his_emr_api_lab 1.1.19 → 1.1.22

data/app/services/lab/orders_service.rb

@@ -1,212 +0,0 @@
-# frozen_string_literal: true
-
-module Lab
-  ##
-  # Manage lab orders.
-  #
-  # Lab orders are just ordinary openmrs orders with extra metadata that
-  # separates them from other orders. Lab orders have an order type of 'Lab'
-  # with the order's test type as the order's concept. The order's start
-  # date is the day the order is made. Additional information pertaining to
-  # the order is stored as observations that point to the order. The
-  # specimen types, requesting clinician, target lab, and reason for test
-  # are saved as observations to the order. Refer to method #order_test for
-  # more information.
-  module OrdersService
-    class << self
-      ##
-      # Create a lab order.
-      #
-      # Parameters schema:
-      #
-      #     {
-      #       encounter_id: {
-      #         type: :integer,
-      #         required: :false,
-      #         description: 'Attach order to this if program_id and patient_id are not provided'
-      #       },
-      #       program_id: { type: :integer, required: false },
-      #       patient_id: { type: :integer, required: false }
-      #       specimen: { type: :object, properties: { concept_id: :integer }, required: %i[concept_id] },
-      #       test_type_ids: {
-      #         type: :array,
-      #         items: {
-      #           type: :object,
-      #           properties: { concept_id: :integer },
-      #           required: %i[concept_id]
-      #         }
-      #       },
-      #       start_date: { type: :datetime }
-      #       accession_number: { type: :string }
-      #       target_lab: { type: :string },
-      #       reason_for_test_id: { type: :integer },
-      #       requesting_clinician: { type: :string }
-      #     }
-      #
-      # encounter_id: is an ID of the encounter the lab order is to be created under
-      # test_type_id: is a concept_id of the name of test being ordered
-      # specimen_type_id: is a list of IDs for the specimens to be tested (can be ommited)
-      # target_lab: is the name of the lab where test will be carried out
-      # reason_for_test_id: is a concept_id for a (standard) reason of why the test is being carried out
-      # requesting_clinician: Name of the clinician requesting the test (defaults to current user)
-      def order_test(order_params)
-        Order.transaction do
-          encounter = find_encounter(order_params)
-          order = create_order(encounter, order_params)
-
-          Lab::TestsService.create_tests(order, order_params[:date], order_params[:tests])
-
-          Lab::LabOrderSerializer.serialize_order(
-            order, requesting_clinician: add_requesting_clinician(order, order_params),
-                   reason_for_test: add_reason_for_test(order, order_params),
-                   target_lab: add_target_lab(order, order_params)
-          )
-        end
-      end
-
-      def update_order(order_id, params)
-        specimen_id = params.dig(:specimen, :concept_id)
-        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')
-          raise ::UnprocessableEntityError, "Can't change order specimen once set"
-        end
-
-        if specimen_id.to_i != order.concept_id
-          Rails.logger.debug("Updating order ##{order.order_id}")
-          order.update!(concept_id: specimen_id,
-                        discontinued: true,
-                        discontinued_by: User.current.user_id,
-                        discontinued_date: params[:date]&.to_date || Time.now,
-                        discontinued_reason_non_coded: 'Sample drawn/updated')
-        end
-
-        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
-
-        Lab::LabOrderSerializer.serialize_order(order)
-      end
-
-      def void_order(order_id, reason)
-        order = Lab::LabOrder.includes(%i[requesting_clinician reason_for_test target_lab], tests: [:result])
