his_emr_api_lab 1.1.5 → 1.1.9

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 666ea51bb7ff2938b6d4fd733a619a49cf600aed37c330c8be3f9680bdc4e94e
+  metadata.gz: a13cacbcc7be1a44baac082c8ade406f20538dabe21c26b3b2ef249cd9ee22cd
+  data.tar.gz: 9b0a9cfb4676982b299600078fa0421133af14a0b8d15dd49ac9ca1933fad7e0
 SHA512:
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+  metadata.gz: 93092265b1d1cde16121ff005c901387e357040e32b05b3dff508564cde3832f8451e6805c7ca47c772abf90a47757a6cfd9a95084962b148cbdf7819f3a3493
+  data.tar.gz: d2d1dded33ca89b66ad8d99c477fa373f6cc8c33958cc17192fb1a7691abaf4802ebc800c63006ff46d64e527a630ce263c0edddc1db368d67b2848406fd997c

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

@@ -44,6 +44,9 @@ class Lab::Lims::Api::RestApi
 
   def consume_orders(*_args, patient_id: nil, **_kwargs)
     orders_pending_updates(patient_id).each do |order|
+      mapping = Lab::LimsOrderMapping.find_by(order_id: order.order_id)
+      next if mapping.nil? || check_and_fix_duplicate!(mapping, order)
+
       order_dto = Lab::Lims::OrderSerializer.serialize_order(order)
 
       if order_dto['priority'].nil? || order_dto['sample_type'].casecmp?('not_specified')
@@ -405,4 +408,24 @@ class Lab::Lims::Api::RestApi
 
     orders
   end
+
+  # Checks for duplicates previously created due to this proving orders that have
+  # not been pushed to LIMS as orders awaiting updates.
+  def check_and_fix_duplicate!(mapping, order)
+    duplicate_orders = Lab::LabOrder.where(accession_number: mapping.lims_id)
+                                    .where.not(order_id: mapping.order_id)
+    return false if duplicate_orders.size.zero?
+
+    unless order.discontinued
+      order.void('Duplicate created due to bug in HIS-EMR-API-Lab v1.1.7')
+      mapping.destroy
+      return true
+    end
+
+    duplicate_orders.each do |duplicate_order|
+      duplicate_order.void("Has duplicate that contains updates ##{order.order_id}: Duplicate was created by bug in HIS-EMR-API-Lab v1.1.7")
+    end
+
+    true
+  end
 end

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

@@ -12,7 +12,7 @@ module Lab
 
       class << self
         def preferred_api
-          emr_api_application('lims_api', 'couchdb')
+          emr_api_application('lims_api')
         end
 
         ##

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

@@ -32,7 +32,7 @@ module Lab
       def specimen_type_id
         lims_specimen_name = self['sample_type']&.strip&.downcase
 
-        if %w[specimen_not_collected not_assigned not_specified].include?(lims_specimen_name)
+        if lims_specimen_name.nil? || %w[specimen_not_collected not_assigned not_specified].include?(lims_specimen_name)
           return ConceptName.select(:concept_id).find_by_name!('Unknown').concept_id
         end
 

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

@@ -58,6 +58,9 @@ module Lab
             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)
+          elsif order_dto[:_id] && Lab::LimsOrderMapping.where(lims_id: order_dto[:_id]).exists?
+            Rails.logger.warn("Duplicate accession number found: #{order_dto[:_id]}, skipping order...")
+            nil
           else
             Rails.logger.info("Creating order ##{order_dto['accession_number']} in LIMS")
             update = lims_api.create_order(order_dto)

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

@@ -45,7 +45,7 @@ module Lab
 
       def self.start_worker(worker_name)
         Rails.logger = LoggerMultiplexor.new(log_path("#{worker_name}.log"), $stdout)
-        ActiveRecord::Base.logger = Rails.logger
+        # ActiveRecord::Base.logger = Rails.logger
         Rails.logger.level = :debug
 
         File.open(log_path("#{worker_name}.lock"), File::RDWR | File::CREAT, 0o644) do |fout|

data/db/migrate/20210807111531_add_default_to_lims_order_mapping.rb

@@ -0,0 +1,7 @@
+class AddDefaultToLimsOrderMapping < ActiveRecord::Migration[5.2]
+  def up
+    change_column :lab_lims_order_mappings, :revision, :string, limit: 256, default: nil, null: true
+  end
+
+  def down; end
+end

data/lib/lab/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Lab
-  VERSION = '1.1.5'
+  VERSION = '1.1.9'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: his_emr_api_lab
 version: !ruby/object:Gem::Version
-  version: 1.1.5
+  version: 1.1.9
 platform: ruby
 authors:
 - Elizabeth Glaser Pediatric Foundation Malawi
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-07-21 00:00:00.000000000 Z
+date: 2021-08-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: couchrest
@@ -290,6 +290,7 @@ files:
 - db/migrate/20210326195504_add_order_revision_to_lims_order_mapping.rb
 - db/migrate/20210407071728_create_lab_lims_failed_imports.rb
 - db/migrate/20210610095024_fix_numeric_results_value_type.rb
+- db/migrate/20210807111531_add_default_to_lims_order_mapping.rb
 - lib/auto12epl.rb
 - lib/couch_bum/couch_bum.rb
 - lib/generators/lab/install/USAGE
@@ -330,7 +331,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.8
+rubygems_version: 3.1.4
 signing_key: 
 specification_version: 4
 summary: Lab extension for the HIS-EMR-API