRATION_SOURCE']}"
+                    else raise "Invalid MIGRATION_SOURCE: #{ENV.fetch('MIGRATION_SOURCE', nil)}"
                     end
 
         worker = MigrationWorker.new(api_class)

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

@@ -1,12 +1,12 @@
 # frozen_string_literal: true
 
-require_relative './exceptions'
+require_relative 'exceptions'
 
 module Lab
   module Lims
     ##
     # LIMS' Data Transfer Object for orders
-    class OrderDTO < ActiveSupport::HashWithIndifferentAccess
+    class OrderDto < ActiveSupport::HashWithIndifferentAccess
       include Utils
 
       ##
@@ -15,10 +15,10 @@ module Lab
         ActiveSupport::HashWithIndifferentAccess.new(
           program_id: lab_program.program_id,
           accession_number: self['tracking_number'],
-          patient_id: patient_id,
+          patient_id:,
           specimen: { concept_id: specimen_type_id },
           tests: self['tests']&.map { |test| { concept_id: test_type_id(test) } },
-          requesting_clinician: requesting_clinician,
+          requesting_clinician:,
           date: start_date,
           target_lab: facility_name(self['receiving_facility']),
           order_location: facility_name(self['sending_facility']),

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

@@ -1,13 +1,13 @@
 # frozen_string_literal: true
 
-require_relative './config'
-require_relative './order_dto'
-require_relative './utils'
+require_relative 'config'
+require_relative 'order_dto'
+require_relative 'utils'
 
 module Lab
   module Lims
     ##
-    # Serializes a LabOrder into a LIMS OrderDTO.
+    # Serializes a LabOrder into a LIMS OrderDto.
     module OrderSerializer
       class << self
         include Utils
@@ -15,8 +15,8 @@ module Lab
         def serialize_order(order)
           serialized_order = Lims::Utils.structify(Lab::LabOrderSerializer.serialize_order(order))
 
-          Lims::OrderDTO.new(
-            _id: Lab::LimsOrderMapping.find_by(order: order)&.lims_id || serialized_order.accession_number,
+          Lims::OrderDto.new(
+            _id: Lab::LimsOrderMapping.find_by(order:)&.lims_id || serialized_order.accession_number,
             tracking_number: serialized_order.accession_number,
             sending_facility: current_facility_name,
             receiving_facility: serialized_order.target_lab,
@@ -39,9 +39,9 @@ module Lab
         private
 
         def format_order_location(encounter_id)
-          location_id = Encounter.select(:location_id).where(encounter_id: encounter_id)
+          location_id = Encounter.select(:location_id).where(encounter_id:)
           location = Location.select(:name)
-                             .where(location_id: location_id)
+                             .where(location_id:)
                              .first
 
           location&.name
@@ -53,7 +53,7 @@ module Lab
           name = PersonName.find_by_person_id(patient_id)
           national_id = PatientIdentifier.joins(:type)
                                          .merge(PatientIdentifierType.where(name: 'National ID'))
-                                         .where(patient_id: patient_id)
+                                         .where(patient_id:)
                                          .first
           phone_number = PersonAttribute.joins(:type)
                                         .merge(PersonAttributeType.where(name: 'Cell phone Number'))
@@ -86,7 +86,7 @@ module Lab
         def find_arv_number(patient_id)
           PatientIdentifier.joins(:type)
                            .merge(PatientIdentifierType.where(name: 'ARV Number'))
-                           .where(patient_id: patient_id)
+                           .where(patient_id:)
                            .first&.identifier
         end
 
