his_emr_api_lab 1.1.2 → 1.1.6

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: e2202cc31522b4ae92847b3102841cfcf0c65a9e389fde480e3e787f1ef49ec7
-  data.tar.gz: a82291c66cdd6fb651e0917dc68e5b28b6dcedeb124973ab57f9f60187b4c920
+  metadata.gz: ec3adbde37c8f4213c049a83371cd30deb35a4833e3f95d5ace57bf9e2344e02
+  data.tar.gz: 2b676b2060b642493906794747160939e9d5cec15e94f87cb35e486434e4a7cd
 SHA512:
-  metadata.gz: 7da2c231dba9fa4b013890becd128b0a8694fe797b510e9baa37638d1437133cc11e27e2479938eda921ccfe6c23583544092cb477372b5db298922913035c72
-  data.tar.gz: cb8fbf9e9c71d187e0085b42f0fe5299976dc4309d672c815c231cdb096548d9b53b9b0f222f453b66a41a8d18b759f2d8d295c46c899206d7c7ffcee500bb6c
+  metadata.gz: 232dbd10ff1f15f18432d3421e99ecce64ab5855c30fc0d6f028bfe3cce291f29d5954453c0f7bc6f9d9c27a5990ac16299677721188d4d0b981734ba23d283f
+  data.tar.gz: 2f823d4b6edc2494f405002dc6681eb895ec7e961c817dd7c02b6688e286edf9a72b9467651d39d743d74a4bee094a4590150020002c3028a69d8534696af8de

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

@@ -38,6 +38,9 @@ module Lab
         end
 
         def create_order(order)
+          order = order.dup
+          order.delete('_id')
+
           bum.couch_rest :post, '/', order
         end
 

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

@@ -59,6 +59,9 @@ 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
 

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

@@ -11,15 +11,19 @@ module Lab
       class ConfigNotFound < RuntimeError; end
 
       class << self
+        def preferred_api
+          emr_api_application('lims_api', 'couchdb')
+        end
+
         ##
         # Returns LIMS' couchdb configuration file for the current environment (Rails.env)
         def couchdb
           config_path = begin
-                          find_config_path('couchdb.yml')
-                        rescue ConfigNotFound => e
-                          Rails.logger.error("Failed to find default LIMS couchdb config: #{e.message}")
-                          find_config_path('couchdb-lims.yml') # This can be placed in HIS-EMR-API/config
-                        end
+            find_config_path('couchdb.yml')
+          rescue ConfigNotFound => e
+            Rails.logger.error("Failed to find default LIMS couchdb config: #{e.message}")
+            find_config_path('couchdb-lims.yml') # This can be placed in HIS-EMR-API/config
+          end
 
           Rails.logger.debug("Using LIMS couchdb config: #{config_path}")
 
@@ -64,9 +68,7 @@ module Lab
           @emr_api_application ||= YAML.load_file(Rails.root.join('config', 'application.yml'))
 
           @emr_api_application.fetch(param) do
-            unless fallback
-              raise ConfigNotFound, "Missing config param: #{param}"
-            end
+            raise ConfigNotFound, "Missing config param: #{param}" unless fallback
 
             fallback
           end
@@ -83,9 +85,7 @@ module Lab
             Rails.root.parent.join("nlims_controller/config/#{filename}")
           ]
 
-          if filename == 'couchdb.yml'
-            paths = [Rails.root.join('config/lims-couchdb.yml'), *paths]
-          end
+          paths = [Rails.root.join('config/lims-couchdb.yml'), *paths] if filename == 'couchdb.yml'
 
           paths.each do |path|
             Rails.logger.debug("Looking for LIMS couchdb config at: #{path}")

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

@@ -69,9 +69,7 @@ module Lab
       end
 
       def start_date
-        if self['date_created'].blank?
-          raise LimsException, 'Order missing created date'
-        end
+        raise LimsException, 'Order missing created date' if self['date_created'].blank?
 
         Utils.parse_date(self['date_created'])
       end
@@ -85,7 +83,7 @@ module Lab
 
       # Translates a LIMS sample priority to a concept_id
       def reason_for_test
-        return unknown_concept.concept_id unless self['priority']
+        return nil unless self['priority']
 
         name = case self['priority']
                when %r{Reapet / Missing}i then 'Repeat / Missing'

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

@@ -64,7 +64,7 @@ module Lab
             first_name: name&.given_name,
             last_name: name&.family_name,
             id: national_id&.identifier,
-            phone_number: phone_number&.value,
+            phone_number: phone_number&.value || 'Unknown',
             gender: person.gender,
             email: nil
           }
@@ -83,9 +83,7 @@ module Lab
         end
 
         def format_sample_status_trail(order)
-          if order.concept_id == ConceptName.find_by_name!('Unknown').concept_id
-            return []
-          end
+          return [] if order.concept_id == ConceptName.find_by_name!('Unknown').concept_id
 
           user = User.find(order.discontinued_by || order.creator)
           drawn_by = PersonName.find_by_person_id(user.user_id)

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

@@ -17,7 +17,12 @@ module Lab
         loop do
           logger.info('Looking for new orders to push to LIMS...')
           orders = orders_pending_sync(batch_size).all
-          orders.each { |order| push_order(order) }
+          orders.each do |order|
+            push_order(order)
+          rescue GatewayError => e
+            logger.error("Failed to push order ##{order.accession_number}: #{e.class} - #{e.message}")
+            sleep(Lab::Lims::Config.updates_poll_frequency)
+          end
 