-                             .find(order_id)
-
-        order.requesting_clinician&.void(reason)
-        order.reason_for_test&.void(reason)
-        order.target_lab&.void(reason)
-
-        order.tests.each { |test| test.void(reason) }
-        voided = order.void(reason)
-
-        voided
-      end
-
-      private
-
-      ##
-      # Extract an encounter from the given parameters.
-      #
-      # Uses an encounter_id to retrieve an encounter if provided else
-      # a 'Lab' encounter is created using the provided program_id and
-      # patient_id.
-      def find_encounter(order_params)
-        return Encounter.find(order_params[:encounter_id]) if order_params[:encounter_id]
-
-        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
-
-        Encounter.create!(
-          patient_id: order_params[:patient_id],
-          program_id: program_id,
-          type: EncounterType.find_by_name!(Lab::Metadata::ENCOUNTER_TYPE_NAME),
-          encounter_datetime: order_params[:date] || Date.today,
-          provider_id: order_params[:provider_id] || User.current.person.person_id
-        )
-      end
-
-      def create_order(encounter, params)
-        Lab::LabOrder.create!(
-          order_type: OrderType.find_by_name!(Lab::Metadata::ORDER_TYPE_NAME),
-          concept_id: params.dig(:specimen, :concept_id) || unknown_concept_id,
-          encounter_id: encounter.encounter_id,
-          patient_id: encounter.patient_id,
-          start_date: params[:date]&.to_date || Date.today,
-          auto_expire_date: params[:end_date],
-          accession_number: params[:accession_number] || next_accession_number,
-          orderer: User.current&.user_id
-        )
-      end
-
-      ##
-      # Attach the requesting clinician to an order
-      def add_requesting_clinician(order, params)
-        create_order_observation(
-          order,
-          Lab::Metadata::REQUESTING_CLINICIAN_CONCEPT_NAME,
-          params[:date],
-          value_text: params['requesting_clinician']
-        )
-      end
-
-      ##
-      # Attach a reason for the order/test
-      #
-      # Examples of reasons include: Routine, Targeted, Confirmatory, Repeat, or Stat.
-      def add_reason_for_test(order, params)
-        create_order_observation(
-          order,
-          Lab::Metadata::REASON_FOR_TEST_CONCEPT_NAME,
-          params[:date],
-          value_coded: params[:reason_for_test_id]
-        )
-      end
-
-      ##
-      # Attach the lab where the test is going to get carried out.
-      def add_target_lab(order, params)
-        return nil unless params['target_lab']
-
-        create_order_observation(
-          order,
-          Lab::Metadata::TARGET_LAB_CONCEPT_NAME,
-          params[:date],
-          value_text: params['target_lab']
-        )
-      end
-
-      def create_order_observation(order, concept_name, date, **values)
-        Observation.create!(
-          order: order,
-          encounter_id: order.encounter_id,
-          person_id: order.patient_id,
-          concept_id: ConceptName.find_by_name!(concept_name).concept_id,
-          obs_datetime: date&.to_time || Time.now,
-          **values
-        )
-      end
-
-      def next_accession_number(date = nil)
-        Lab::AccessionNumberService.next_accession_number(date)
-      end
-
-      def unknown_concept_id
-        ConceptName.find_by_name!('Unknown').concept_id
-      end
-
-      def update_reason_for_test(order, concept_id)
-        raise InvalidParameterError, "Reason for test can't be blank" if concept_id.blank?
-
-        return if order.reason_for_test&.value_coded == concept_id
-
-        raise InvalidParameterError, "Can't change reason for test once set" if order.reason_for_test&.value_coded
-
-        order.reason_for_test&.delete
-        add_reason_for_test(order, date: order.start_date, reason_for_test_id: concept_id)
-      end
-    end
-  end
-end

