mahis_emr_api_lab 1.2.0

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Files changed (90) hide show
  1. checksums.yaml +7 -0
  2. data/MIT-LICENSE +20 -0
  3. data/README.md +71 -0
  4. data/Rakefile +32 -0
  5. data/app/controllers/lab/application_controller.rb +6 -0
  6. data/app/controllers/lab/labels_controller.rb +17 -0
  7. data/app/controllers/lab/orders_controller.rb +78 -0
  8. data/app/controllers/lab/reasons_for_test_controller.rb +9 -0
  9. data/app/controllers/lab/results_controller.rb +20 -0
  10. data/app/controllers/lab/specimen_types_controller.rb +15 -0
  11. data/app/controllers/lab/test_result_indicators_controller.rb +9 -0
  12. data/app/controllers/lab/test_types_controller.rb +15 -0
  13. data/app/controllers/lab/tests_controller.rb +25 -0
  14. data/app/controllers/lab/users_controller.rb +32 -0
  15. data/app/jobs/lab/application_job.rb +4 -0
  16. data/app/jobs/lab/push_order_job.rb +12 -0
  17. data/app/jobs/lab/update_patient_orders_job.rb +32 -0
  18. data/app/jobs/lab/void_order_job.rb +17 -0
  19. data/app/mailers/lab/application_mailer.rb +6 -0
  20. data/app/models/lab/application_record.rb +5 -0
  21. data/app/models/lab/lab_accession_number_counter.rb +13 -0
  22. data/app/models/lab/lab_acknowledgement.rb +6 -0
  23. data/app/models/lab/lab_encounter.rb +7 -0
  24. data/app/models/lab/lab_order.rb +58 -0
  25. data/app/models/lab/lab_result.rb +31 -0
  26. data/app/models/lab/lab_test.rb +19 -0
  27. data/app/models/lab/lims_failed_import.rb +4 -0
  28. data/app/models/lab/lims_order_mapping.rb +10 -0
  29. data/app/models/lab/order_extension.rb +14 -0
  30. data/app/serializers/lab/lab_order_serializer.rb +56 -0
  31. data/app/serializers/lab/result_serializer.rb +36 -0
  32. data/app/serializers/lab/test_serializer.rb +52 -0
  33. data/app/services/lab/accession_number_service.rb +77 -0
  34. data/app/services/lab/acknowledgement_service.rb +47 -0
  35. data/app/services/lab/concepts_service.rb +82 -0
  36. data/app/services/lab/json_web_token_service.rb +20 -0
  37. data/app/services/lab/labelling_service/order_label.rb +106 -0
  38. data/app/services/lab/lims/acknowledgement_serializer.rb +29 -0
  39. data/app/services/lab/lims/acknowledgement_worker.rb +37 -0
  40. data/app/services/lab/lims/api/blackhole_api.rb +21 -0
  41. data/app/services/lab/lims/api/couchdb_api.rb +53 -0
  42. data/app/services/lab/lims/api/mysql_api.rb +316 -0
  43. data/app/services/lab/lims/api/rest_api.rb +434 -0
  44. data/app/services/lab/lims/api/ws_api.rb +121 -0
  45. data/app/services/lab/lims/api_factory.rb +19 -0
  46. data/app/services/lab/lims/config.rb +105 -0
  47. data/app/services/lab/lims/exceptions.rb +11 -0
  48. data/app/services/lab/lims/migrator.rb +216 -0
  49. data/app/services/lab/lims/order_dto.rb +105 -0
  50. data/app/services/lab/lims/order_serializer.rb +251 -0
  51. data/app/services/lab/lims/pull_worker.rb +314 -0
  52. data/app/services/lab/lims/push_worker.rb +152 -0
  53. data/app/services/lab/lims/utils.rb +91 -0
  54. data/app/services/lab/lims/worker.rb +94 -0
  55. data/app/services/lab/metadata.rb +26 -0
  56. data/app/services/lab/notification_service.rb +72 -0
  57. data/app/services/lab/orders_search_service.rb +72 -0
  58. data/app/services/lab/orders_service.rb +330 -0
  59. data/app/services/lab/results_service.rb +166 -0
  60. data/app/services/lab/tests_service.rb +105 -0
  61. data/app/services/lab/user_service.rb +62 -0
  62. data/config/routes.rb +28 -0
  63. data/db/migrate/20210126092910_create_lab_lab_accession_number_counters.rb +12 -0
  64. data/db/migrate/20210310115457_create_lab_lims_order_mappings.rb +15 -0
  65. data/db/migrate/20210323080140_change_lims_id_to_string_in_lims_order_mapping.rb +15 -0
  66. data/db/migrate/20210326195504_add_order_revision_to_lims_order_mapping.rb +5 -0
  67. data/db/migrate/20210407071728_create_lab_lims_failed_imports.rb +19 -0
  68. data/db/migrate/20210610095024_fix_numeric_results_value_type.rb +20 -0
  69. data/db/migrate/20210807111531_add_default_to_lims_order_mapping.rb +7 -0
  70. data/lib/auto12epl.rb +201 -0
  71. data/lib/couch_bum/couch_bum.rb +92 -0
  72. data/lib/generators/lab/install/USAGE +9 -0
  73. data/lib/generators/lab/install/install_generator.rb +19 -0
  74. data/lib/generators/lab/install/templates/rswag-ui-lab.rb +5 -0
  75. data/lib/generators/lab/install/templates/start_worker.rb +32 -0
  76. data/lib/generators/lab/install/templates/swagger.yaml +714 -0
  77. data/lib/lab/engine.rb +13 -0
  78. data/lib/lab/version.rb +5 -0
  79. data/lib/logger_multiplexor.rb +38 -0
  80. data/lib/mahis_emr_api_lab.rb +6 -0
  81. data/lib/tasks/lab_tasks.rake +25 -0
  82. data/lib/tasks/loaders/data/reasons-for-test.csv +7 -0
  83. data/lib/tasks/loaders/data/test-measures.csv +225 -0
  84. data/lib/tasks/loaders/data/tests.csv +161 -0
  85. data/lib/tasks/loaders/loader_mixin.rb +53 -0
  86. data/lib/tasks/loaders/metadata_loader.rb +26 -0
  87. data/lib/tasks/loaders/reasons_for_test_loader.rb +23 -0
  88. data/lib/tasks/loaders/specimens_loader.rb +65 -0
  89. data/lib/tasks/loaders/test_result_indicators_loader.rb +54 -0
  90. metadata +331 -0
@@ -0,0 +1,434 @@
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+ # frozen_string_literal: true
