his_emr_api_lab 0.0.2

data/lib/tasks/loaders/loader_mixin.rb

@@ -0,0 +1,53 @@
+# frozen_string_literal: true
+
+module Lab
+  module Loaders
+    module LoaderMixin
+      def self.included(_mod)
+        User.current = User.find_by_username('admin') || User.first
+        Location.current = Location.find_by_name('Registration') || Location.first
+      end
+
+      CONCEPT_DATATYPE_CODED = 2
+      CONCEPT_CLASS_TEST = 1
+
+      def find_or_create_concept(name, is_set: false)
+        # Filter out concept_names with voided concepts
+        concept = ConceptName.joins(:concept).find_by_name(name)
+        return concept if concept
+
+        ConceptName.create!(
+          concept: Concept.create!(
+            short_name: name,
+            datatype_id: CONCEPT_DATATYPE_CODED,
+            class_id: CONCEPT_CLASS_TEST,
+            is_set: is_set,
+            uuid: SecureRandom.uuid,
+            creator: User.current.user_id,
+            date_created: Time.now
+          ),
+          name: name,
+          locale: 'en',
+          concept_name_type: 'FULLY_SPECIED',
+          uuid: SecureRandom.uuid,
+          creator: User.current.user_id,
+          date_created: Time.now
+        )
+      end
+
+      def add_concept_to_set(set_concept_id:, concept_id:)
+        set = ConceptSet.find_by(concept_set: set_concept_id, concept_id: concept_id)
+        return set if set
+
+        ConceptSet.create!(concept_set: set_concept_id,
+                           concept_id: concept_id,
+                           creator: User.current.user_id,
+                           date_created: Time.now)
+      end
+
+      def data_path(filename)
+        "#{__dir__}/data/#{filename}"
+      end
+    end
+  end
+end

data/lib/tasks/loaders/metadata_loader.rb

@@ -0,0 +1,26 @@
+# frozen_string_literal: true
+
+require_relative 'reasons_for_test_loader'
+require_relative 'specimens_loader'
+require_relative 'test_result_indicators_loader'
+
+module Lab
+  module Loaders
+    module MetadataLoader
+      def self.load
+        unless Program.where(name: 'Laboratory program').exists?
+          Program.create(name: 'Laboratory program',
+                         description: 'Manage Lab information',
+                         creator: 1,
+                         uuid: SecureRandom.uuid)
+        end
+
+        SpecimensLoader.load
+        TestResultIndicatorsLoader.load
+        ReasonsForTestLoader.load
+      end
+    end
+  end
+end
+
+Lab::Loaders::MetadataLoader.load

data/lib/tasks/loaders/reasons_for_test_loader.rb

@@ -0,0 +1,23 @@
+# frozen_string_literal: true
+
+require_relative './loader_mixin'
+
+module Lab
+  module Loaders
+    module ReasonsForTestLoader
+      class << self
+        include LoaderMixin
+
+        def load
+          CSV.open(data_path('reasons-for-test.csv'), headers: :first_row) do |csv|
+            csv.each do |row|
+              puts "Adding reason for test: #{row['reason_name']}"
+              add_concept_to_set(set_concept_id: find_or_create_concept(Lab::Metadata::REASON_FOR_TEST_CONCEPT_NAME).concept_id,
+                                 concept_id: find_or_create_concept(row['reason_name']).concept_id)
+            end
+          end
+        end
+      end
+    end
+  end
+end

data/lib/tasks/loaders/specimens_loader.rb

@@ -0,0 +1,65 @@
+# frozen_string_literal: true
+
+require 'csv'
+require_relative './loader_mixin'
+
+module Lab
+  module Loaders
+    ##
+    # Load specimens and their tests into the database
+    module SpecimensLoader
+      class << self
+        include LoaderMixin
+      
+        def load
+          puts "------- Loading tests and specimens ---------"
+          CSV.open(data_path('tests.csv'), headers: :first_row) do |csv|
+            csv.each_with_object({}) do |row, test_types|
+              specimen_name = row['specimen_name']
+              test_name = row['test_name']
+
+              ActiveRecord::Base.transaction do
+                test_type = test_types[test_name] || create_test_type(test_name)
+                create_specimen_type(specimen_name, test_type)
+
+                test_types[test_name] ||= test_type
+              end
+
+              puts "Created test #{test_name} <--< #{specimen_name}"
+            rescue StandardError => e
+              puts "Error: #{test_name}: #{e}"
+            end
+          end
+        end
+
+        def test_type_concept_id
+          find_or_create_concept(Lab::Metadata::TEST_TYPE_CONCEPT_NAME).concept_id
+        end
+
+        def specimen_type_concept_id
+          find_or_create_concept(Lab::Metadata::SPECIMEN_TYPE_CONCEPT_NAME).concept_id
+        end
+
+
+        def create_test_type(name)
+          concept_id = find_or_create_concept(name, is_set: true).concept_id
+
+          add_concept_to_set(set_concept_id: test_type_concept_id, concept_id: concept_id)
+        rescue StandardError => e
+          raise "Failed to create test type `#{name}`: #{e}"
+        end
+
+        def create_specimen_type(name, test_type)
+          concept_id = find_or_create_concept(name).concept_id
+
+          [
+            add_concept_to_set(set_concept_id: specimen_type_concept_id, concept_id: concept_id),
+            add_concept_to_set(set_concept_id: test_type.concept_id, concept_id: concept_id)
+          ]
+        rescue StandardError => e
+          raise "Failed to create specimen type `#{name}`: #{e}"
+        end
+      end
+    end
+  end
+end