@@ -209,8 +209,8 @@ module Lab
         end
 
         def current_district
-          district = current_health_center.city_village\
-                       || current_health_center.parent&.name\
+          district = current_health_center.city_village \
+                       || current_health_center.parent&.name \
                        || GlobalProperty.find_by_property('current_health_center_district')&.property_value
 
           return district if district

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

@@ -17,10 +17,10 @@ module Lab
 
       ##
       # Pulls orders from the LIMS queue and writes them to the local database
-      def pull_orders(batch_size: 10_000, **kwargs)
+      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, **kwargs) 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])
@@ -137,7 +137,7 @@ module Lab
         person = Person.find(local_patient.id)
         person_name = PersonName.find_by_person_id(local_patient.id)
 
-        unless (person.gender.blank? && lims_patient['gender'].blank?)\
+        unless (person.gender.blank? && lims_patient['gender'].blank?) \
           || person.gender&.first&.casecmp?(lims_patient['gender']&.first)
           diff[:gender] = { local: person.gender, lims: lims_patient['gender'] }
         end
@@ -154,8 +154,8 @@ module Lab
       end
 
       def names_match?(name1, name2)
-        name1 = name1&.gsub(/'/, '')&.strip
-        name2 = name2&.gsub(/'/, '')&.strip
+        name1 = name1&.gsub("'", '')&.strip
+        name2 = name2&.gsub("'", '')&.strip
 
         return true if name1.blank? && name2.blank?
 
@@ -229,10 +229,11 @@ module Lab
 
           creator = format_result_entered_by(test_results['result_entered_by'])
 
-          ResultsService.create_results(test.id,  { provider_id: User.current.person_id,
-                                                    date: Utils.parse_date(test_results['date_result_entered'], result_date),
-                                                    comments: "LIMS import: Entered by: #{creator}",
-                                                    measures: measures } )
+          ResultsService.create_results(test.id, { provider_id: User.current.person_id,
+                                                   date: Utils.parse_date(test_results['date_result_entered'],
+                                                                          order[:order_date].to_s),
+                                                   comments: "LIMS import: Entered by: #{creator}",
+                                                   measures: })
         end
       end
 
@@ -241,7 +242,7 @@ module Lab
         test_concept = Utils.find_concept_by_name(test_name)
         raise "Unknown test name, #{test_name}!" unless test_concept
 
-        LabTest.find_by(order_id: order_id, value_coded: test_concept.concept_id)
+        LabTest.find_by(order_id:, value_coded: test_concept.concept_id)
       end
 
       def find_measure(_order, indicator_name, value)
@@ -256,7 +257,7 @@ module Lab
 
         ActiveSupport::HashWithIndifferentAccess.new(
           indicator: { concept_id: indicator.concept_id },
-          value_type: value_type,
+          value_type:,
           value: value_type == 'numeric' ? value.to_f : value,
           value_modifier: value_modifier.blank? ? '=' : value_modifier
         )
@@ -292,7 +293,7 @@ module Lab
         LimsFailedImport.create!(lims_id: order_dto[:_id],
                                  tracking_number: order_dto[:tracking_number],
                                  patient_nhid: order_dto[:patient][:id],
-                                 reason: reason,
+                                 reason:,
                                  diff: diff&.to_json)
       end
 
@@ -301,7 +302,7 @@ module Lab
       end
 
       def find_order_mapping_by_lims_id(lims_id)
-        mapping = Lab::LimsOrderMapping.find_by(lims_id: lims_id)
+        mapping = Lab::LimsOrderMapping.find_by(lims_id:)
         return nil unless mapping
 
         return mapping if Lab::LabOrder.where(order_id: mapping.order_id).exists?