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+ require 'rest-client'
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+
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+ class Lab::Lims::Api::RestApi
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+ class LimsApiError < StandardError; end
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+
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+ class AuthenticationTokenExpired < LimsApiError; end
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+
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+ class InvalidParameters < LimsApiError; end
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+
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+ def initialize(config)
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+ @config = config
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+ end
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+
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+ def create_order(order_dto)
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+ response = in_authenticated_session do |headers|
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+ Rails.logger.info("Pushing order ##{order_dto[:tracking_number]} to LIMS")
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+
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+ if order_dto['sample_type'].casecmp?('not_specified')
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+ RestClient.post(expand_uri('request_order', api_version: 'v2'), make_create_params(order_dto), headers)
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+ else
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+ RestClient.post(expand_uri('create_order'), make_create_params(order_dto), headers)
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+ end
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+ end
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+
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+ data = JSON.parse(response.body)
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+ update_order_results(order_dto) unless data['message'].casecmp?('Order already available')
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+
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+ ActiveSupport::HashWithIndifferentAccess.new(
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+ id: order_dto.fetch(:_id, order_dto[:tracking_number]),
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+ rev: 0,
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+ tracking_number: order_dto[:tracking_number]
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+ )
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+ end
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+
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+ def acknowledge(acknowledgement_dto)
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+ Rails.logger.info("Acknowledging order ##{acknowledgement_dto} in LIMS")
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+ response = in_authenticated_session do |headers|
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+ RestClient.post(expand_uri('/acknowledge/test/results/recipient'), acknowledgement_dto, headers)
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+ end
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+ Rails.logger.info("Acknowledged order ##{acknowledgement_dto} in LIMS. Response: #{response}")
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+ JSON.parse(response)
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+ end
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+
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+ def update_order(_id, order_dto)
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+ in_authenticated_session do |headers|
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+ RestClient.post(expand_uri('update_order'), make_update_params(order_dto), headers)
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+ end
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+
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+ update_order_results(order_dto)
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+
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+ { tracking_number: order_dto[:tracking_number] }
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+ end
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+
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+ def consume_orders(*_args, patient_id: nil, **_kwargs)
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+ orders_pending_updates(patient_id).each do |order|
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+ order_dto = Lab::Lims::OrderSerializer.serialize_order(order)
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+
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+ if order_dto['priority'].nil? || order_dto['sample_type'].casecmp?('not_specified')
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+ patch_order_dto_with_lims_order!(order_dto, find_lims_order(order.accession_number))
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+ end
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+
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+ if order_dto['test_results'].empty?