data/app/services/lab/results_service.rb

@@ -1,122 +0,0 @@
-# frozen_string_literal: true
-
-module Lab
-  module ResultsService
-    class << self
-      ##
-      # Attach results to a test
-      #
-      # Params:
-      #   test_id: The tests id (maps to obs_id of the test's observation in OpenMRS)
-      #   params: A hash comprising the following fields
-      #     - encounter_id: Encounter to create result under (can be ommitted but provider_id has to specified)
-      #     - provider_id: Specify a provider for an encounter the result is going to be created under
-      #     - date: Retrospective date when the result was received (can be ommitted, defaults to today)
-      #     - measures: An array of measures. A measure is an object of the following structure
-      #         - indicator: An object that has a concept_id field (concept_id of the indicator)
-      #         - value_type: An enum that's limited to 'numeric', 'boolean', 'text', and 'coded'
-      def create_results(test_id, params)
-        ActiveRecord::Base.transaction do
-          test = Lab::LabTest.find(test_id)
-          encounter = find_encounter(test, encounter_id: params[:encounter_id],
-                                           date: params[:date]&.to_date,
-                                           provider_id: params[:provider_id])
-
-          results_obs = create_results_obs(encounter, test, params[:date], params[:comments])
-          params[:measures].map { |measure| add_measure_to_results(results_obs, measure, params[:date]) }
-
-          Lab::ResultSerializer.serialize(results_obs)
-        end
-      end
-
-      private
-
-      def find_encounter(test, encounter_id: nil, date: nil, provider_id: nil)
-        return Encounter.find(encounter_id) if encounter_id
-
-        Encounter.create!(
-          patient_id: test.person_id,
-          program_id: test.encounter.program_id,
-          type: EncounterType.find_by_name!(Lab::Metadata::ENCOUNTER_TYPE_NAME),
-          encounter_datetime: date || Date.today,
-          provider_id: provider_id || User.current.user_id
-        )
-      end
-
-      # Creates the parent observation for results to which the different measures are attached
-      def create_results_obs(encounter, test, date, comments = nil)
-        void_existing_results_obs(encounter, test)
-
-        Lab::LabResult.create!(
-          person_id: encounter.patient_id,
-          encounter_id: encounter.encounter_id,
-          concept_id: test_result_concept.concept_id,
-          order_id: test.order_id,
-          obs_group_id: test.obs_id,
-          obs_datetime: date&.to_datetime || DateTime.now,
-          comments: comments
-        )
-      end
-
-      def void_existing_results_obs(encounter, test)
-        result = Lab::LabResult.find_by(person_id: encounter.patient_id,
-                                        concept_id: test_result_concept.concept_id,
-                                        obs_group_id: test.obs_id)
-        return unless result
-
-        result.measures.map { |child_obs| child_obs.void("Updated/overwritten by #{User.current.username}") }
-        result.void("Updated/overwritten by #{User.current.username}")
-      end
-
-      def test_result_concept
-        ConceptName.find_by_name!(Lab::Metadata::TEST_RESULT_CONCEPT_NAME)
-      end
-
-      def add_measure_to_results(results_obs, params, date)
-        validate_measure_params(params)
-
-        Observation.create!(
-          person_id: results_obs.person_id,
-          encounter_id: results_obs.encounter_id,
-          order_id: results_obs.order_id,
-          concept_id: params[:indicator][:concept_id],
-          obs_group_id: results_obs.obs_id,
-          obs_datetime: date&.to_datetime || DateTime.now,
-          **make_measure_value(params)
-        )
-      end
-
-      def validate_measure_params(params)
-        raise InvalidParameterError, 'measures.value is required' if params[:value].blank?
-
-        if params[:indicator]&.[](:concept_id).blank?
-          raise InvalidParameterError, 'measures.indicator.concept_id is required'
-        end
-
-        params
-      end
-
-      # Converts user provided measure values to observation_values
-      def make_measure_value(params)
-        obs_value = { value_modifier: params[:value_modifier] }
-        value_type = params[:value_type] || 'text'
-
-        case value_type.downcase
-        when 'numeric' then obs_value.merge(value_numeric: params[:value])
-        when 'boolean' then obs_value.merge(value_boolean: parse_boolen_value(params[:value]))
-        when 'coded' then obs_value.merge(value_coded: params[:value]) # Should we be collecting value_name_coded_id?
-        when 'text' then obs_value.merge(value_text: params[:value])
-        else raise InvalidParameterError, "Invalid value_type: #{params[:value_type]}"
-        end
-      end
-
-      def parse_boolen_value(string)
-        case string.downcase
-        when 'true' then true
-        when 'false' then false
-        else raise InvalidParameterError, "Invalid boolean value: #{string}"
-        end
-      end
-    end
-  end
-end