           # Doing this after .each above to stop ActiveRecord from executing
           # an extra request to the database (ActiveRecord's lazy evaluation

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

@@ -2,6 +2,8 @@
 
 require 'logger_multiplexor'
 
+require_relative './api/couchdb_api'
+
 module Lab
   module Lims
     ##
@@ -19,8 +21,7 @@ module Lab
 
       def self.start_push_worker
         start_worker('push_worker') do
-          api = Lims::Api::RestApi.new(Lab::Lims::Config.rest_api)
-          worker = PushWorker.new(api)
+          worker = PushWorker.new(lims_api)
 
           worker.push_orders # (wait: true)
         end
@@ -28,8 +29,7 @@ module Lab
 
       def self.start_pull_worker
         start_worker('pull_worker') do
-          api = Lims::Api::RestApi.new(Lab::Lims::Config.rest_api)
-          worker = PullWorker.new(api)
+          worker = PullWorker.new(lims_api)
 
           worker.pull_orders
         end
@@ -37,8 +37,7 @@ module Lab
 
       def self.start_realtime_pull_worker
         start_worker('realtime_pull_worker') do
-          api = Lims::Api::WsApi.new(Lab::Lims::Config.updates_socket)
-          worker = PullWorker.new(api)
+          worker = PullWorker.new(Lims::Api::WsApi.new(Lab::Lims::Config.updates_socket))
 
           worker.pull_orders
         end
@@ -71,6 +70,14 @@ module Lab
         Rails.logger.warn("Check for realtime updates failed: #{e.message}")
         false
       end
+
+      def self.lims_api
+        case Lims::Config.preferred_api
+        when /couchdb/i then Api::CouchDbApi.new(config: Lab::Lims::Config.couchdb)
+        when /rest/i then Api::RestApi.new(Lab::Lims::Config.rest_api)
+        else raise "Invalid LIMS API in application.yml, expected 'rest' or 'couchdb'"
+        end
+      end
     end
   end
 end

data/app/services/lab/orders_service.rb

@@ -66,9 +66,7 @@ module Lab
 
       def update_order(order_id, params)
         specimen_id = params.dig(:specimen, :concept_id)
-        unless specimen_id
-          raise ::InvalidParameterError, 'Specimen concept_id is required'
-        end
+        raise ::InvalidParameterError, 'Specimen concept_id is required' unless specimen_id
 
         order = Lab::LabOrder.find(order_id)
         if order.concept_id != unknown_concept_id && !params[:force_update]&.casecmp?('true')
@@ -84,7 +82,7 @@ module Lab
                         discontinued_reason_non_coded: 'Sample drawn/updated')
         end
 
-        if params.key?(:reason_for_test_id)
+        if params[:reason_for_test_id]
           Rails.logger.debug("Updating reason for test on order ##{order.order_id}")
           update_reason_for_test(order, params[:reason_for_test_id])
         end
@@ -116,13 +114,9 @@ module Lab
       # a 'Lab' encounter is created using the provided program_id and
       # patient_id.
       def find_encounter(order_params)
-        if order_params[:encounter_id]
-          return Encounter.find(order_params[:encounter_id])
-        end
+        return Encounter.find(order_params[:encounter_id]) if order_params[:encounter_id]
 
-        unless order_params[:patient_id]
-          raise InvalidParameterError, 'encounter_id or patient_id required'
-        end
+        raise InvalidParameterError, 'encounter_id or patient_id required' unless order_params[:patient_id]
 
         program_id = order_params[:program_id] || Program.find_by_name!(Lab::Metadata::LAB_PROGRAM_NAME).program_id
 
@@ -203,17 +197,13 @@ module Lab
       end
 
       def update_reason_for_test(order, concept_id)
-        if concept_id.blank?
-          raise InvalidParameterError, "Reason for test can't be blank"
-        end
+        raise InvalidParameterError, "Reason for test can't be blank" if concept_id.blank?
 
         return if order.reason_for_test&.value_coded == concept_id
 
-        unless order.reason_for_test&.value_coded.nil?
-          raise InvalidParameterError, "Can't change reason for test once set"
-        end
+        raise InvalidParameterError, "Can't change reason for test once set" if order.reason_for_test&.value_coded
 
-        order.reason_for_test.delete
+        order.reason_for_test&.delete
         add_reason_for_test(order, date: order.start_date, reason_for_test_id: concept_id)
       end
     end

data/db/migrate/20210807111531_add_default_to_lims_order_mapping.rb

@@ -0,0 +1,7 @@
+class AddDefaultToLimsOrderMapping < ActiveRecord::Migration[5.2]
+  def up
+    ActiveRecord::Base.connection.execute('ALTER TABLE lab_lims_order_mappings MODIFY revision VARCHAR(256) DEFAULT NULL')
+  end
+
+  def down; end
+end

data/lib/lab/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Lab
-  VERSION = '1.1.2'
+  VERSION = '1.1.6'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: his_emr_api_lab
 version: !ruby/object:Gem::Version
-  version: 1.1.2
+  version: 1.1.6
 platform: ruby
 authors:
 - Elizabeth Glaser Pediatric Foundation Malawi
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-07-15 00:00:00.000000000 Z
+date: 2021-08-07 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