his_emr_api_lab 1.0.5 → 1.1.3

data/app/services/lab/metadata.rb

@@ -10,6 +10,7 @@ module Lab
     TEST_RESULT_CONCEPT_NAME = 'Lab test result'
     TEST_RESULT_INDICATOR_CONCEPT_NAME = 'Lab test result indicator'
     TEST_TYPE_CONCEPT_NAME = 'Test type'
+    UNKNOWN_SPECIMEN = 'Unknown'
 
     # Encounter
     ENCOUNTER_TYPE_NAME = 'Lab'

data/app/services/lab/orders_search_service.rb

@@ -5,6 +5,14 @@ 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
@@ -17,6 +25,16 @@ module Lab
         orders.map { |order| Lab::LabOrderSerializer.serialize_order(order) }
       end
 
+      def find_orders_without_results(patient_id: nil)
+        results_query = Lab::LabResult.all
+        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
+      end
+
       def filter_orders_by_date(orders, date: nil, end_date: nil)
         date = date&.to_date
         end_date = end_date&.to_date
@@ -53,6 +71,8 @@ module Lab
           popped_params[filter.to_sym] = params.delete(filter)
         end
       end
+
+      def fetch_results(order); end
     end
   end
 end

data/app/services/lab/orders_service.rb

@@ -66,20 +66,27 @@ module Lab
 
       def update_order(order_id, params)
         specimen_id = params.dig(:specimen, :concept_id)
-        unless specimen_id
-          raise ::InvalidParameterError, 'Specimen concept_id is required'
-        end
+        raise ::InvalidParameterError, 'Specimen concept_id is required' unless specimen_id
 
         order = Lab::LabOrder.find(order_id)
-        unless order.concept_id == unknown_concept_id || params[:force_update]&.to_s&.casecmp?('true')
-          raise ::UnprocessableEntityError
+        if order.concept_id != unknown_concept_id && !params[:force_update]&.casecmp?('true')
+          raise ::UnprocessableEntityError, "Can't change order specimen once set"
+        end
+
+        if specimen_id.to_i != order.concept_id
+          Rails.logger.debug("Updating order ##{order.order_id}")
+          order.update!(concept_id: specimen_id,
+                        discontinued: true,
+                        discontinued_by: User.current.user_id,
+                        discontinued_date: params[:date]&.to_date || Time.now,
+                        discontinued_reason_non_coded: 'Sample drawn/updated')
+        end
+
+        if params[:reason_for_test_id]
+          Rails.logger.debug("Updating reason for test on order ##{order.order_id}")
+          update_reason_for_test(order, params[:reason_for_test_id])
         end
 
-        order.update!(concept_id: specimen_id,
-                      discontinued: true,
-                      discontinued_by: User.current.user_id,
-                      discontinued_date: params[:date]&.to_date || Date.today,
-                      discontinued_reason_non_coded: 'Sample drawn/updated')
         Lab::LabOrderSerializer.serialize_order(order)
       end
 
@@ -92,8 +99,10 @@ module Lab
         order.target_lab&.void(reason)
 
         order.tests.each { |test| test.void(reason) }
+        voided = order.void(reason)
+        Lab::VoidOrderJob.perform_later(order_id)
 
-        order.void(reason)
+        voided
       end
 
       private
@@ -105,13 +114,9 @@ module Lab
       # a 'Lab' encounter is created using the provided program_id and
       # patient_id.
       def find_encounter(order_params)
-        if order_params[:encounter_id]
-          return Encounter.find(order_params[:encounter_id])
-        end
+        return Encounter.find(order_params[:encounter_id]) if order_params[:encounter_id]
 
-        unless order_params[:patient_id]
-          raise InvalidParameterError, 'encounter_id or patient_id required'
-        end
+        raise InvalidParameterError, 'encounter_id or patient_id required' unless order_params[:patient_id]
 
         program_id = order_params[:program_id] || Program.find_by_name!(Lab::Metadata::LAB_PROGRAM_NAME).program_id
 
@@ -157,7 +162,7 @@ module Lab
           order,
           Lab::Metadata::REASON_FOR_TEST_CONCEPT_NAME,
           params[:date],
-          value_coded: params['reason_for_test_id']
+          value_coded: params[:reason_for_test_id]
         )
       end
 