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+ begin
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+ patch_order_dto_with_lims_results!(order_dto, find_lims_results(order.accession_number))
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+ rescue InvalidParameters => e # LIMS responds with a 401 when a result is not found :(
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+ Rails.logger.error("Failed to fetch results for ##{order.accession_number}: #{e.message}")
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+ end
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+ end
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+
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+ yield order_dto, OpenStruct.new(last_seq: 0)
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+ rescue LimsApiError => e
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+ Rails.logger.error("Failed to fetch updates for ##{order.accession_number}: #{e.class} - #{e.message}")
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+ sleep(1)
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+ end
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+ end
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+
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+ def delete_order(_id, order_dto)
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+ tracking_number = order_dto.fetch('tracking_number')
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+
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+ order_dto['tests'].each do |test|
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+ Rails.logger.info("Voiding test '#{test}' (#{tracking_number}) in LIMS")
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+ in_authenticated_session do |headers|
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+ date_voided, voided_status = find_test_status(order_dto, test, 'Voided')
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+ params = make_void_test_params(tracking_number, test, voided_status['updated_by'], date_voided)
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+ RestClient.post(expand_uri('update_test'), params, headers)
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+ end
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+ end
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+ end
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+
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+ def verify_tracking_number(tracking_number)
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+ find_lims_order(tracking_number)
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+ rescue InvalidParameters => e
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+ Rails.logger.error("Failed to verify tracking number #{tracking_number}: #{e.message}")
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+ false
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+ end
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+
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+ private
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+
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+ attr_reader :config
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+
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+ MAX_LIMS_RETRIES = 5 # LIMS API Calls can only fail this number of times before we give up on it
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+
104
+ ##
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+ # Execute LIMS API calls within an authenticated session.
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+ #
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+ # Method automatically checks authenticates with LIMS if necessary and passes
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+ # down the necessary headers for authentication to the REST call being made.
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+ #
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+ # Example:
111
+ #
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+ # response = in_authenticated_session do |headers|
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+ # RestClient.get(expand_uri('query_results_by_tracking_number/XXXXXX'), headers)
114
+ # end
115
+ #
116
+ # pp JSON.parse(response.body) if response.code == 200
117
+ def in_authenticated_session
118
+ retries ||= MAX_LIMS_RETRIES
119
+
120
+ self.authentication_token = authenticate unless authentication_token
121
+
122
+ response = yield 'token' => authentication_token, 'Content-type' => 'application/json'
123
+ check_response!(response)
124
+ rescue AuthenticationTokenExpired => e
125
+ self.authentication_token = nil
126
+ retry if (retries -= 1).positive?
127
+ rescue RestClient::ExceptionWithResponse => e
128
+ Rails.logger.error("LIMS Error: #{e.response&.code} - #{e.response&.body}")
129
+ raise e unless e.response&.code == 401
130
+
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+ self.authentication_token = nil
132
+ retry if (retries -= 1).positive?
133
+ end
134
+
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+ def authenticate
136
+ username = config.fetch(:username)
137
+ password = config.fetch(:password)
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+
139
+ Rails.logger.debug("Authenticating with LIMS as: #{username}")
140
+ response = RestClient.get(expand_uri("re_authenticate/#{username}/#{password}"),
141
+ headers: { 'Content-type' => 'application/json' })
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+ response_body = JSON.parse(response.body)
143
+
144
+ if response_body['status'] == 401
145
+ Rails.logger.error("Failed to authenticate with LIMS as #{config.fetch(:username)}: #{response_body['message']}")
146
+ raise LimsApiError, 'LIMS authentication failed'
147
+ end
148
+
149
+ response_body['data']['token']
150
+ end
151
+
152
+ def authentication_token=(token)
153
+ Thread.current[:lims_authentication_token] = token
154
+ end
155
+
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+ def authentication_token
157
+ Thread.current[:lims_authentication_token]
158
+ end
159
+
160
+ ##
161
+ # Examines a response from LIMS to check if token has expired.
