his_emr_api_lab 1.1.18 → 1.1.21

checksums.yaml

@@ -1,7 +1,7 @@
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data/app/controllers/lab/results_controller.rb

@@ -11,7 +11,7 @@ module Lab
                                                   :value_modifier,
                                                   { indicator: [:concept_id] }] }])
 
-      result = Lab::ResultsService.create_results(params[:test_id], result_params)
+      result = Lab::ResultsService.create_results(params[:test_id], result_params, 'user entered')
 
       render json: result, status: :created
     end

data/app/models/lab/lab_order.rb

@@ -35,6 +35,10 @@ module Lab
             class_name: 'Observation',
             foreign_key: :order_id
 
+    has_one :mapping,
+            class_name: '::Lab::LimsOrderMapping',
+            foreign_key: :order_id
+
     default_scope do
       joins(:order_type)
         .merge(OrderType.where(name: Lab::Metadata::ORDER_TYPE_NAME))

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

@@ -188,6 +188,9 @@ class Lab::Lims::Api::RestApi
       last_name: order_dto.fetch(:patient).fetch(:last_name),
       phone_number: order_dto.fetch(:patient).fetch(:phone_number),
       gender: order_dto.fetch(:patient).fetch(:gender),
+      arv_number: order_dto.fetch(:patient).fetch(:arv_number),
+      art_regimen: order_dto.fetch(:patient).fetch(:art_regimen),
+      art_start_date: order_dto.fetch(:patient).fetch(:art_start_date),
       national_patient_id: order_dto.fetch(:patient).fetch(:id),
       requesting_clinician: requesting_clinician(order_dto),
       sample_type: order_dto.fetch(:sample_type),

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

@@ -64,12 +64,40 @@ module Lab
             first_name: name&.given_name,
             last_name: name&.family_name,
             id: national_id&.identifier,
+            arv_number: find_arv_number(patient_id),
+            art_regimen: find_current_regimen(patient_id),
+            art_start_date: find_art_start_date(patient_id),
             phone_number: phone_number&.value || 'Unknown',
             gender: person.gender,
             email: nil
           }
         end
 
+        def find_current_regimen(patient_id)
+          regimen_data = ActiveRecord::Base.connection.select_one <<~SQL
+            SELECT patient_current_regimen(#{patient_id}, current_date()) regimen
+          SQL
+          return nil if regimen_data.blank?
+
+          regimen_data['regimen']
+        end
+
+        def find_arv_number(patient_id)
+          PatientIdentifier.joins(:type)
+                           .merge(PatientIdentifierType.where(name: 'ARV Number'))
+                           .where(patient_id: patient_id)
+                           .first&.identifier
+        end
+
+        def find_art_start_date(patient_id)
+          start_date = ActiveRecord::Base.connection.select_one <<~SQL
+            SELECT date_antiretrovirals_started(#{patient_id}, current_date()) AS earliest_date
+          SQL
+          return nil if start_date.blank?
+
+          start_date['earliest_date']
+        end
+
         def format_sample_type(name)
           return 'not_specified' if name.casecmp?('Unknown')
 

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

@@ -204,10 +204,10 @@ 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'], order[:order_date].to_s),
-                                                 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: measures } )
         end
       end
 

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

@@ -57,7 +57,11 @@ module Lab
           elsif mapping
             Rails.logger.info("Updating order ##{order_dto[:accession_number]} in LIMS")
             lims_api.update_order(mapping.lims_id, order_dto)
-            mapping.update(pushed_at: Time.now)
+            if order_dto['test_results'].nil? || order_dto['test_results'].empty?
+              mapping.update(pushed_at: Time.now)             
+            else
+              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.
@@ -67,7 +71,7 @@ module Lab
             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'],
-                                          pushed_at: Time.now)
+                                          pushed_at: Time.now, result_push_status: false)
           end
         end
 
