his_emr_api_lab 1.1.4 → 1.1.8

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 956381a9da4af7bdc49a3f35ad2e7b155d241ae3f45dd08888f20d21ca376ca5
+  metadata.gz: e5421bf2b632a395fa9870ba1a3e855aea8033f8c54034bda352fdf23409812e
+  data.tar.gz: 4cd24426fa0f0a5fe39c416bb0f35f28769c36b95eac72a8abca7579efd75c58
 SHA512:
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-  data.tar.gz: a00e126ff73058474f17bce296259e8ce5c5619ba441611074c0b1a5a6c1e269846f7296185e0d323bf798c4c626069693e2912bee5837307253d8bc5553053e
+  metadata.gz: 54815cf740ce0c0882752a341df21acbd51bde4102b0dcd2ddd581575efb70b9aa1284295dda7e6cb78b5e6355a3c983d5b41acf5f8f40fe8318737a6cce08a5
+  data.tar.gz: b516dd7ac285004b6d4e5125b73e159adf180a07b1cf0470ae4380d02ad274b72d2a68ec697c99deb3f4e8a5f057ec9d0682925e1d1a72b6986852285feea996

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')
@@ -59,6 +62,9 @@ class Lab::Lims::Api::RestApi
       end
 
       yield order_dto, OpenStruct.new(last_seq: 0)
+    rescue LimsApiError => e
+      Rails.logger.error("Failed to fetch updates for ##{order.accession_number}: #{e.class} - #{e.message}")
+      sleep(1)
     end
   end
 
@@ -402,4 +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/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 = '1.1.4'
+  VERSION = '1.1.8'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: his_emr_api_lab
 version: !ruby/object:Gem::Version
-  version: 1.1.4
+  version: 1.1.8
 platform: ruby
 authors:
 - Elizabeth Glaser Pediatric Foundation Malawi
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-07-21 00:00:00.000000000 Z
+date: 2021-08-20 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