162
+ #
163
+ # LIMS' doesn't properly use HTTP status codes; the codes are embedded in the
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+ # response body. 200 is used for success responses and 401 for everything else.
165
+ # We have this work around to examine the response body and
166
+ # throw errors accordingly. The following are the errors thrown:
167
+ #
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+ # Lims::AuthenticationTokenExpired
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+ # Lims::InvalidParameters
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+ # Lims::ApiError - Thrown when we couldn't make sense of the error
171
+ def check_response!(response)
172
+ body = JSON.parse(response.body)
173
+ return response if body['status'] == 200
174
+
175
+ Rails.logger.error("Lims Api Error: #{response.body}")
176
+
177
+ raise LimsApiError, "#{body['status']} - #{body['message']}" if body['status'] != 401
178
+
179
+ if body['message'].match?(/token expired/i)
180
+ raise AuthenticationTokenExpired, "Authentication token expired: #{body['message']}"
181
+ end
182
+
183
+ raise InvalidParameters, body['message']
184
+ end
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+
186
+ ##
187
+ # Takes a LIMS API relative URI and converts it to a full URL.
188
+ def expand_uri(uri, api_version: 'v1')
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+ protocol = config.fetch(:protocol)
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+ host = config.fetch(:host)
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+ port = config.fetch(:port)
192
+ uri = uri.gsub(%r{^/+}, '')
193
+
194
+ "#{protocol}://#{host}:#{port}/api/#{api_version}/#{uri}"
195
+ end
196
+
197
+ ##
198
+ # Converts an OrderDTO to parameters for POST /create_order
199
+ def make_create_params(order_dto)
200
+ {
201
+ tracking_number: order_dto.fetch(:tracking_number),
202
+ district: current_district,
203
+ health_facility_name: order_dto.fetch(:sending_facility),
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+ first_name: order_dto.fetch(:patient).fetch(:first_name),
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+ last_name: order_dto.fetch(:patient).fetch(:last_name),
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+ phone_number: order_dto.fetch(:patient).fetch(:phone_number),
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+ gender: order_dto.fetch(:patient).fetch(:gender),
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+ arv_number: order_dto.fetch(:patient).fetch(:arv_number),
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+ art_regimen: order_dto.fetch(:patient).fetch(:art_regimen),
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+ art_start_date: order_dto.fetch(:patient).fetch(:art_start_date),
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+ date_of_birth: order_dto.fetch(:patient).fetch(:dob),
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+ national_patient_id: order_dto.fetch(:patient).fetch(:id),
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+ requesting_clinician: requesting_clinician(order_dto),
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+ sample_type: order_dto.fetch(:sample_type),
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+ tests: order_dto.fetch(:tests),
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+ date_sample_drawn: sample_drawn_date(order_dto),
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+ sample_priority: order_dto.fetch(:priority) || 'Routine',
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+ sample_status: order_dto.fetch(:sample_status),
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+ target_lab: order_dto.fetch(:receiving_facility),
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+ order_location: order_dto.fetch(:order_location) || 'Unknown',
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+ who_order_test_first_name: order_dto.fetch(:who_order_test).fetch(:first_name),
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+ who_order_test_last_name: order_dto.fetch(:who_order_test).fetch(:last_name)
223
+ }
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+ end
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+
226
+ ##
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+ # Converts an OrderDTO to parameters for POST /update_order
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+ def make_update_params(order_dto)
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+ date_updated, status = sample_drawn_status(order_dto)
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+
231
+ {
232
+ tracking_number: order_dto.fetch(:tracking_number),
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+ who_updated: status.fetch(:updated_by),
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+ date_updated: date_updated,
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+ specimen_type: order_dto.fetch(:sample_type),
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+ status: 'specimen_collected'
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+ }
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+ end
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+
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+ def current_district
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+ health_centre = Location.current_health_center
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+ raise 'Current health centre not set' unless health_centre
243
+
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+ district = health_centre.district || Lab::Lims::Config.application['district']
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+
246
+ unless district
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+ health_centre_name = "##{health_centre.id} - #{health_centre.name}"
248
+ raise "Current health centre district not set: #{health_centre_name}"
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+ end
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+
251
+ district
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+ end
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+
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+ ##
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+ # Extracts sample drawn status from an OrderDTO
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+ def sample_drawn_status(order_dto)
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+ order_dto[:sample_statuses].each do |trail_entry|
258
+ date, status = trail_entry.each_pair.find { |_date, status| status['status'].casecmp?('Drawn') }
259
+ next unless date
260
+
261
+ return Date.strptime(date, '%Y%m%d%H%M%S').strftime('%Y-%m-%d'), status
262
+ end
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+
264
+ [order_dto['date_created'], nil]
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+ end
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+
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+ ##
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+ # Extracts a sample drawn date from a LIMS OrderDTO.