data/lib/tasks/loaders/test_result_indicators_loader.rb

@@ -0,0 +1,54 @@
+# frozen_string_literal: true
+
+require 'csv'
+require_relative './loader_mixin'
+
+module Lab
+  module Loaders
+    ##
+    # Load specimens and their tests into the database
+    module TestResultIndicatorsLoader
+      class << self
+        include LoaderMixin
+      
+        def load
+          puts "------- Loading measures ------------"
+          CSV.open(data_path('test-measures.csv'), headers: :first_row) do |csv|
+            csv.each_with_object({}) do |row, test_measures|
+              test_name = row['test_name']
+              measure_name = row['measure_name']
+
+              ActiveRecord::Base.transaction do
+                measure_concept = find_or_create_concept(measure_name)
+                add_measure_to_test(test_name, measure_concept)
+              end
+
+              puts "Created measure #{test_name} <--< #{measure_name}"
+            rescue StandardError => e
+              puts "Error: #{measure_name}: #{e}"
+            end
+          end
+        end
+
+        def create_test_type(name)
+          concept_id = find_or_create_concept(name, is_set: true).concept_id
+
+          create_concept_set(concept_set: test_type_concept_id, concept_id: concept_id)
+        rescue StandardError => e
+          raise "Failed to create test type `#{name}`: #{e}"
+        end
+
+        def add_measure_to_test(test_name, measure_concept)
+          [
+            add_concept_to_set(set_concept_id: find_or_create_concept(Lab::Metadata::TEST_RESULT_INDICATOR_CONCEPT_NAME).concept_id,
+                               concept_id: measure_concept.concept_id),
+            add_concept_to_set(set_concept_id: measure_concept.concept_id,
+                               concept_id: find_or_create_concept(test_name).concept_id)
+          ]
+        rescue StandardError => e
+          raise "Failed to create measure for test `#{name}`: #{e}"
+        end
+      end
+    end
+  end
+end

metadata

@@ -0,0 +1,296 @@
+--- !ruby/object:Gem::Specification
+name: his_emr_api_lab
+version: !ruby/object:Gem::Version
+  version: 0.0.2
+platform: ruby
+authors:
+- Elizabeth Glaser Pediatric Foundation Malawi
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2021-04-07 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: couchrest
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.0.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.0.0
+- !ruby/object:Gem::Dependency
+  name: rails
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 5.2.4
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 5.2.4.3
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 5.2.4
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 5.2.4.3
+- !ruby/object:Gem::Dependency
+  name: bcrypt
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 3.1.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 3.1.0
+- !ruby/object:Gem::Dependency
+  name: factory_bot_rails
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 6.1.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 6.1.0
+- !ruby/object:Gem::Dependency
+  name: faker
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.16.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.16.0
+- !ruby/object:Gem::Dependency
+  name: rspec-rails
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 5.0.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 5.0.0
+- !ruby/object:Gem::Dependency
+  name: rswag-api
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.4.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.4.0
+- !ruby/object:Gem::Dependency
+  name: rswag-specs
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.4.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.4.0
+- !ruby/object:Gem::Dependency
+  name: rswag-ui
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.4.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.4.0
+- !ruby/object:Gem::Dependency
+  name: rubocop
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.79.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.79.0
+- !ruby/object:Gem::Dependency
+  name: rubocop-rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.41.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.41.0
+- !ruby/object:Gem::Dependency
+  name: shoulda-matchers
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 4.5.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 4.5.0
+- !ruby/object:Gem::Dependency
+  name: sqlite3
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.4.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.4.0
+description: |
+  This adds a lab interface to the OpenMRS compatible core API provided by
+  [HIS-EMR-API](https://github.com/EGPAFMalawiHIS/HIS-EMR-API).
+email:
+- emrdevelopersmalawi@pedaids.org
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- MIT-LICENSE
+- README.md
+- Rakefile
+- app/controllers/lab/application_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/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/lims/api.rb
+- app/services/lab/lims/config.rb
+- app/services/lab/lims/order_dto.rb
+- app/services/lab/lims/order_serializer.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
+- 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
+homepage: https://github.com/EGPAFMalawiHIS/his_emr_api_lab
+licenses:
+- MIT
+metadata:
+  source_code_uri: https://github.com/EGPAFMalawiHIS/his_emr_api_lab
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubygems_version: 3.0.8
+signing_key: 
+specification_version: 4
+summary: Lab extension for the HIS-EMR-API
+test_files: []