his_emr_api_lab 2.1.2 → 2.1.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: e3ab952d0c5ba09a760b554c079873884b9b937bd4822e822c0b1317ca52694c
+  metadata.gz: 2086e2372ae3182efa9a1eb56d5dfe0845f770800f25891dec98af02530d7953
+  data.tar.gz: cebae46dd81f29f128b6904ccaa7dbefc780b0dfcc57d9f2e1f3087f86cfc830
 SHA512:
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-  data.tar.gz: 395df3bcfe287ffbe505df72c6d4256715210147a5b933d464c1ec9c617999ead6b0d9cc90eb5e903dc82ccf274ac9afc482cffd2c767756d6c2f0be499ef315
+  metadata.gz: 6381879cefbb24c3226d2a68f458e26cea19bcf3db7f4b50fb97a14afc7b94958f2e76178d8f1fa0f4abd6ff976ddaa0ca5ce3f26fb309414117f0b82c872389
+  data.tar.gz: b6bede3239bb94db739c4ea1f7cf817a4eb217b9c5ba77bb9b3678dcb1b3edba44f41f71c8e0db00d9f1d333458a49376d8bb57a631473ed35ef4d3641293399

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/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 = order.voided.zero? ? 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] = {}
 
@@ -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/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/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/lib/lab/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Lab
-  VERSION = '2.1.2'
+  VERSION = '2.1.4'
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: his_emr_api_lab
 version: !ruby/object:Gem::Version
-  version: 2.1.2
+  version: 2.1.4
 platform: ruby
 authors:
 - Elizabeth Glaser Pediatric Foundation Malawi