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+ def sample_drawn_date(order_dto)
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+ sample_drawn_status(order_dto).first
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+ end
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+
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+ ##
274
+ # Extracts the requesting clinician from a LIMS OrderDTO
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+ def requesting_clinician(order_dto)
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+ orderer = order_dto[:who_order_test]
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+
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+ "#{orderer[:first_name]} #{orderer[:last_name]}"
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+ end
280
+
281
+ def find_lims_order(tracking_number)
282
+ response = in_authenticated_session do |headers|
283
+ Rails.logger.info("Fetching order ##{tracking_number}")
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+ RestClient.get(expand_uri("query_order_by_tracking_number/#{tracking_number}"), headers)
285
+ end
286
+
287
+ Rails.logger.info("Order ##{tracking_number} found... Parsing...")
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+ JSON.parse(response).fetch('data')
289
+ end
290
+
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+ def find_lims_results(tracking_number)
292
+ response = in_authenticated_session do |headers|
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+ Rails.logger.info("Fetching results for order ##{tracking_number}")
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+ RestClient.get(expand_uri("query_results_by_tracking_number/#{tracking_number}"), headers)
295
+ end
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+
297
+ Rails.logger.info("Result for order ##{tracking_number} found... Parsing...")
298
+ JSON.parse(response).fetch('data').fetch('results')
299
+ end
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+
301
+ ##
302
+ # Make a copy of the order_dto with the results from LIMS parsed
303
+ # and appended to it.
304
+ def patch_order_dto_with_lims_results!(order_dto, results)
305
+ order_dto.merge!(
306
+ '_id' => order_dto[:tracking_number],
307
+ '_rev' => 0,
308
+ 'test_results' => results.each_with_object({}) do |result, formatted_results|
309
+ test_name, measures = result
310
+ result_date = measures.delete('result_date')
311
+
312
+ formatted_results[test_name] = {
313
+ results: measures.each_with_object({}) do |measure, processed_measures|
314
+ processed_measures[measure[0]] = { 'result_value' => measure[1] }
315
+ end,
316
+ result_date: result_date,
317
+ result_entered_by: {}
318
+ }
319
+ end
320
+ )
321
+ end
322
+
323
+ def patch_order_dto_with_lims_order!(order_dto, lims_order)
324
+ order_dto.merge!(
325
+ 'sample_type' => lims_order['other']['sample_type'],
326
+ 'sample_status' => lims_order['other']['specimen_status'],
327
+ 'priority' => lims_order['other']['priority']
328
+ )
329
+ end
330
+
331
+ def update_order_results(order_dto)
332
+ return nil if order_dto['test_results'].nil? || order_dto['test_results'].empty?
