mahis_emr_api_lab 1.2.3 → 1.2.5

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: 22fcdf2407609885b81df63de7be75ff20156f6b0b6d8de6a6eb8974d54915ae
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+  metadata.gz: e95ee315519fcf1d77d9b337b449921c05489cf7842bf2f74e730f61fd298233aba7b87c0a819b6bcac9f39c58c87703c5ed76a9b7b1f31b60573d3fcceb8b14
+  data.tar.gz: 3326b887701a0fdf285bb37f2a2daa56500f4b81875080cb711bc25b046370e94c6e198c837e7521415b69ccc0cbfe01cb0c18096e09196f2b79468eaf15fbba

data/app/controllers/lab/labels_controller.rb

@@ -2,7 +2,8 @@
 
 module Lab
   class LabelsController < ApplicationController
-    skip_before_action :authenticate
+    _callbacks = _process_action_callbacks.map(&:filter)
+    skip_before_action :authenticate if _callbacks.include?(:authenticate)
 
     def print_order_label
       order_id = params.require(:order_id)

data/app/controllers/lab/users_controller.rb

@@ -3,7 +3,8 @@
 # This controller handles creation and authentication of LIMS User
 module Lab
   class UsersController < ::ApplicationController
-    skip_before_action :authenticate
+     _callbacks = _process_action_callbacks.map(&:filter)
+    skip_before_action :authenticate if _callbacks.include?(:authenticate)
     # create a LIMS User that will be responsible for sending lab results
     def create
       user_params = params.permit(:username, :password)

data/app/models/lab/lab_result.rb

@@ -2,6 +2,10 @@
 
 module Lab
   class LabResult < Observation
+    def children
+      Observation.where(obs_group_id: obs_id, voided: 0)
+    end
+    
     alias measures children
 
     default_scope do

data/app/services/lab/lims/api/{couchdb_api.rb → couch_db_api.rb}

@@ -33,7 +33,7 @@ module Lab
           bum.binge_changes(since: from, limit: 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

@@ -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'],

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

@@ -1,4 +1,5 @@
 # frozen_string_literal: true
+
 require 'rest-client'
 
 class Lab::Lims::Api::RestApi
@@ -8,6 +9,8 @@ class Lab::Lims::Api::RestApi
 
   class InvalidParameters < LimsApiError; end
 
+  START_DATE = Time.parse('2024-09-03').freeze
+
   def initialize(config)
     @config = config
   end
@@ -195,7 +198,7 @@ class Lab::Lims::Api::RestApi
   end
 
   ##
-  # Converts an OrderDTO to parameters for POST /create_order
+  # Converts an OrderDto to parameters for POST /create_order
   def make_create_params(order_dto)
     {
       tracking_number: order_dto.fetch(:tracking_number),
@@ -224,7 +227,7 @@ class Lab::Lims::Api::RestApi
   end
 
   ##
-  # Converts an OrderDTO to parameters for POST /update_order
+  # Converts an OrderDto to parameters for POST /update_order
   def make_update_params(order_dto)
     date_updated, status = sample_drawn_status(order_dto)
 
@@ -240,7 +243,7 @@ class Lab::Lims::Api::RestApi
   def current_district
     health_centre = Location.current_health_center
     raise 'Current health centre not set' unless health_centre
-    
+
     district = health_centre.district || Lab::Lims::Config.application['district']
 
     unless district
@@ -252,7 +255,7 @@ class Lab::Lims::Api::RestApi
   end
 
   ##
-  # Extracts sample drawn status from an OrderDTO
+  # Extracts sample drawn status from an OrderDto
   def sample_drawn_status(order_dto)
     order_dto[:sample_statuses].each do |trail_entry|
       date, status = trail_entry.each_pair.find { |_date, status| status['status'].casecmp?('Drawn') }
@@ -265,13 +268,13 @@ class Lab::Lims::Api::RestApi
   end
 
   ##
-  # Extracts a sample drawn date from a LIMS OrderDTO.
+  # Extracts a sample drawn date from a LIMS OrderDto.
   def sample_drawn_date(order_dto)
     sample_drawn_status(order_dto).first
   end
 
   ##
-  # Extracts the requesting clinician from a LIMS OrderDTO
+  # Extracts the requesting clinician from a LIMS OrderDto
   def requesting_clinician(order_dto)
     orderer = order_dto[:who_order_test]
 
@@ -406,7 +409,7 @@ class Lab::Lims::Api::RestApi
     Rails.logger.debug('Looking for orders without a specimen')
     unknown_specimen = ConceptName.where(name: Lab::Metadata::UNKNOWN_SPECIMEN)
                                   .select(:concept_id)
-    orders = Lab::LabOrder.where(concept_id: unknown_specimen)
+    orders = Lab::LabOrder.where(concept_id: unknown_specimen, date_created: START_DATE..(Date.today + 1.day))
                           .where.not(accession_number: Lab::LimsOrderMapping.select(:lims_id))
     orders = orders.where(patient_id: patient_id) if patient_id
 
@@ -418,16 +421,17 @@ class Lab::Lims::Api::RestApi
     # Lab::OrdersSearchService.find_orders_without_results(patient_id: patient_id)
     #                         .where.not(accession_number: Lab::LimsOrderMapping.select(:lims_id).where("pulled_at IS NULL"))
     Lab::OrdersSearchService.find_orders_without_results(patient_id: patient_id)
-                             .where(order_id: Lab::LimsOrderMapping.select(:order_id))
+                            .where(order_id: Lab::LimsOrderMapping.select(:order_id), date_created: START_DATE..(Date.today + 1.day))
   end
 
   def orders_without_reason(patient_id = nil)
     Rails.logger.debug('Looking for orders without a reason for test')
     orders = Lab::LabOrder.joins(:reason_for_test)
                           .merge(Observation.where(value_coded: nil, value_text: nil))
+                          .where(date_created: START_DATE..(Date.today + 1.day))
                           .limit(1000)
                           .where.not(accession_number: Lab::LimsOrderMapping.select(:lims_id))
-    orders = orders.where(patient_id: patient_id) if patient_id
+    orders = orders.where(patient_id: patient_id, date_created: START_DATE..(Date.today + 1.day)) if patient_id
 
     orders
   end

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

@@ -2,10 +2,12 @@
 
 module Lab
   module Lims
-    class LimsException < StandardError; end
-    class DuplicateNHID < LimsException; end
-    class MissingAccessionNumber < LimsException; end
-    class UnknownSpecimenType < LimsException; end
-    class UnknownTestType < LimsException; end
+    module Exceptions
+      class LimsException < StandardError; end
+      class DuplicateNHID < LimsException; end
+      class MissingAccessionNumber < LimsException; end
+      class UnknownSpecimenType < LimsException; end
+      class UnknownTestType < LimsException; end
+    end
   end
 end

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

@@ -29,7 +29,7 @@ require 'lab/lab_test'
 require 'lab/lims_order_mapping'
 require 'lab/lims_failed_import'
 
-require_relative './api/couchdb_api'
+require_relative './api/couch_db_api'
 require_relative './config'
 require_relative './pull_worker'
 require_relative './utils'
@@ -82,7 +82,7 @@ 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

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

@@ -6,7 +6,7 @@ module Lab
   module Lims
     ##
     # LIMS' Data Transfer Object for orders
-    class OrderDTO < ActiveSupport::HashWithIndifferentAccess
+    class OrderDto < ActiveSupport::HashWithIndifferentAccess
       include Utils
 
       ##

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

@@ -7,14 +7,14 @@ 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
 
         def serialize_order(order)
           serialized_order = Lims::Utils.structify(Lab::LabOrderSerializer.serialize_order(order))
-          Lims::OrderDTO.new(
+          Lims::OrderDto.new(
             _id: Lab::LimsOrderMapping.find_by(order: order)&.lims_id || serialized_order.accession_number,
             tracking_number: serialized_order.accession_number,
             sending_facility: current_facility_name,