data/app/services/lab/tests_service.rb

@@ -1,93 +0,0 @@
-# frozen_string_literal: true
-
-module Lab
-  ##
-  # Manage tests that have been ordered through the ordering service.
-  module TestsService
-    class << self
-      def find_tests(filters)
-        tests = Lab::LabTest.all
-
-        tests = filter_tests(tests, test_type_id: filters.delete(:test_type_id),
-                                    patient_id: filters.delete(:patient_id))
-
-        tests = filter_tests_by_results(tests) if %w[1 true].include?(filters[:pending_results]&.downcase)
-
-        tests = filter_tests_by_order(tests, accession_number: filters.delete(:accession_number),
-                                             order_date: filters.delete(:order_date),
-                                             specimen_type_id: filters.delete(:specimen_type_id))
-
-        tests.map { |test| Lab::TestSerializer.serialize(test) }
-      end
-
-      def create_tests(order, date, tests_params)
-        raise InvalidParameterError, 'tests are required' if tests_params.nil? || tests_params.empty?
-
-        Lab::LabTest.transaction do
-          tests_params.map do |params|
-            test = Lab::LabTest.create!(
-              concept_id: ConceptName.find_by_name!(Lab::Metadata::TEST_TYPE_CONCEPT_NAME)
-                                     .concept_id,
-              encounter_id: order.encounter_id,
-              order_id: order.order_id,
-              person_id: order.patient_id,
-              obs_datetime: date&.to_time || Time.now,
-              value_coded: params[:concept_id]
-            )
-
-            Lab::TestSerializer.serialize(test, order: order)
-          end
-        end
-      end
-
-      private
-
-      ##
-      # Filter a LabTests Relation.
-      def filter_tests(tests, test_type_id: nil, patient_id: nil)
-        tests = tests.where(value_coded: test_type_id) if test_type_id
-        tests = tests.where(person_id: patient_id) if patient_id
-
-        tests
-      end
-
-      ##
-      # Filter out any tests having results
-      def filter_tests_by_results(tests)
-        tests.where.not(obs_id: Lab::LabResult.all.select(:obs_group_id))
-      end
-
-      ##
-      # Filter LabTests Relation using their parent orders parameters.
-      def filter_tests_by_order(tests, accession_number: nil, order_date: nil, specimen_type_id: nil)
-        return tests unless accession_number || order_date || specimen_type_id
-
-        lab_orders = filter_orders(Lab::LabOrder.all, accession_number: accession_number,
-                                                      order_date: order_date,
-                                                      specimen_type_id: specimen_type_id)
-        tests.joins(:order).merge(lab_orders)
-      end
-
-      def filter_orders(orders, accession_number: nil, order_date: nil, specimen_type_id: nil)
-        if order_date
-          order_date = order_date.to_date
-          orders = orders.where('start_date >= ? AND start_date < ?', order_date, order_date + 1.day)
-        end
-
-        orders = orders.where(accession_number: accession_number) if accession_number
-        orders = orders.where(concept_id: specimen_type_id) if specimen_type_id
-
-        orders
-      end
-
-      def create_test(order, date, test_type_id)
-        create_order_observation(
-          order,
-          Lab::Metadata::TEST_TYPE_CONCEPT_NAME,
-          date,
-          value_coded: test_type_id
-        )
-      end
-    end
-  end
-end

