his_emr_api_lab 2.1.3 → 2.1.4.pre.alpha

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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+  metadata.gz: 306b46064eb5c58668eb1f4598d99258f1e76b69db42b90abe33d35ddd2434b0
+  data.tar.gz: f367e1fdf5101dd25a2e64f83f61ac6eeffe4fee2007846da5037c18083d1b96
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+  data.tar.gz: 47fdae979daa748c4dbc6fd1c291594b857a40b45e4f3adea3ecaae8fcb54275c2c77485e8bf2f2c222eddea66a1518f3c396236dbd56f4b4afcd9b16bfd4e76

data/app/jobs/lab/process_lab_result_job.rb

@@ -6,6 +6,7 @@ module Lab
   class ProcessLabResultJob < ApplicationJob
     queue_as :default
     def perform(results_obs_id, serializer, result_enter_by)
+      Rails.logger.info("Lab::ProcessLabResultJob: Processing result completion for #{serializer}")
       results_obs = Lab::LabResult.find(results_obs_id)
       Lab::ResultsService.process_result_completion(results_obs, serializer, result_enter_by)
     end

data/app/serializers/lab/lab_order_serializer.rb

@@ -21,7 +21,7 @@ module Lab
           order_date: order.date_created,
           location_id: encounter.location_id,
           program_id: encounter.program_id,
-          program_name: program.name,
+          program_name: program&.name,
           # order_date: order.start_date,
           patient_id: order.patient_id,
           accession_number: order.accession_number,

data/app/serializers/lab/result_serializer.rb

@@ -7,11 +7,11 @@ module Lab
     def self.serialize(result)
       result.children.map do |measure|
         value, value_type = read_value(measure)
-        concept_name = ConceptName.find_by_concept_id(measure.concept_id)
-        
-        program_id = ""
+        # Get the test catalog name instead of any random concept name
+        concept_name = get_test_catalog_concept_name(measure.concept_id)
+        program_id = ''
         if measure.obs_id.present?
-          obs = Observation.find(measure.obs_id)
+          obs = Observation.unscope(where: :obs_group_id).find(measure.obs_id)
           encounter = Encounter.find(obs.encounter_id)
           program_id = encounter.program_id
         end
@@ -19,8 +19,8 @@ module Lab
         {
           id: measure.obs_id,
           indicator: {
-            concept_id: concept_name&.concept_id,
-            name: concept_name&.name
+            concept_id: measure.concept_id,
+            name: concept_name
           },
           date: measure.obs_datetime,
           value:,
@@ -31,6 +31,12 @@ module Lab
       end
     end
 
+    def self.get_test_catalog_concept_name(concept_id)
+      return nil unless concept_id
+
+      ::ConceptAttribute.find_by(concept_id:, attribute_type: ConceptAttributeType.test_catalogue_name)&.value_reference
+    end
+
     def self.read_value(measure)
       %w[value_numeric value_coded value_boolean value_text].each do |field|
         value = measure.send(field) if measure.respond_to?(field)

data/app/services/lab/concepts_service.rb

@@ -9,7 +9,7 @@ module Lab
         FROM concept_set cs
                 INNER JOIN concept_name cn ON cn.concept_id = cs.concept_id
                 INNER JOIN concept_attribute ca ON ca.value_reference = #{ActiveRecord::Base.connection.quote(nlims_code)}
-            AND ca.attribute_type_id = 20
+            AND ca.attribute_type_id = #{ConceptAttributeType.nlims_code.concept_attribute_type_id}
         WHERE cs.concept_id IN (SELECT concept_set.concept_id
                                 FROM concept_set
                                 WHERE concept_set.concept_set IN (SELECT concept_name.concept_id
@@ -22,8 +22,8 @@ module Lab
                                                                             FROM concept_name
                                                                             WHERE concept_name.voided = 0
                                                                               AND concept_name.name = 'Test type')
-                                            AND concept_set.concept_id = ca.concept_id
                                             )
+        AND cs.concept_set = ca.concept_id
         GROUP BY cn.concept_id
       SQL
     end
@@ -61,7 +61,7 @@ module Lab
         INNER JOIN concept_attribute ca2 ON ca.concept_id = ca2.concept_id
           AND ca2.attribute_type_id = #{ConceptAttributeType.nlims_code.concept_attribute_type_id}
         WHERE ca.attribute_type_id = #{ConceptAttributeType.test_catalogue_name.concept_attribute_type_id}
-        AND ca.concept_id IN (#{concept_set.select(:concept_id).to_sql})
+        AND ca.concept_id IN (#{concept_set.select(:concept_set).to_sql})
         GROUP BY ca.concept_id
       SQL
     end

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

@@ -341,7 +341,7 @@ module Lab
         def nlims_order_exists?(tracking_number)
           response = in_authenticated_session do |headers|
             Rails.logger.info("Verifying order ##{tracking_number}")
-            RestClient.get(expand_uri("orders/#{tracking_number}", api_version: 'v2'), headers)
+            RestClient.get(expand_uri("orders/#{tracking_number}/exists", api_version: 'v2'), headers)
           end
 
           Rails.logger.info("Order ##{tracking_number} verified... Parsing...")