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

@@ -60,10 +60,10 @@ module Lab
             Rails.logger.info("Updating order ##{order_dto[:accession_number]} in LIMS")
             lims_api.update_order(mapping.lims_id, order_dto)
             if order_dto['test_results'].nil? || order_dto['test_results'].empty?
-              mapping.update(pushed_at: Time.now)             
+              mapping.update(pushed_at: Time.now)
             else
-              mapping.update(pushed_at: Time.now, result_push_status: true)  
-           end
+              mapping.update(pushed_at: Time.now, result_push_status: true)
+            end
           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.
@@ -72,7 +72,7 @@ module Lab
           else
             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'],
+            Lab::LimsOrderMapping.create!(order:, lims_id: update['id'], revision: update['rev'],
                                           pushed_at: Time.now, result_push_status: false)
           end
         end
@@ -107,7 +107,7 @@ module Lab
                      .joins(:mapping)
                      .where('orders.discontinued_date > :last_updated
                              OR obs.date_created > orders.date_created AND lab_lims_order_mappings.result_push_status = 0',
-                            last_updated: last_updated)
+                            last_updated:)
                      .group('orders.order_id')
                      .order(discontinued_date: :desc, date_created: :desc)
       end

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

@@ -8,7 +8,7 @@ module Lab
     # Various helper methods for modules in the Lims namespaces...
     module Utils
       LIMS_LOG_PATH = Rails.root.join('log', 'lims')
-      FileUtils.mkdir_p(LIMS_LOG_PATH) unless File.exist?(LIMS_LOG_PATH)
+      FileUtils.mkdir_p(LIMS_LOG_PATH)
 
       def logger
         Rails.logger
@@ -49,17 +49,15 @@ module Lab
         god_user = User.first
 
         person = Person.create!(creator: god_user.user_id)
-        PersonName.create!(person: person, given_name: 'Lab', family_name: 'Daemon', creator: god_user.user_id)
+        PersonName.create!(person:, given_name: 'Lab', family_name: 'Daemon', creator: god_user.user_id)
 
-        User.create!(username: 'lab_daemon', person: person, creator: god_user.user_id)
+        User.create!(username: 'lab_daemon', person:, creator: god_user.user_id)
       end
 
       def self.parse_date(str_date, fallback_date = nil)
         str_date = str_date&.to_s
 
-        if str_date.blank? && fallback_date.blank?
-          raise "Can't parse blank date"
-        end
+        raise "Can't parse blank date" if str_date.blank? && fallback_date.blank?
 
         return parse_date(fallback_date) if str_date.blank?
 

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

@@ -2,7 +2,7 @@
 
 require 'logger_multiplexor'
 
-require_relative './api/couchdb_api'
+require_relative 'api/couchdb_api'
 
 module Lab
   module Lims

data/app/services/lab/orders_search_service.rb

@@ -11,8 +11,8 @@ module Lab
                               .where(filters)
                               .order(start_date: :desc)
 
-        orders = filter_orders_by_status(orders, pop_filters(extra_filters, :status))
-        orders = filter_orders_by_date(orders, extra_filters)
+        orders = filter_orders_by_status(orders, **pop_filters(extra_filters, :status))
+        orders = filter_orders_by_date(orders, **extra_filters)
 
         orders.map { |order| Lab::LabOrderSerializer.serialize_order(order) }
       end
@@ -22,7 +22,7 @@ module Lab
         results_query = results_query.where(person_id: patient_id) if patient_id
 
         query = Lab::LabOrder.where.not(order_id: results_query.select(:order_id))
-        query = query.where(patient_id: patient_id) if patient_id
+        query = query.where(patient_id:) if patient_id
 
         query
       end

data/app/services/lab/orders_service.rb

@@ -196,7 +196,7 @@ module Lab
 
         Encounter.create!(
           patient_id: order_params[:patient_id],
-          program_id: program_id,
+          program_id:,
           type: EncounterType.find_by_name!(Lab::Metadata::ENCOUNTER_TYPE_NAME),
           encounter_datetime: order_params[:date] || Date.today,
           provider_id: order_params[:provider_id] || User.current.person.person_id
@@ -220,7 +220,7 @@ module Lab
       end
 
       def accession_number_exists?(accession_number)
-        Lab::LabOrder.where(accession_number: accession_number).exists?
+        Lab::LabOrder.where(accession_number:).exists?
       end
 
       def nlims_accession_number_exists?(accession_number)
@@ -269,14 +269,14 @@ module Lab
         )
       end
 
