his_emr_api_lab 0.0.2

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data/MIT-LICENSE

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+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

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+![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
+```
+
+## Contributing
+
+Contribution directions go here.
+
+## License
+
+The gem is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).

data/Rakefile

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+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

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+# frozen_string_literal: true
+
+module Lab
+  class ApplicationController < ::ApplicationController
+  end
+end

data/app/controllers/lab/orders_controller.rb

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+# 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
+
+      render json: orders, status: :created
+    end
+
+    def update
+      specimen = params.require(:specimen).permit(:concept_id)
+
+      order = OrdersService.update_order(params[:id], specimen: specimen)
+
+      render json: order
+    end
+
+    def index
+      filters = params.permit(%i[patient_id accession_number date status])
+
+      render json: OrdersSearchService.find_orders(filters)
+    end
+
+    def destroy
+      OrdersService.void_order(params[:id], params[:reason])
+
+      render status: :no_content
+    end
+  end
+end

data/app/controllers/lab/reasons_for_test_controller.rb

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+# 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

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+# 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)
+
+      render json: result, status: :created
+    end
+  end
+end

data/app/controllers/lab/specimen_types_controller.rb

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+# 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

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+# 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

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+# 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

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+# 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(Order.find(order_id), date, test_concepts)
+
+    render json: tests, status: :created
+  end
+
+  def service
+    Lab::TestsService
+  end
+end

data/app/jobs/lab/application_job.rb

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+module Lab
+  class ApplicationJob < ActiveJob::Base
+  end
+end

data/app/mailers/lab/application_mailer.rb

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+module Lab
+  class ApplicationMailer < ActionMailer::Base
+    default from: 'from@example.com'
+    layout 'mailer'
+  end
+end

data/app/models/lab/application_record.rb

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+module Lab
+  class ApplicationRecord < ActiveRecord::Base
+    self.abstract_class = true
+  end
+end

data/app/models/lab/lab_accession_number_counter.rb

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+# 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

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+# 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

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+# 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
+
+    default_scope { joins(:order_type).merge(OrderType.where(name: Lab::Metadata::ORDER_TYPE_NAME)) }
+
+    def self.prefetch_relationships
+      includes(:reason_for_test,
+               :requesting_clinician,
+               :target_lab,
+               tests: [:result])
+    end
+  end
+end

data/app/models/lab/lab_result.rb

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+# 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
+  end
+end

data/app/models/lab/lab_test.rb

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+# 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
+  end
+end

data/app/models/lab/lims_failed_import.rb

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+module Lab
+  class LimsFailedImport < ApplicationRecord
+  end
+end

data/app/models/lab/lims_order_mapping.rb

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+# 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

data/app/serializers/lab/lab_order_serializer.rb

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+# frozen_string_literal: true
+
+module Lab
+  module LabOrderSerializer
+    def self.serialize_order(order, tests: nil, requesting_clinician: nil, reason_for_test: nil, target_lab: nil)
+      tests ||= order.tests
+      requesting_clinician ||= order.requesting_clinician
+      reason_for_test ||= order.reason_for_test
+      target_lab ||= order.target_lab
+
+      ActiveSupport::HashWithIndifferentAccess.new(
+        {
+          id: order.order_id,
+          order_id: order.order_id, # Deprecated: Link to :id
+          encounter_id: order.encounter_id,
+          order_date: order.start_date,
+          patient_id: order.patient_id,
+          accession_number: order.accession_number,
+          specimen: {
+            concept_id: order.concept_id,
+            name: concept_name(order.concept_id)
+          },
+          requesting_clinician: requesting_clinician&.value_text,
+          target_lab: target_lab&.value_text,
+          reason_for_test: {
+            concept_id: reason_for_test&.value_coded,
+            name: concept_name(reason_for_test&.value_coded)
+          },
+          tests: tests.map do |test|
+            result_obs = test.children.first
+
+            {
+              id: test.obs_id,
+              concept_id: test.value_coded,
+              name: concept_name(test.value_coded),
+              result: result_obs && ResultSerializer.serialize(result_obs)
+            }
+          end
+        }
+      )
+    end
+
+    def self.concept_name(concept_id)
+      return concept_id unless concept_id
+
+      ConceptName.select(:name).find_by_concept_id(concept_id)&.name
+    end
+  end
+end