333
+
334
+ order_dto['test_results'].each do |test_name, results|
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+ Rails.logger.info("Pushing result for order ##{order_dto['tracking_number']}")
336
+ in_authenticated_session do |headers|
337
+ params = make_update_test_params(order_dto['tracking_number'], test_name, results)
338
+
339
+ RestClient.post(expand_uri('update_test'), params, headers)
340
+ end
341
+ end
342
+ end
343
+
344
+ def make_update_test_params(tracking_number, test_name, results, test_status = 'Drawn')
345
+ {
346
+ tracking_number: tracking_number,
347
+ test_name: test_name,
348
+ result_date: results['result_date'],
349
+ time_updated: results['result_date'],
350
+ who_updated: {
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+ first_name: results[:result_entered_by][:first_name],
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+ last_name: results[:result_entered_by][:last_name],
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+ id_number: results[:result_entered_by][:id]
354
+ },
355
+ test_status: test_status,
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+ results: results['results']&.each_with_object({}) do |measure, formatted_results|
357
+ measure_name, measure_value = measure
358
+
359
+ formatted_results[measure_name] = measure_value['result_value']
360
+ end
361
+ }
362
+ end
363
+
364
+ def find_test_status(order_dto, target_test, target_status)
365
+ order_dto['test_statuses'].each do |test, statuses|
366
+ next unless test.casecmp?(target_test)
367
+
368
+ statuses.each do |date, status|
369
+ next unless status['status'].casecmp?(target_status)
370
+
371
+ return [Date.strptime(date, '%Y%m%d%H%M%S'), status]
372
+ end
373
+ end
374
+
375
+ nil
376
+ end
377
+
378
+ def make_void_test_params(tracking_number, test_name, voided_by, void_date = nil)
379
+ void_date ||= Time.now
380
+
381
+ {
382
+ tracking_number: tracking_number,
383
+ test_name: test_name,
384
+ time_updated: void_date,
385
+ who_updated: {
386
+ first_name: voided_by[:first_name],
387
+ last_name: voided_by[:last_name],
388
+ id_number: voided_by[:id]
389
+ },
390
+ test_status: 'voided'
391
+ }
392
+ end
393
+
394
+ def orders_pending_updates(patient_id = nil)
395
+ Rails.logger.info('Looking for orders that need to be updated...')
396
+ orders = {}
397
+
398
+ orders_without_specimen(patient_id).each { |order| orders[order.order_id] = order }
399
+ orders_without_results(patient_id).each { |order| orders[order.order_id] = order }
400
+ orders_without_reason(patient_id).each { |order| orders[order.order_id] = order }
401
+
402
+ orders.values
403
+ end
404
+
405
+ def orders_without_specimen(patient_id = nil)
406
+ Rails.logger.debug('Looking for orders without a specimen')
407
+ unknown_specimen = ConceptName.where(name: Lab::Metadata::UNKNOWN_SPECIMEN)
408
+ .select(:concept_id)
409
+ orders = Lab::LabOrder.where(concept_id: unknown_specimen)
410
+ .where.not(accession_number: Lab::LimsOrderMapping.select(:lims_id))
411
+ orders = orders.where(patient_id: patient_id) if patient_id
412
+
413
+ orders
414
+ end
415
+
416
+ def orders_without_results(patient_id = nil)
417
+ Rails.logger.debug('Looking for orders without a result')
418
+ # Lab::OrdersSearchService.find_orders_without_results(patient_id: patient_id)
419
+ # .where.not(accession_number: Lab::LimsOrderMapping.select(:lims_id).where("pulled_at IS NULL"))
420
+ Lab::OrdersSearchService.find_orders_without_results(patient_id: patient_id)
421
+ .where(order_id: Lab::LimsOrderMapping.select(:order_id))
422
+ end
423
+
424
+ def orders_without_reason(patient_id = nil)
425
+ Rails.logger.debug('Looking for orders without a reason for test')
426
+ orders = Lab::LabOrder.joins(:reason_for_test)
427
+ .merge(Observation.where(value_coded: nil, value_text: nil))
428
+ .limit(1000)
429
+ .where.not(accession_number: Lab::LimsOrderMapping.select(:lims_id))
430
+ orders = orders.where(patient_id: patient_id) if patient_id
431
+
432
+ orders
433
+ end
434
+ end
@@ -0,0 +1,121 @@
1
+ # frozen_string_literal: true
2
+
3
+ require 'socket.io-client-simple'
4
+
5
+ module Lab
6
+ module Lims
7
+ module Api
8
+ ##
9
+ # Retrieve results from LIMS only through a websocket
10
+ class WsApi
11
+ def initialize(config)
12
+ @config = config
13
+ @results_queue = []
14
+ @socket = nil
15
+ end
16
+
17
+ def consume_orders(**_kwargs)
18
+ loop do
19
+ results = fetch_results
20
+ unless results
21
+ Rails.logger.debug('No results available... Waiting for results...')
