his_emr_api_lab 2.1.2 → 2.1.4.pre.beta

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: e3ab952d0c5ba09a760b554c079873884b9b937bd4822e822c0b1317ca52694c
+  metadata.gz: 2cb84913a3c09866a51aa40a98812803bfee6f66a36c3e5c7ea4bdcb9a530724
+  data.tar.gz: 833074b20f473b97b515a11392fc768dabc0b3289b1717474e08b903120c6216
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+  metadata.gz: fa6487f57604f5ee24b2fc15e730dfc765cea9eff12051d1875560aa49832e36dc7ffab4320517eeb1f6ffe0ccb706b0e40e4bffc0bcb56d3055b77c9f72c650
+  data.tar.gz: 02a6a0b02074c8fcec8c3d9dbeaeee0a29ea6f96a62f30459f96ee904720c72a854d8251bfb111c5e6e80ae6552a658dabb409547b92119062ada27723d2d0bf

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/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

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

@@ -11,3 +11,14 @@ module Lab
     end
   end
 end
+
+
+module Lab
+  module Lims
+      class LimsException < StandardError; end
+      class DuplicateNHID < LimsException; end
+      class MissingAccessionNumber < LimsException; end
+      class UnknownSpecimenType < LimsException; end
+      class UnknownTestType < LimsException; 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/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/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

@@ -78,9 +78,8 @@ module Lab
       end
 
       def self.find_concept_by_name(name)
-        ConceptName.joins(:concept)
-                   .merge(Concept.all) # Filter out voided
-                   .where(name: CGI.unescapeHTML(name))
+        ConceptName.joins("INNER JOIN concept_attribute ON concept_attribute.concept_id = concept_name.concept_id")
+                   .where("concept_attribute.value_reference = ?", CGI.unescapeHTML(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

@@ -35,7 +35,11 @@ module Lab
           serializer = Lab::ResultSerializer.serialize(results_obs)
         end
 
-        ProcessLabResultJob.perform_later(results_obs.id, serializer, result_enter_by)
+        # 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)
 
         Rails.logger.info("Lab::ResultsService: Result created for test #{test_id} #{serializer}")
         serializer
@@ -78,12 +82,14 @@ 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)
 
         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.encounter_type = EncounterType.find_by_name!(Lab::Metadata::ENCOUNTER_TYPE_NAME)
+        encounter.type = encounter_type
+        encounter.encounter_type = encounter_type if (encounter&.encounter_type.nil? || encounter&.type.nil?)
         encounter.encounter_datetime = date || Date.today
         encounter.provider_id = provider_id || User.current.user_id if Encounter.column_names.include?('provider_id')
 

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 = '2.1.2'
+  VERSION = '2.1.4-beta'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: his_emr_api_lab
 version: !ruby/object:Gem::Version
-  version: 2.1.2
+  version: 2.1.4.pre.beta
 platform: ruby
 authors:
 - Elizabeth Glaser Pediatric Foundation Malawi
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2026-01-22 00:00:00.000000000 Z
+date: 2026-01-29 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: