his_emr_api_lab 1.1.21 → 1.1.22

checksums.yaml

@@ -1,7 +1,7 @@
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metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: his_emr_api_lab
 version: !ruby/object:Gem::Version
-  version: 1.1.21
+  version: 1.1.22
 platform: ruby
 authors:
 - Elizabeth Glaser Pediatric Foundation Malawi
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-06-13 00:00:00.000000000 Z
+date: 2022-06-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: couchrest
@@ -234,86 +234,7 @@ email:
 executables: []
 extensions: []
 extra_rdoc_files: []
-files:
-- MIT-LICENSE
-- README.md
-- Rakefile
-- app/controllers/lab/application_controller.rb
-- app/controllers/lab/labels_controller.rb
-- app/controllers/lab/orders_controller.rb
-- app/controllers/lab/reasons_for_test_controller.rb
-- app/controllers/lab/results_controller.rb
-- app/controllers/lab/specimen_types_controller.rb
-- app/controllers/lab/test_result_indicators_controller.rb
-- app/controllers/lab/test_types_controller.rb
-- app/controllers/lab/tests_controller.rb
-- app/jobs/lab/application_job.rb
-- app/jobs/lab/push_order_job.rb
-- app/jobs/lab/update_patient_orders_job.rb
-- app/jobs/lab/void_order_job.rb
-- app/mailers/lab/application_mailer.rb
-- app/models/lab/application_record.rb
-- app/models/lab/lab_accession_number_counter.rb
-- app/models/lab/lab_encounter.rb
-- app/models/lab/lab_order.rb
-- app/models/lab/lab_result.rb
-- app/models/lab/lab_test.rb
-- app/models/lab/lims_failed_import.rb
-- app/models/lab/lims_order_mapping.rb
-- app/serializers/lab/lab_order_serializer.rb
-- app/serializers/lab/result_serializer.rb
-- app/serializers/lab/test_serializer.rb
-- app/services/lab/accession_number_service.rb
-- app/services/lab/concepts_service.rb
-- app/services/lab/labelling_service/order_label.rb
-- app/services/lab/lims/api/blackhole_api.rb
-- app/services/lab/lims/api/couchdb_api.rb
-- app/services/lab/lims/api/mysql_api.rb
-- app/services/lab/lims/api/rest_api.rb
-- app/services/lab/lims/api/ws_api.rb
-- app/services/lab/lims/api_factory.rb
-- app/services/lab/lims/config.rb
-- app/services/lab/lims/exceptions.rb
-- app/services/lab/lims/migrator.rb
-- app/services/lab/lims/order_dto.rb
-- app/services/lab/lims/order_serializer.rb
-- app/services/lab/lims/pull_worker.rb
-- app/services/lab/lims/push_worker.rb
-- app/services/lab/lims/utils.rb
-- app/services/lab/lims/worker.rb
-- app/services/lab/metadata.rb
-- app/services/lab/orders_search_service.rb
-- app/services/lab/orders_service.rb
-- app/services/lab/results_service.rb
-- app/services/lab/tests_service.rb
-- config/routes.rb
-- db/migrate/20210126092910_create_lab_lab_accession_number_counters.rb
-- db/migrate/20210310115457_create_lab_lims_order_mappings.rb
-- db/migrate/20210323080140_change_lims_id_to_string_in_lims_order_mapping.rb
-- 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
-- lib/generators/lab/install/install_generator.rb
-- lib/generators/lab/install/templates/rswag-ui-lab.rb
-- lib/generators/lab/install/templates/start_worker.rb
-- lib/generators/lab/install/templates/swagger.yaml
-- lib/his_emr_api_lab.rb
-- lib/lab/engine.rb
-- lib/lab/version.rb
-- lib/logger_multiplexor.rb
-- lib/tasks/lab_tasks.rake
-- lib/tasks/loaders/data/reasons-for-test.csv
-- lib/tasks/loaders/data/test-measures.csv
-- lib/tasks/loaders/data/tests.csv
-- lib/tasks/loaders/loader_mixin.rb
-- lib/tasks/loaders/metadata_loader.rb
-- lib/tasks/loaders/reasons_for_test_loader.rb
-- lib/tasks/loaders/specimens_loader.rb
-- lib/tasks/loaders/test_result_indicators_loader.rb
+files: []
 homepage: https://github.com/EGPAFMalawiHIS/his_emr_api_lab
 licenses:
 - MIT

data/MIT-LICENSE

@@ -1,20 +0,0 @@
-Copyright 2020 Walter Kaunda
-
-Permission is hereby granted, free of charge, to any person obtaining
-a copy of this software and associated documentation files (the
-"Software"), to deal in the Software without restriction, including
-without limitation the rights to use, copy, modify, merge, publish,
-distribute, sublicense, and/or sell copies of the Software, and to
-permit persons to whom the Software is furnished to do so, subject to
-the following conditions:
-
-The above copyright notice and this permission notice shall be
-included in all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
-LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
-OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
-WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

@@ -1,71 +0,0 @@
-![Ruby](https://github.com/EGPAFMalawiHIS/HIS-EMR-API-Lab/workflows/Ruby/badge.svg?branch=development)
-# Lab
-
-A Rails engine for [HIS-EMR-API](https://github.com/EGPAFMalawiHIS/HIS-EMR-API)
-compatible applications that provides an API for managing various lab
-activities.
-
-## Usage
-
-The engine provides an API that provides the following functionalities:
-
-  - Search/Retrieve test types
-  - Search/Retrieve sample types for a given test
-  - Order lab tests
-  - Attach a result to a test
-
-For details on how to perform these operations please see the
-[API docs](https://raw.githack.com/EGPAFMalawiHIS/HIS-EMR-API-Lab/development/docs/api.html).
-
-## Installation
-
-Add this line to your application's Gemfile:
-
-```ruby
-gem 'lab', git: 'https://github.com/EGPAFMalawiHIS/HIS-EMR-API-Lab', branch: 'development'
-```
-
-And then execute:
-
-```bash
-$ bundle install lab
-```
-
-Or install it yourself as:
-
-```bash
-$ gem install lab
-```
-
-Finally run:
-
-```bash
-$ bundle exec rails lab:install
-```
-
-## Configuration
-
-This module in most cases should work without any configuration, however to enable
-certain features some configuration may be required. Visit the
-[configuration](./docs/configuration.md) page to learn how to configure the
-application.
-
-## Contributing
-
-Fork this application create a branch for the contribution you want to make,
-push your changes to the branch and then issue a pull request. You may want
-to create a new first on our repository, so that your pull request references
-this issue.
-
-If you are fixing a bug, it will be nice to add a unit test that exposes
-the bug. Although this is not a requirement in most cases.
-
-Be sure to follow [this](https://github.com/rubocop/ruby-style-guide) Ruby
-style guide. We don't necessarily look for strict adherence to the guidelines
-but too much a departure from it is frowned upon. For example, you will be forgiven
-for writing a method with 15 to 20 lines if you clearly justify why you couldn't
-break that method into multiple smaller methods.
-
-## License
-
-The gem is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).

data/Rakefile

@@ -1,32 +0,0 @@
-begin
-  require 'bundler/setup'
-rescue LoadError
-  puts 'You must `gem install bundler` and `bundle install` to run rake tasks'
-end
-
-require 'rdoc/task'
-
-RDoc::Task.new(:rdoc) do |rdoc|
-  rdoc.rdoc_dir = 'rdoc'
-  rdoc.title    = 'Lab'
-  rdoc.options << '--line-numbers'
-  rdoc.rdoc_files.include('README.md')
-  rdoc.rdoc_files.include('lib/**/*.rb')
-end
-
-APP_RAKEFILE = File.expand_path("spec/dummy/Rakefile", __dir__)
-load 'rails/tasks/engine.rake'
-
-load 'rails/tasks/statistics.rake'
-
-require 'bundler/gem_tasks'
-
-require 'rake/testtask'
-
-Rake::TestTask.new(:test) do |t|
-  t.libs << 'spec'
-  t.pattern = 'spec/**/*_spec.rb'
-  t.verbose = false
-end
-
-task default: :test

data/app/controllers/lab/application_controller.rb

@@ -1,6 +0,0 @@
-# frozen_string_literal: true
-
-module Lab
-  class ApplicationController < ::ApplicationController
-  end
-end