22
+ sleep(Lab::Lims::Config.updates_poll_frequency)
23
+ next
24
+ end
25
+
26
+ Rails.logger.info("Received result for ##{results['tracking_number']}")
27
+ order = find_order(results['tracking_number'])
28
+ next unless order
29
+
30
+ Rails.logger.info("Updating result for order ##{order.order_id}")
31
+ yield make_order_dto(order, results), OpenStruct.new(last_seq: 1)
32
+ end
33
+ end
34
+
35
+ private
36
+
37
+ def initialize_socket
38
+ Rails.logger.debug('Establishing connection to socket...')
39
+ socket = SocketIO::Client::Simple.connect(socket_url)
40
+ socket.on(:connect, &method(:on_socket_connect))
41
+ socket.on(:disconnect, &method(:on_socket_disconnect))
42
+ socket.on(:results, &method(:on_results_received))
43
+ end
44
+
45
+ def socket_url
46
+ @config.fetch('url')
47
+ end
48
+
49
+ def on_socket_connect
50
+ Rails.logger.debug('Connection to LIMS results socket established...')
51
+ end
52
+
53
+ def on_socket_disconnect
54
+ Rails.logger.debug('Connection to LIMS results socket lost...')
55
+ @socket = nil
56
+ end
57
+
58
+ def on_results_received(result)
59
+ Rails.logger.debug("Received result from LIMS: #{result}")
60
+ tracking_number = result['tracking_number']
61
+
62
+ Rails.logger.debug("Queueing result for order ##{tracking_number}")
63
+ @results_queue.push(result)
64
+ end
65
+
66
+ def order_exists?(tracking_number)
67
+ Rails.logger.debug("Looking for order for result ##{tracking_number}")
68
+ orders = OrdersSearchService.find_orders_without_results
69
+ .where(accession_number: tracking_number)
70
+ # The following ensures that the order was previously pushed to LIMS
71
+ # or was received from LIMS
72
+ Lab::LimsOrderMapping.where.not(order: orders).exists?
73
+ end
74
+
75
+ def fetch_results
76
+ loop do
77
+ @socket ||= initialize_socket
78
+
79
+ results = @results_queue.shift
80
+ return nil unless results
81
+
82
+ unless order_exists?(results['tracking_number'])
83
+ Rails.logger.debug("Ignoring result for order ##{tracking_number}")
84
+ next
85
+ end
86
+
87
+ return results
88
+ end
89
+ end
90
+
91
+ def find_order(lims_id)
92
+ mapping = Lab::LimsOrderMapping.where(lims_id: lims_id).select(:order_id)
93
+ Lab::LabOrder.find_by(order_id: mapping)
94
+ end
95
+
96
+ def make_order_dto(order, results)
97
+ Lab::Lims::OrderSerializer
98
+ .serialize_order(order)
99
+ .merge(
100
+ id: order.accession_number,
101
+ test_results: {
102
+ results['test_name'] => {
103
+ results: results['results'].each_with_object({}) do |measure, formatted_measures|
104
+ measure_name, measure_value = measure
105
+
106
+ formatted_measures[measure_name] = { result_value: measure_value }
107
+ end,
108
+ result_date: results['date_updated'],
109
+ result_entered_by: {
110
+ first_name: results['who_updated']['first_name'],
111
+ last_name: results['who_updated']['last_name'],
112
+ id: results['who_updated']['id_number']
113
+ }
114
+ }
115
+ }
116
+ )
117
+ end
118
+ end
119
+ end
120
+ end
121
+ end
@@ -0,0 +1,19 @@
1
+ # frozen_string_literal: true
2
+
3
+ module Lab
4
+ module Lims
5
+ ##
6
+ # Creates LIMS Apis based on current configuration
7
+ module ApiFactory
8
+ def self.create_api
9
+ return Lab::Lims::Api::BlackholeApi.new if Rails.env.casecmp?('test')
10
+
11
+ case Lab::Lims::Config.preferred_api
12
+ when /rest/i then Lab::Lims::Api::RestApi.new(Lab::Lims::Config.rest_api)
13
+ when /couchdb/ then Lab::Lims::Api::CouchDbApi.new(config: Lab::Lims::Config.couchdb_api)
14
+ else raise "Invalid lims_api configuration: #{Lab::Lims::Config.preferred_api}"
15
+ end
16
+ end
17
+ end
18
+ end
19
+ end
@@ -0,0 +1,105 @@
1
+ # frozen_string_literal: true
2
+
3
+ module Lab
4
+ module Lims
5
+ ##
6
+ # Load LIMS' configuration files
7
+ module Config
8
+ # TODO: Replace this maybe with `Rails.application.configuration.lab.lims`
9
+ # so that we do not have to directly mess with configuration files.