@@ -97,8 +101,9 @@ module Lab
                                             .last_updated
 
         Lab::LabOrder.left_joins(:results)
+                     .joins(:mapping)
                      .where('orders.discontinued_date > :last_updated
-                             OR obs.date_created > :last_updated',
+                             OR obs.date_created > orders.date_created AND lab_lims_order_mappings.result_push_status = 0',
                             last_updated: last_updated)
                      .group('orders.order_id')
                      .order(discontinued_date: :desc, date_created: :desc)

data/app/services/lab/results_service.rb

@@ -15,7 +15,10 @@ module Lab
       #     - measures: An array of measures. A measure is an object of the following structure
       #         - indicator: An object that has a concept_id field (concept_id of the indicator)
       #         - value_type: An enum that's limited to 'numeric', 'boolean', 'text', and 'coded'
-      def create_results(test_id, params)
+      #   result_enter_by: A string that specifies who created the result
+      def create_results(test_id, params, result_enter_by = 'LIMS')
+        serializer = {}
+        results_obs = {}
         ActiveRecord::Base.transaction do
           test = Lab::LabTest.find(test_id)
           encounter = find_encounter(test, encounter_id: params[:encounter_id],
@@ -24,13 +27,34 @@ module Lab
 
           results_obs = create_results_obs(encounter, test, params[:date], params[:comments])
           params[:measures].map { |measure| add_measure_to_results(results_obs, measure, params[:date]) }
+          OrderExtension.create!(creator: User.current, value: result_enter_by, order_id: results_obs.order_id,
+                                 date_created: Time.now)
 
-          Lab::ResultSerializer.serialize(results_obs)
+          serializer = Lab::ResultSerializer.serialize(results_obs)
         end
+        NotificationService.new.create_notification(result_enter_by, prepare_notification_message(results_obs, serializer, result_enter_by))
+        Rails.logger.info("Lab::ResultsService: Result created for test #{test_id} #{serializer}")
+        serializer
       end
 
       private
 
+      def prepare_notification_message(result, values, result_enter_by)
+        { Type: result_enter_by,
+          'Test type': ConceptName.find_by(concept_id: result.test.value_coded)&.name,
+          'Accession number': Order.find(result.order_id)&.accession_number,
+          'ARV-Number': find_arv_number(result.person_id),
+          PatientID: result.person_id,
+          Result: values }.as_json
+      end
+
+      def find_arv_number(patient_id)
+        PatientIdentifier.joins(:type)
+                         .merge(PatientIdentifierType.where(name: 'ARV Number'))
+                         .where(patient_id: patient_id)
+                         .first&.identifier
+      end
+
       def find_encounter(test, encounter_id: nil, date: nil, provider_id: nil)
         return Encounter.find(encounter_id) if encounter_id
 
@@ -64,6 +88,7 @@ module Lab
                                         obs_group_id: test.obs_id)
         return unless result
 
+        OrderExtension.find_by(order_id: result.order_id)&.void("Updated/overwritten by #{User.current.username}")
         result.measures.map { |child_obs| child_obs.void("Updated/overwritten by #{User.current.username}") }
         result.void("Updated/overwritten by #{User.current.username}")
       end

data/lib/lab/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Lab
-  VERSION = '1.1.18'
+  VERSION = '1.1.21'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: his_emr_api_lab
 version: !ruby/object:Gem::Version
-  version: 1.1.18
+  version: 1.1.21
 platform: ruby
 authors:
 - Elizabeth Glaser Pediatric Foundation Malawi
-autorequire:
+autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-11-09 00:00:00.000000000 Z
+date: 2022-06-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: couchrest
@@ -319,7 +319,7 @@ 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
@@ -334,8 +334,9 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.9
-signing_key:
+rubyforge_project: 
+rubygems_version: 2.7.6
+signing_key: 
 specification_version: 4
 summary: Lab extension for the HIS-EMR-API
 test_files: []