data/app/controllers/lab/labels_controller.rb

@@ -1,17 +0,0 @@
-# frozen_string_literal: true
-
-module Lab
-  class LabelsController < ApplicationController
-    skip_before_action :authenticate
-
-    def print_order_label
-      order_id = params.require(:order_id)
-
-      label = LabellingService::OrderLabel.new(order_id)
-      send_data(label.print, type: 'application/label; charset=utf-8',
-                             stream: false,
-                             filename: "#{SecureRandom.hex(24)}.lbl",
-                             disposition: 'inline')
-    end
-  end
-end

data/app/controllers/lab/orders_controller.rb

@@ -1,38 +0,0 @@
-# frozen_string_literal: true
-
-module Lab
-  class OrdersController < ApplicationController
-    def create
-      order_params_list = params.require(:orders)
-      orders = order_params_list.map do |order_params|
-        OrdersService.order_test(order_params)
-      end
-
-      orders.each { |order| Lab::PushOrderJob.perform_later(order.fetch(:order_id)) }
-
-      render json: orders, status: :created
-    end
-
-    def update
-      specimen = params.require(:specimen).permit(:concept_id)
-      order = OrdersService.update_order(params[:id], specimen: specimen, force_update: params[:force_update])
-      Lab::PushOrderJob.perform_later(order.fetch(:order_id))
-
-      render json: order
-    end
-
-    def index
-      filters = params.permit(%i[patient_id accession_number date status])
-
-      Lab::UpdatePatientOrdersJob.perform_later(filters[:patient_id]) if filters[:patient_id]
-      render json: OrdersSearchService.find_orders(filters)
-    end
-
-    def destroy
-      OrdersService.void_order(params[:id], params[:reason])
-      Lab::VoidOrderJob.perform_later(params[:id])
-
-      render status: :no_content
-    end
-  end
-end

data/app/controllers/lab/reasons_for_test_controller.rb

@@ -1,9 +0,0 @@
-# frozen_string_literal: true
-
-module Lab
-  class ReasonsForTestController < ApplicationController
-    def index
-      render json: ConceptsService.reasons_for_test
-    end
-  end
-end

data/app/controllers/lab/results_controller.rb

@@ -1,19 +0,0 @@
-# frozen_string_literal: true
-
-module Lab
-  class ResultsController < ApplicationController
-    def create
-      result_params = params.require(:result)
-                            .permit([:encounter_id,
-                                     :date,
-                                     { measures: [:value,
-                                                  :value_type,
-                                                  :value_modifier,
-                                                  { indicator: [:concept_id] }] }])
-
-      result = Lab::ResultsService.create_results(params[:test_id], result_params, 'user entered')
-
-      render json: result, status: :created
-    end
-  end
-end

data/app/controllers/lab/specimen_types_controller.rb

@@ -1,15 +0,0 @@
-# frozen_string_literal: true
-
-module Lab
-  class SpecimenTypesController < ApplicationController
-    def index
-      filters = params.permit(%w[name test_type])
-
-      specimen_types = ConceptsService.specimen_types(name: filters['name'],
-                                                      test_type: filters['test_type'])
-                                      .as_json(only: %w[concept_id name])
-
-      render json: specimen_types
-    end
-  end
-end

data/app/controllers/lab/test_result_indicators_controller.rb

@@ -1,9 +0,0 @@
-# frozen_string_literal: true
-
-class Lab::TestResultIndicatorsController < ApplicationController
-  def index
-    test_type_id = params.require(:test_type_id)
-
-    render json: Lab::ConceptsService.test_result_indicators(test_type_id)
-  end
-end

data/app/controllers/lab/test_types_controller.rb

@@ -1,15 +0,0 @@
-# frozen_string_literal: true
-
-module Lab
-  class TestTypesController < ApplicationController
-    def index
-      filters = params.permit(%w[name specimen_type])
-
-      test_types = ConceptsService.test_types(name: filters['name'],
-                                              specimen_type: filters['specimen_type'])
-                                  .as_json(only: %w[concept_id name])
-
-      render json: test_types
-    end
-  end
-end

data/app/controllers/lab/tests_controller.rb

@@ -1,26 +0,0 @@
-# frozen_string_literal: true
-
-class Lab::TestsController < ::ApplicationController
-  def index
-    filters = params.permit(%i[order_date accession_number patient_id test_type_id specimen_type_id pending_results])
-
-    tests = service.find_tests(filters)
-    render json: tests
-  end
-
-  # Add a specimen to an existing order
-  def create
-    test_params = params.permit(:order_id, :date, tests: [:concept_id])
-    order_id, test_concepts = test_params.require(%i[order_id tests])
-    date = test_params[:date] || Date.today
-
-    tests = service.create_tests(Lab::LabOrder.find(order_id), date, test_concepts)
-    Lab::PushOrderJob.perform_later(order_id)
-
-    render json: tests, status: :created
-  end
-
-  def service
-    Lab::TestsService
-  end
-end

