his_emr_api_lab 0.0.7 → 0.0.12

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: '064059e7286ba44485e1707c2be889126776e15125732859bc41c682d4784002'
+  metadata.gz: 38f48eba209b710d53ac07d89c95e335f9578a2b2b2137550b8b48f0032355f9
+  data.tar.gz: e6930b341721036f4aaeb8ab64551eb1ed4d35e6b80314d181488265e1cda0ba
 SHA512:
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-  data.tar.gz: 8c1b11e868f38fcd9c61d275b2bd74783dd698eaaea2ee88d2819b76c944c36972856090a239f7087b3c96a65de7104fd65347ce7128f3c76d799768dbd80253
+  metadata.gz: 2f9873af33a53537e59143efd1bf6b36fe5af1201be7cd463c42d14417babfb31640f3a46e12bd5dc73d709fa6075ea619a1faf868143f1f3f9a641341342c85
+  data.tar.gz: dbc656255bdb6c160a71771c06532d533ec90f38a6d7e37f5d1880564dcacf874097fe2c5ce424da60602117674135fec6859dda4380f3c4ef20cf4fd3235777

data/app/services/lab/labelling_service/order_label.rb

@@ -27,7 +27,7 @@ module Lab
                                '',
                                drawer,
                                '',
-                               specimen,
+                               tests,
                                reason_for_test,
                                order.accession_number,
                                order.accession_number)
@@ -36,7 +36,7 @@ module Lab
       def reason_for_test
         return 'Unknown' unless order.reason_for_test
 
-        ConceptName.find_by_concept_id(order.reason_for_test.value_coded)&.name || 'Unknown'
+        short_concept_name(order.reason_for_test.value_coded) || 'Unknown'
       end
 
       def patient
@@ -60,11 +60,14 @@ module Lab
       def drawer
         return 'N/A' if order.concept_id == unknown_concept.concept_id
 
-        name = PersonName.find_by_person_id(order.creator)
-        return "#{name.given_name} #{name.family_name}" if name
+        drawer_id = order.discontinued_by || order.creator
+        draw_date = (order.discontinued_date || order.start_date).strftime('%d/%^b/%Y %H:%M:%S')
 
-        user = User.find(order.creator)
-        user&.username || 'N/A'
+        name = PersonName.find_by_person_id(drawer_id)
+        return "#{name.given_name} #{name.family_name} #{draw_date}" if name
+
+        user = User.find_by_user_id(drawer_id)
+        user ? "#{user.username} #{draw_date}" : 'N/A'
       end
 
       def specimen
@@ -73,6 +76,24 @@ module Lab
         ConceptName.find_by_concept_id(order.concept_id)&.name || 'Unknown'
       end
 
+      def tests
+        tests = order.tests.map do |test|
+          name = short_concept_name(test.value_coded) || 'Unknown'
+
+          next 'VL' if name.match?(/Viral load/i)
+
+          name.size > 7 ? name[0..6] : name
+        end
+
+        tests.join(', ')
+      end
+
+      def short_concept_name(concept_id)
+        ConceptName.where(concept_id: concept_id)
+                   .min_by { |concept| concept.name.size }
+                   &.name
+      end
+
       def unknown_concept
         ConceptName.find_by_name('Unknown')
       end

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

@@ -0,0 +1,34 @@
+# frozen_string_literal: true
+
+require_relative './api'
+require_relative './order_dto'
+
+module Lab
+  module Lims
+    ##
+    # Manage LIMS orders that failed to import
+    module FailedImports
+      class << self
+        ##
+        # Retrieve all imports that failed
+        def failed_imports(start_id = 0, limit = 20)
+          Lab::LimsFailedImport.where('id >= ?', start_id).limit(limit)
+        end
+
+        ##
+        # Forcefully imports a failed import into a patient
+        def force_import(failed_import_id, _patient_id)
+          failed_import = Lab::LimsFailedImport.find(failed_import_id)
+          order_dto = Lab::Lims::OrderDTO.new(lims_api.find_order(failed_import.lims_id))
+          byebug
+        end
+
+        private
+
+        def lims_api
+          @lims_api ||= Lab::Lims::Api.new
+        end
+      end
+    end
+  end
+end

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

@@ -44,7 +44,7 @@ module Lab
   module Lims
     module Migrator
       class MigratorApi < Api
-        MAX_THREADS = 6
+        MAX_THREADS = (ENV.fetch('MIGRATION_WORKERS') { 6 }).to_i
 
         attr_reader :rejections
 

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

@@ -69,6 +69,10 @@ module Lab
       end
 
       def start_date
+        if self['date_created'].blank?
+          raise LimsException, 'Order missing created date'
+        end
+
         Utils.parse_date(self['date_created'])
       end
 

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

@@ -66,6 +66,8 @@ module Lab
           Date.strptime(str_date, '%d-%m-%Y').strftime('%Y-%m-%d')
         elsif str_date.match?(/(\d{4}\d{2}\d{2})\d+/)
           Date.strptime(str_date, '%Y%m%d').strftime('%Y-%m-%d')
+        elsif str_date.match?(%r{\d{2}/\d{2}/\d{4}})
+          str_date.to_date.to_s
         else
           Rails.logger.warn("Invalid date: #{str_date}")
           parse_date(fallback_date)

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

@@ -28,7 +28,9 @@ module Lab
           fout.write("Worker ##{Process.pid} started at #{Time.now}")
           worker = new(Api.new)
           worker.pull_orders
-          worker.push_orders
+          # TODO: Verify that names being pushed to LIMS are of the correct format (ie matching
+          # LIMS naming conventions). Enable pushing when that is done
+          # worker.push_orders
         end
       end
 

data/lib/lab/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Lab
-  VERSION = '0.0.7'
+  VERSION = '0.0.12'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: his_emr_api_lab
 version: !ruby/object:Gem::Version
-  version: 0.0.7
+  version: 0.0.12
 platform: ruby
 authors:
 - Elizabeth Glaser Pediatric Foundation Malawi
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-04-27 00:00:00.000000000 Z
+date: 2021-04-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: couchrest
@@ -252,6 +252,7 @@ files:
 - app/services/lab/lims/api.rb
 - app/services/lab/lims/config.rb
 - app/services/lab/lims/exceptions.rb
+- app/services/lab/lims/failed_imports.rb
 - app/services/lab/lims/migrator.rb
 - app/services/lab/lims/order_dto.rb
 - app/services/lab/lims/order_serializer.rb