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

@@ -214,7 +214,7 @@ module Lab
           end
 
           next if test.result || test_results['results'].blank?
-
+          
           result_date = Time.now
           measures = test_results['results'].map do |indicator, value|
             measure = find_measure(order, indicator, value)

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

@@ -10,6 +10,7 @@ module Lab
       include Utils # for logger
 
       SECONDS_TO_WAIT_FOR_ORDERS = 30
+      START_DATE = Time.parse('2024-09-03').freeze
 
       def initialize(lims_api)
         @lims_api = lims_api
@@ -23,7 +24,7 @@ module Lab
           logger.debug("Found #{orders.size} orders...")
           orders.each do |order|
             push_order(order)
-          rescue GatewayError => e
+          rescue StandardError => e
             logger.error("Failed to push order ##{order.accession_number}: #{e.class} - #{e.message}")
           rescue StandardError => e
             logger.error("Failed to push order ##{order.id}: #{order&.accession_number} : #{e.class} - #{e.message}")
@@ -94,6 +95,7 @@ module Lab
         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))
                      .where("accession_number IS NOT NULL AND accession_number !=''")
+                     .where(date_created: START_DATE..(Date.today + 1.day))
                      .order(date_created: :desc)
       end
 

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

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

data/app/services/lab/orders_service.rb

@@ -148,8 +148,7 @@ module Lab
                  'arv_number': find_arv_number(order.patient_id),
                  'patient_id': result.person_id,
                  'ordered_by': order&.provider&.person&.name,
-                 'rejection_reason': order_params['comments']
-                }.as_json
+                 'rejection_reason': order_params['comments'] }.as_json
         NotificationService.new.create_notification('LIMS', data)
       end
 
@@ -197,7 +196,6 @@ module Lab
         return Encounter.find(encounter_id) if order_params[:encounter] || order_params[:encounter_id]
         raise StandardError, 'encounter_id|uuid or patient_id|uuid required' unless order_params[:patient]
 
-
         encounter = Encounter.new
         encounter.patient = Patient.find(patient_id)
         encounter.encounter_type = EncounterType.find_by_name!(Lab::Metadata::ENCOUNTER_TYPE_NAME)
@@ -263,7 +261,6 @@ module Lab
       #
       # Examples of reasons include: Routine, Targeted, Confirmatory, Repeat, or Stat.
       def add_reason_for_test(order, params)
-
         reason = params[:reason_for_test_id] || params[:reason_for_test]
 
         reason = Concept.find(reason)
@@ -289,6 +286,8 @@ module Lab
       end
 
       def create_order_observation(order, concept_name, date, **values)
+        creator = User.find_by(username: 'lab_daemon')
+        User.current ||= creator
         Observation.create!(
           order: order,
           encounter_id: order.encounter_id,

data/lib/lab/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Lab
-  VERSION = '1.2.3'
+  VERSION = '1.2.5'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: mahis_emr_api_lab
 version: !ruby/object:Gem::Version
-  version: 1.2.3
+  version: 1.2.5
 platform: ruby
 authors:
 - Elizabeth Glaser Pediatric Foundation Malawi
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2024-08-26 00:00:00.000000000 Z
+date: 2025-06-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: couchrest
@@ -254,7 +254,7 @@ files:
 - app/services/lab/lims/acknowledgement_serializer.rb
 - app/services/lab/lims/acknowledgement_worker.rb
 - app/services/lab/lims/api/blackhole_api.rb
-- app/services/lab/lims/api/couchdb_api.rb
+- app/services/lab/lims/api/couch_db_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
@@ -309,7 +309,7 @@ licenses:
 - MIT
 metadata:
   source_code_uri: https://github.com/EGPAFMalawiHIS/his_emr_api_lab
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -324,8 +324,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.4.17
-signing_key: 
+rubygems_version: 3.4.1
+signing_key:
 specification_version: 4
 summary: Lab extension for the HIS-EMR-API
 test_files: []