data/app/jobs/lab/application_job.rb

@@ -1,4 +0,0 @@
-module Lab
-  class ApplicationJob < ActiveJob::Base
-  end
-end

data/app/jobs/lab/push_order_job.rb

@@ -1,12 +0,0 @@
-# frozen_string_literal: true
-
-module Lab
-  ##
-  # Push an order to LIMS.
-  class PushOrderJob < ApplicationJob
-    def perform(order_id)
-      push_worker = Lab::Lims::PushWorker.new(Lab::Lims::ApiFactory.create_api)
-      push_worker.push_order_by_id(order_id)
-    end
-  end
-end

data/app/jobs/lab/update_patient_orders_job.rb

@@ -1,32 +0,0 @@
-# frozen_string_literal: true
-
-module Lab
-  ##
-  # Fetches updates on a patient's orders from external sources.
-  class UpdatePatientOrdersJob < ApplicationJob
-    queue_as :default
-
-    def perform(patient_id)
-      Rails.logger.info('Initialising LIMS REST API...')
-
-      User.current = Lab::Lims::Utils.lab_user
-      Location.current = Location.find_by_name('ART clinic')
-
-      lockfile = Rails.root.join('tmp', "update-patient-orders-#{patient_id}.lock")
-
-      done = File.open(lockfile, File::RDWR | File::CREAT) do |lock|
-        unless lock.flock(File::LOCK_NB | File::LOCK_EX)
-          Rails.logger.info('Another update patient job is already running...')
-          break false
-        end
-
-        worker = Lab::Lims::PullWorker.new(Lab::Lims::ApiFactory.create_api)
-        worker.pull_orders(patient_id: patient_id)
-
-        true
-      end
-
-      File.unlink(lockfile) if done
-    end
-  end
-end

data/app/jobs/lab/void_order_job.rb

@@ -1,17 +0,0 @@
-# frozen_string_literal: true
-
-module Lab
-  class VoidOrderJob < ApplicationJob
-    queue_as :default
-
-    def perform(order_id)
-      Rails.logger.info("Voiding order ##{order_id} in LIMS")
-
-      User.current = Lab::Lims::Utils.lab_user
-      Location.current = Location.find_by_name('ART clinic')
-
-      worker = Lab::Lims::PushWorker.new(Lab::Lims::ApiFactory.create_api)
-      worker.push_order(Lab::LabOrder.unscoped.find(order_id))
-    end
-  end
-end

data/app/mailers/lab/application_mailer.rb

@@ -1,6 +0,0 @@
-module Lab
-  class ApplicationMailer < ActionMailer::Base
-    default from: 'from@example.com'
-    layout 'mailer'
-  end
-end

data/app/models/lab/application_record.rb

@@ -1,5 +0,0 @@
-module Lab
-  class ApplicationRecord < ActiveRecord::Base
-    self.abstract_class = true
-  end
-end

data/app/models/lab/lab_accession_number_counter.rb

@@ -1,13 +0,0 @@
-# frozen_string_literal: true
-
-module Lab
-  # Used to keep track of counters for accession numbers.
-  #
-  # An accession number is just a prefix plus a running encounter
-  # that's reset at the end of the day
-  class LabAccessionNumberCounter < ApplicationRecord
-    self.table_name = :lab_accession_number_counters
-
-    validates_presence_of :date, :value
-  end
-end

data/app/models/lab/lab_encounter.rb

@@ -1,7 +0,0 @@
-# frozen_string_literal: true
-
-module Lab
-  class LabEncounter < ::Encounter
-    default_scope { joins(:type).merge(EncounterType.where('name LIKE ?', ENCOUNTER_TYPE_NAME)) }
-  end
-end