@@ -190,6 +195,17 @@ module Lab
       def unknown_concept_id
         ConceptName.find_by_name!('Unknown').concept_id
       end
+
+      def update_reason_for_test(order, concept_id)
+        raise InvalidParameterError, "Reason for test can't be blank" if concept_id.blank?
+
+        return if order.reason_for_test&.value_coded == concept_id
+
+        raise InvalidParameterError, "Can't change reason for test once set" if order.reason_for_test&.value_coded
+
+        order.reason_for_test&.delete
+        add_reason_for_test(order, date: order.start_date, reason_for_test_id: concept_id)
+      end
     end
   end
 end

data/lib/lab/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Lab
-  VERSION = '1.0.5'
+  VERSION = '1.1.3'
 end

data/lib/tasks/loaders/data/reasons-for-test.csv

@@ -3,4 +3,5 @@
 "Repeat / Missing"
 "Targeted"
 "Confirmatory"
+"Stat"
 "Other"

data/lib/tasks/loaders/data/tests.csv

@@ -86,8 +86,6 @@ Blood,HbA1c,"2019-11-19 14:05:31"
 Blood,Microalbumin,"2019-11-19 14:05:31"
 Blood,Microprotein,"2019-11-19 14:05:31"
 Blood,"Von Willebrand Factor","2019-11-19 14:05:31"
-Blood,"HIV_viral_load","2021-04-13 00:00:00"
-Blood,"Viral laod","2021-04-11 00:00:00"
 Blood,"Viral Load","2019-11-19 14:05:31"
 Blood,"Urine Lam","2019-11-19 14:05:31"
 Blood,"Protein and Sugar","2021-04-16"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: his_emr_api_lab
 version: !ruby/object:Gem::Version
-  version: 1.0.5
+  version: 1.1.3
 platform: ruby
 authors:
 - Elizabeth Glaser Pediatric Foundation Malawi
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-06-23 00:00:00.000000000 Z
+date: 2021-07-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: couchrest
@@ -58,6 +58,20 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: 5.2.4.3
+- !ruby/object:Gem::Dependency
+  name: socket.io-client-simple
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.2.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.2.1
 - !ruby/object:Gem::Dependency
   name: bcrypt
   requirement: !ruby/object:Gem::Requirement
@@ -234,6 +248,8 @@ files:
 - app/controllers/lab/test_types_controller.rb
 - app/controllers/lab/tests_controller.rb
 - app/jobs/lab/application_job.rb
+- app/jobs/lab/update_patient_orders_job.rb
+- app/jobs/lab/void_order_job.rb
 - app/mailers/lab/application_mailer.rb
 - app/models/lab/application_record.rb
 - app/models/lab/lab_accession_number_counter.rb
@@ -251,12 +267,15 @@ files:
 - app/services/lab/labelling_service/order_label.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/config.rb
 - app/services/lab/lims/exceptions.rb
-- app/services/lab/lims/failed_imports.rb
 - app/services/lab/lims/migrator.rb
 - app/services/lab/lims/order_dto.rb
 - app/services/lab/lims/order_serializer.rb
+- app/services/lab/lims/pull_worker.rb
+- app/services/lab/lims/push_worker.rb
 - app/services/lab/lims/utils.rb
 - app/services/lab/lims/worker.rb
 - app/services/lab/metadata.rb

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

@@ -1,33 +0,0 @@
-# frozen_string_literal: true
-
-require_relative './order_dto'
-
-module Lab
-  module Lims
-    ##
-    # Manage LIMS orders that failed to import
-    module FailedImports
-      class << self
-        ##
-        # Retrieve all imports that failed
-        def failed_imports(start_id = 0, limit = 20)
-          Lab::LimsFailedImport.where('id >= ?', start_id).limit(limit)
-        end
-
-        ##
-        # Forcefully imports a failed import into a patient
-        def force_import(failed_import_id, _patient_id)
-          failed_import = Lab::LimsFailedImport.find(failed_import_id)
-          order_dto = Lab::Lims::OrderDTO.new(lims_api.find_order(failed_import.lims_id))
-          byebug
-        end
-
-        private
-
-        def lims_api
-          @lims_api ||= Lab::Lims::Api.new
-        end
-      end
-    end
-  end
-end