data/config/routes.rb

@@ -1,17 +0,0 @@
-# frozen_string_literal: true
-
-Lab::Engine.routes.draw do
-  resources :orders, path: 'api/v1/lab/orders'
-  resources :tests, path: 'api/v1/lab/tests', except: %i[update] do # ?pending=true to select tests without results?
-    resources :results, only: %i[index create destroy]
-  end
-
-  get 'api/v1/lab/labels/order', to: 'labels#print_order_label'
-
-  # Metadata
-  # TODO: Move the following to namespace /concepts
-  resources :specimen_types, only: %i[index], path: 'api/v1/lab/specimen_types'
-  resources :test_result_indicators, only: %i[index], path: 'api/v1/lab/test_result_indicators'
-  resources :test_types, only: %i[index], path: 'api/v1/lab/test_types'
-  resources :reasons_for_test, only: %i[index], path: 'api/v1/lab/reasons_for_test'
-end

data/db/migrate/20210126092910_create_lab_lab_accession_number_counters.rb

@@ -1,12 +0,0 @@
-class CreateLabLabAccessionNumberCounters < ActiveRecord::Migration[5.2]
-  def change
-    create_table :lab_accession_number_counters do |t|
-      t.date :date
-      t.bigint :value
-
-      t.timestamps
-
-      t.index %i[date], unique: true
-    end
-  end
-end

data/db/migrate/20210310115457_create_lab_lims_order_mappings.rb

@@ -1,15 +0,0 @@
-class CreateLabLimsOrderMappings < ActiveRecord::Migration[5.2]
-  def change
-    create_table :lab_lims_order_mappings do |t|
-      t.integer :lims_id, null: false, unique: true
-      t.integer :order_id, null: false, unique: true
-      t.datetime :pushed_at
-      t.datetime :pulled_at
-
-      t.timestamps
-
-      t.foreign_key :orders, primary_key: :order_id, column: :order_id
-      t.index :lims_id
-    end
-  end
-end

data/db/migrate/20210323080140_change_lims_id_to_string_in_lims_order_mapping.rb

@@ -1,15 +0,0 @@
-# frozen_string_literal: true
-
-class ChangeLimsIdToStringInLimsOrderMapping < ActiveRecord::Migration[5.2]
-  def change
-    reversible do |direction|
-      direction.up do
-        change_column :lab_lims_order_mappings, :lims_id, :string, null: false
-      end
-
-      direction.down do
-        change_column :lab_lims_order_mappings, :lims_id, :integer, null: false
-      end
-    end
-  end
-end

data/db/migrate/20210326195504_add_order_revision_to_lims_order_mapping.rb

@@ -1,5 +0,0 @@
-class AddOrderRevisionToLimsOrderMapping < ActiveRecord::Migration[5.2]
-  def change
-    add_column :lab_lims_order_mappings, :revision, :string
-  end
-end

data/db/migrate/20210407071728_create_lab_lims_failed_imports.rb

@@ -1,19 +0,0 @@
-# frozen_string_literal: true
-
-class CreateLabLimsFailedImports < ActiveRecord::Migration[5.2]
-  def change
-    create_table :lab_lims_failed_imports do |t|
-      t.string :lims_id, null: false
-      t.string :tracking_number, null: false
-      t.string :patient_nhid, null: false
-      t.string :reason, null: false
-      t.string :diff, limit: 2048
-
-      t.timestamps
-
-      t.index :lims_id
-      t.index :patient_nhid
-      t.index :tracking_number
-    end
-  end
-end

data/db/migrate/20210610095024_fix_numeric_results_value_type.rb

@@ -1,20 +0,0 @@
-class FixNumericResultsValueType < ActiveRecord::Migration[5.2]
-  def up
-    results = Lab::LabResult.all.includes(:children)
-
-    ActiveRecord::Base.connection.transaction do
-      results.each do |result|
-        result.children.each do |measure|
-          next unless measure.value_text&.match?(/^[+-]?((\d+(\.\d+)?)|\.\d+)$/)
-
-          puts "Updating result value type for result measure ##{measure.obs_id}"
-          measure.value_numeric = measure.value_text
-          measure.value_text = nil
-          measure.save!
-        end
-      end
-    end
-  end
-
-  def down; end
-end

data/db/migrate/20210807111531_add_default_to_lims_order_mapping.rb

@@ -1,7 +0,0 @@
-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