data/app/models/lab/lab_order.rb

@@ -1,58 +0,0 @@
-# frozen_string_literal: true
-
-module Lab
-  class LabOrder < ::Order
-    class << self
-      def make_obs_concept_filter(concept_name)
-        concept = ConceptName.where(name: concept_name).select(:concept_id)
-
-        -> { where(concept: concept) }
-      end
-    end
-
-    has_many :tests,
-             make_obs_concept_filter(Lab::Metadata::TEST_TYPE_CONCEPT_NAME),
-             class_name: '::Lab::LabTest',
-             foreign_key: :order_id
-
-    has_many :results,
-             make_obs_concept_filter(Lab::Metadata::TEST_RESULT_CONCEPT_NAME),
-             class_name: 'Observation',
-             foreign_key: :order_id
-
-    has_one :reason_for_test,
-            make_obs_concept_filter(Lab::Metadata::REASON_FOR_TEST_CONCEPT_NAME),
-            class_name: 'Observation',
-            foreign_key: :order_id
-
-    has_one :requesting_clinician,
-            make_obs_concept_filter(Lab::Metadata::REQUESTING_CLINICIAN_CONCEPT_NAME),
-            class_name: 'Observation',
-            foreign_key: :order_id
-
-    has_one :target_lab,
-            make_obs_concept_filter(Lab::Metadata::TARGET_LAB_CONCEPT_NAME),
-            class_name: 'Observation',
-            foreign_key: :order_id
-
-    has_one :mapping,
-            class_name: '::Lab::LimsOrderMapping',
-            foreign_key: :order_id
-
-    default_scope do
-      joins(:order_type)
-        .merge(OrderType.where(name: Lab::Metadata::ORDER_TYPE_NAME))
-        .where.not(concept_id: ConceptName.where(name: 'Tests ordered').select(:concept_id))
-    end
-
-    scope :drawn, -> { where.not(concept_id: ConceptName.where(name: 'Unknown').select(:concept_id)) }
-    scope :not_drawn, -> { where(concept_id: ConceptName.where(name: 'Unknown').select(:concept_id)) }
-
-    def self.prefetch_relationships
-      includes(:reason_for_test,
-               :requesting_clinician,
-               :target_lab,
-               tests: [:result])
-    end
-  end
-end

data/app/models/lab/lab_result.rb

@@ -1,31 +0,0 @@
-# frozen_string_literal: true
-
-module Lab
-  class LabResult < Observation
-    alias measures children
-
-    default_scope do
-      lab_test_concept = ConceptName.where(name: Lab::Metadata::TEST_RESULT_CONCEPT_NAME)
-                                    .select(:concept_id)
-      where(voided: 0, concept: lab_test_concept)
-    end
-
-    belongs_to :test,
-               (lambda do
-                  where(concept: ConceptName.where(name: Lab::Metadata::TEST_TYPE_CONCEPT_NAME)
-                                            .select(:concept_id))
-                end),
-               class_name: 'Observation',
-               foreign_key: :obs_group_id
-
-    def void(reason)
-      children.each do |measure|
-        # Need to have a LabResultMeasure model that privately handles it's children
-        measure.children.each { |provider| provider.void(reason) }
-        measure.void(reason)
-      end
-
-      super(reason)
-    end
-  end
-end

data/app/models/lab/lab_test.rb

@@ -1,19 +0,0 @@
-# frozen_string_literal: true
-
-module Lab
-  class LabTest < ::Observation
-    default_scope do
-      where(concept: ConceptName.where(name: Lab::Metadata::TEST_TYPE_CONCEPT_NAME))
-    end
-
-    has_one :result,
-            -> { where(concept: ConceptName.where(name: Lab::Metadata::TEST_RESULT_CONCEPT_NAME)) },
-            class_name: '::Lab::LabResult',
-            foreign_key: :obs_group_id
-
-    def void(reason)
-      result&.void(reason)
-      super(reason)
-    end
-  end
-end

data/app/models/lab/lims_failed_import.rb

@@ -1,4 +0,0 @@
-module Lab
-  class LimsFailedImport < ApplicationRecord
-  end
-end

data/app/models/lab/lims_order_mapping.rb

@@ -1,10 +0,0 @@
-# frozen_string_literal: true
-
-module Lab
-  class LimsOrderMapping < ApplicationRecord
-    belongs_to :order, class_name: 'LabOrder', foreign_key: 'order_id'
-
-    validates_presence_of :lims_id, :order_id
-    validates_uniqueness_of :lims_id, :order_id
-  end
-end