10
+
11
+ class ConfigNotFound < RuntimeError; end
12
+
13
+ class << self
14
+ def preferred_api
15
+ emr_api_application('lims_api')
16
+ end
17
+
18
+ ##
19
+ # Returns LIMS' couchdb configuration file for the current environment (Rails.env)
20
+ def couchdb
21
+ config_path = begin
22
+ find_config_path('couchdb.yml')
23
+ rescue ConfigNotFound => e
24
+ Rails.logger.error("Failed to find default LIMS couchdb config: #{e.message}")
25
+ find_config_path('couchdb-lims.yml') # This can be placed in HIS-EMR-API/config
26
+ end
27
+
28
+ Rails.logger.debug("Using LIMS couchdb config: #{config_path}")
29
+
30
+ YAML.load_file(config_path)[Rails.env]
31
+ end
32
+
33
+ def rest_api
34
+ @rest_api ||= {
35
+ protocol: emr_api_application('lims_protocol', 'http'),
36
+ host: emr_api_application('lims_host'),
37
+ port: emr_api_application('lims_port'),
38
+ username: emr_api_application('lims_username'),
39
+ password: emr_api_application('lims_password')
40
+ }
41
+ end
42
+
43
+ def updates_socket
44
+ @updates_socket ||= {
45
+ 'url' => emr_api_application('lims_realtime_updates_url')
46
+ }
47
+ end
48
+
49
+ def updates_poll_frequency
50
+ 30 # Seconds
51
+ end
52
+
53
+ def config_file_name
54
+ # if nlims.yml exists return it, else return application.yml
55
+ File.exist?(Rails.root.join('config', 'nlims.yml')) ? 'nlims.yml' : 'application.yml'
56
+ end
57
+
58
+ ##
59
+ # Returns LIMS' application.yml configuration file
60
+ def application
61
+ @application ||= YAML.load_file(find_config_path(config_file_name))
62
+ end
63
+
64
+ ##
65
+ # Returns LIMS' database.yml configuration file
66
+ def database
67
+ @database ||= YAML.load_file(find_config_path('database.yml'))
68
+ end
69
+
70
+ private
71
+
72
+ def emr_api_application(param, fallback = nil)
73
+ @emr_api_application ||= YAML.load_file(Rails.root.join('config', config_file_name))
74
+
75
+ @emr_api_application.fetch(param) do
76
+ raise ConfigNotFound, "Missing config param: #{param}" unless fallback
77
+
78
+ fallback
79
+ end
80
+ end
81
+
82
+ ##
83
+ # Looks for a config file in various LIMS installation directories
84
+ #
85
+ # Returns: a path to a file found
86
+ def find_config_path(filename)
87
+ paths = [
88
+ "#{Dir.home}/apps/nlims_controller/config/#{filename}",
89
+ "/var/www/nlims_controller/config/#{filename}",
90
+ Rails.root.parent.join("nlims_controller/config/#{filename}")
91
+ ]
92
+
93
+ paths = [Rails.root.join('config/lims-couchdb.yml'), *paths] if filename == 'couchdb.yml'
94
+
95
+ paths.each do |path|
96
+ Rails.logger.debug("Looking for LIMS couchdb config at: #{path}")
97
+ return path if File.exist?(path)
98
+ end
99
+
100
+ raise ConfigNotFound, "Could not find a configuration file, checked: #{paths.join(':')}"
101
+ end
102
+ end
103
+ end
104
+ end
105
+ end
@@ -0,0 +1,11 @@
1
+ # frozen_string_literal: true
2
+
3
+ module Lab
4
+ module Lims
5
+ class LimsException < StandardError; end
6
+ class DuplicateNHID < LimsException; end
7
+ class MissingAccessionNumber < LimsException; end
8
+ class UnknownSpecimenType < LimsException; end
9
+ class UnknownTestType < LimsException; end
10
+ end
11
+ end