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/couch_db_api'
+require_relative 'api/couchdb_api'
 require_relative 'config'
 require_relative 'pull_worker'
 require_relative 'utils'

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

@@ -144,10 +144,9 @@ module Lab
         end
 
         def format_test_status_trail(order)
-          tests = order.voided ? order.tests : Lab::LabOrderSerializer.voided_tests(order)
-
+          tests = [0, false].include?(order.voided) ? order.tests : Lab::LabOrderSerializer.voided_tests(order)
           tests.each_with_object({}) do |test, trail|
-            test_name = format_test_name(ConceptName.find_by_concept_id!(test.value_coded).name)
+            test_name = format_test_name(::Concept.find(test.value_coded).test_catalogue_name)
 
             current_test_trail = trail[test_name] = {}
 
@@ -156,7 +155,7 @@ module Lab
               updated_by: find_user(test.creator)
             }
 
-            unless test.voided.zero?
+            unless [0, false].include?(test.voided)
               current_test_trail[test.date_voided.strftime('%Y%m%d%H%M%S')] = {
                 status: 'Voided',
                 updated_by: find_user(test.voided_by)
@@ -209,11 +208,7 @@ module Lab
         end
 
         def format_test_name(test_name)
-          return 'Viral Load' if test_name.casecmp?('HIV Viral load')
-
-          return 'TB' if test_name.casecmp?('TB Program')
-
-          test_name.titleize
+          return test_name
         end
 
         def format_sample_priority(priority)

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

@@ -216,7 +216,7 @@ 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

@@ -51,7 +51,7 @@ module Lab
         mapping = Lab::LimsOrderMapping.find_by(order_id: order.order_id)
 
         ActiveRecord::Base.transaction do
-          if mapping && !order.voided.zero?
+          if mapping && ![0, false].include?(order.voided)
             Rails.logger.info("Deleting order ##{order_dto['accession_number']} from LIMS")
             lims_api.delete_order(mapping.lims_id, order_dto)
             mapping.destroy

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

@@ -78,8 +78,12 @@ module Lab
       end
 
       def self.find_concept_by_name(name)
-        ConceptName.joins("INNER JOIN concept_attribute ON concept_attribute.concept_id = concept_name.concept_id")
-                   .where("concept_attribute.value_reference = ?", CGI.unescapeHTML(name))
+        unescaped_name = CGI.unescapeHTML(name)
+        attribute_type_id = ConceptAttributeType.test_catalogue_name.concept_attribute_type_id
+
+        ConceptName.joins('INNER JOIN concept_attribute ON concept_attribute.concept_id = concept_name.concept_id')
+                   .where('concept_attribute.attribute_type_id = ? AND concept_attribute.value_reference = ? AND concept_name.name = ?',
+                          attribute_type_id, unescaped_name, unescaped_name)
                    .first
       end
     end

data/app/services/lab/orders_service.rb

@@ -234,7 +234,7 @@ module Lab
         encounter.encounter_type = EncounterType.find_by_name!(Lab::Metadata::ENCOUNTER_TYPE_NAME)
         encounter.encounter_datetime = order_params[:date] || Date.today
         encounter.visit = Visit.find_by_uuid(visit) if Encounter.column_names.include?('visit_id')
-        encounter.provider_id = User.current&.person.id if Encounter.column_names.include?('provider_id')
+        encounter.provider_id = User.current&.person&.id if Encounter.column_names.include?('provider_id')
         encounter.program_id = order_params[:program_id] if Encounter.column_names.include?('program_id') && order_params[:program_id].present?
         encounter.save!
         encounter.reload

data/app/services/lab/results_service.rb

@@ -20,7 +20,11 @@ module Lab
         serializer = {}
         results_obs = {}
         ActiveRecord::Base.transaction do
-          test = Lab::LabTest.find(test_id) rescue nil
+          test = begin
+            Lab::LabTest.find(test_id)
+          rescue StandardError
+            nil
+          end
           test = Lab::LabTest.find_by_uuid(test_id) if test.blank?
           encounter = find_encounter(test, encounter_id: params[:encounter_id],
                                            encounter_uuid: params[:encounter],
@@ -37,9 +41,9 @@ module Lab
 
         # force commit all transactions
         ActiveRecord::Base.connection.commit_db_transaction
-        
-        # delay job by a second
-        ProcessLabResultJob.set(wait: 1.second).perform_later(results_obs.id, serializer, result_enter_by)
+
+        # Execute job synchronously
+        ProcessLabResultJob.perform_now(results_obs.id, serializer, result_enter_by)
 