-      def create_order_observation(order, concept_name, date, **values)
+      def create_order_observation(order, concept_name, date, **)
         Observation.create!(
-          order: order,
+          order:,
           encounter_id: order.encounter_id,
           person_id: order.patient_id,
           concept_id: ConceptName.find_by_name!(concept_name).concept_id,
           obs_datetime: date&.to_time || Time.now,
-          **values
+          **
         )
       end
 

data/app/services/lab/results_service.rb

@@ -50,7 +50,7 @@ module Lab
                  PatientID: result.person_id,
                  'Ordered By': order&.provider&.person&.name,
                  Result: values }.as_json
-        NotificationService.new.create_notification(result_enter_by, data) 
+        NotificationService.new.create_notification(result_enter_by, data)
       end
 
       def process_acknowledgement(results, results_enter_by)
@@ -62,7 +62,7 @@ module Lab
       def find_arv_number(patient_id)
         PatientIdentifier.joins(:type)
                          .merge(PatientIdentifierType.where(name: 'ARV Number'))
-                         .where(patient_id: patient_id)
+                         .where(patient_id:)
                          .first&.identifier
       end
 
@@ -89,7 +89,7 @@ module Lab
           order_id: test.order_id,
           obs_group_id: test.obs_id,
           obs_datetime: date&.to_datetime || DateTime.now,
-          comments: comments
+          comments:
         )
       end
 

data/app/services/lab/tests_service.rb

@@ -35,7 +35,7 @@ module Lab
               value_coded: params[:concept_id]
             )
 
-            Lab::TestSerializer.serialize(test, order: order)
+            Lab::TestSerializer.serialize(test, order:)
           end
         end
       end
@@ -62,9 +62,9 @@ module Lab
       def filter_tests_by_order(tests, accession_number: nil, order_date: nil, specimen_type_id: nil)
         return tests unless accession_number || order_date || specimen_type_id
 
-        lab_orders = filter_orders(Lab::LabOrder.all, accession_number: accession_number,
-                                                      order_date: order_date,
-                                                      specimen_type_id: specimen_type_id)
+        lab_orders = filter_orders(Lab::LabOrder.all, accession_number:,
+                                                      order_date:,
+                                                      specimen_type_id:)
         tests.joins(:order).merge(lab_orders)
       end
 
@@ -74,7 +74,7 @@ module Lab
           orders = orders.where('start_date >= ? AND start_date < ?', order_date, order_date + 1.day)
         end
 
-        orders = orders.where(accession_number: accession_number) if accession_number
+        orders = orders.where(accession_number:) if accession_number
         orders = orders.where(concept_id: specimen_type_id) if specimen_type_id
 
         orders

data/db/migrate/20210126092910_create_lab_lab_accession_number_counters.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 class CreateLabLabAccessionNumberCounters < ActiveRecord::Migration[5.2]
   def change
     create_table :lab_accession_number_counters do |t|

data/db/migrate/20210310115457_create_lab_lims_order_mappings.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 class CreateLabLimsOrderMappings < ActiveRecord::Migration[5.2]
   def change
     create_table :lab_lims_order_mappings do |t|

data/db/migrate/20210326195504_add_order_revision_to_lims_order_mapping.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 class AddOrderRevisionToLimsOrderMapping < ActiveRecord::Migration[5.2]
   def change
     add_column :lab_lims_order_mappings, :revision, :string

data/db/migrate/20210610095024_fix_numeric_results_value_type.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 class FixNumericResultsValueType < ActiveRecord::Migration[5.2]
   def up
     results = Lab::LabResult.all.includes(:children)

data/db/migrate/20210807111531_add_default_to_lims_order_mapping.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 class AddDefaultToLimsOrderMapping < ActiveRecord::Migration[5.2]
   def up
     change_column :lab_lims_order_mappings, :revision, :string, limit: 256, default: nil, null: true