         Rails.logger.info("Lab::ResultsService: Result created for test #{test_id} #{serializer}")
         serializer
@@ -55,10 +59,10 @@ module Lab
       def precess_notification_message(result, values, result_enter_by)
         order = Order.find(result.order_id)
         data = { Type: result_enter_by,
-                 Specimen: ConceptName.find_by(concept_id: order.concept_id)&.name,
-                 'Test type': ConceptName.find_by(concept_id: result.test.value_coded)&.name,
+                 Specimen: get_test_catalog_name(order.concept_id) || ConceptName.find_by(concept_id: order.concept_id)&.name,
+                 'Test type': get_test_catalog_name(result.test.value_coded) || ConceptName.find_by(concept_id: result.test.value_coded)&.name,
                  'Accession number': order&.accession_number,
-                 'Orde date': Order.columns.include?('start_date') ? order.start_date : order.date_created,
+                 order_date: Order.columns.include?('start_date') ? order.start_date : order.date_created,
                  'ARV-Number': find_arv_number(result.person_id),
                  PatientID: result.person_id,
                  'Ordered By': Order.columns.include?('provider_id') ? order&.provider&.person&.name : Person.find(order.creator)&.name,
@@ -82,19 +86,21 @@ module Lab
       def find_encounter(test, encounter_id: nil, encounter_uuid: nil, date: nil, provider_id: nil)
         return Encounter.find(encounter_id) if encounter_id
         return Encounter.find_by_uuid(encounter_uuid) if encounter_uuid
-        encounter_type = EncounterType.find_by_name!(Lab::Metadata::ENCOUNTER_TYPE_NAME)
+
+        lab_encounter_type = EncounterType.find_by_name!(Lab::Metadata::ENCOUNTER_TYPE_NAME)
 
         encounter = Encounter.new
         encounter.patient_id = test.person_id
         encounter.program_id = test.encounter.program_id if Encounter.column_names.include?('program_id')
         encounter.visit_id = test.encounter.visit_id if Encounter.column_names.include?('visit_id')
-        encounter.type = encounter_type
-        encounter.encounter_type = encounter_type if (encounter&.encounter_type.nil? || encounter&.type.nil?)
+        # Use bracket notation to set the encounter_type column directly (bypasses association)
+        # This handles both Integer and EncounterType object
+        encounter_type_value = lab_encounter_type.is_a?(Integer) ? lab_encounter_type : lab_encounter_type.encounter_type_id
+        encounter[:encounter_type] = encounter_type_value
         encounter.encounter_datetime = date || Date.today
         encounter.provider_id = provider_id || User.current.user_id if Encounter.column_names.include?('provider_id')
-
         encounter.save!
-
+        encounter.reload
         encounter
       end
 
@@ -130,7 +136,8 @@ module Lab
       def add_measure_to_results(results_obs, params, date)
         validate_measure_params(params)
 
-        concept_id = params[:indicator][:concept_id] || Concept.find_concept_by_uuid(params.dig(:indicator, :concept))&.id
+        concept_id = params[:indicator][:concept_id] || Concept.find_concept_by_uuid(params.dig(:indicator,
+                                                                                                :concept))&.id
 
         Observation.create!(
           person_id: results_obs.person_id,
@@ -174,6 +181,13 @@ module Lab
         else raise InvalidParameterError, "Invalid boolean value: #{string}"
         end
       end
+
+      def get_test_catalog_name(concept_id)
+        return nil unless concept_id
+
+        ::ConceptAttribute.find_by(concept_id:,
+                                   attribute_type: ConceptAttributeType.test_catalogue_name)&.value_reference
+      end
     end
   end
 end

data/db/migrate/20260128111557_add_program_id_to_encounter.rb

@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+# This migration adds the program_id column to the encounter table if it doesn't already exist.
+# The program_id column is used to associate encounters with specific programs (e.g., HIV Program, TB Program).
+class AddProgramIdToEncounter < ActiveRecord::Migration[5.2]
+  def change
+    return if column_exists?(:encounter, :program_id)
+
+    add_column :encounter, :program_id, :integer, after: :encounter_type
+    add_index :encounter, :program_id
+    add_foreign_key :encounter, :program, column: :program_id, primary_key: :program_id
+  end
+end

data/lib/lab/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Lab
-  VERSION = '2.1.3'
+  VERSION = '2.1.4-alpha'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: his_emr_api_lab
 version: !ruby/object:Gem::Version
-  version: 2.1.3
+  version: 2.1.4.pre.alpha
 platform: ruby
 authors:
 - Elizabeth Glaser Pediatric Foundation Malawi
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2026-01-22 00:00:00.000000000 Z
+date: 2026-01-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: couchrest
@@ -270,7 +270,7 @@ 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/couch_db_api.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
@@ -301,6 +301,7 @@ files:
 - db/migrate/20210807111531_add_default_to_lims_order_mapping.rb
 - db/migrate/20260119104240_add_fulfiller_fields_to_orders.rb
 - db/migrate/20260119104241_create_comment_to_fulfiller_concept.rb
+- db/migrate/20260128111557_add_program_id_to_encounter.rb
 - lib/auto12epl.rb
 - lib/couch_bum/couch_bum.rb
 - lib/generators/lab/install/USAGE
@@ -339,9 +340,9 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">="
+  - - ">"
     - !ruby/object:Gem::Version
-      version: '0'
+      version: 1.3.1
 requirements: []
 rubygems_version: 3.4.1
 signing_key: