his_emr_api_lab 1.1.21 → 1.1.22

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Files changed (81) hide show
  1. checksums.yaml +4 -4
  2. metadata +3 -82
  3. data/MIT-LICENSE +0 -20
  4. data/README.md +0 -71
  5. data/Rakefile +0 -32
  6. data/app/controllers/lab/application_controller.rb +0 -6
  7. data/app/controllers/lab/labels_controller.rb +0 -17
  8. data/app/controllers/lab/orders_controller.rb +0 -38
  9. data/app/controllers/lab/reasons_for_test_controller.rb +0 -9
  10. data/app/controllers/lab/results_controller.rb +0 -19
  11. data/app/controllers/lab/specimen_types_controller.rb +0 -15
  12. data/app/controllers/lab/test_result_indicators_controller.rb +0 -9
  13. data/app/controllers/lab/test_types_controller.rb +0 -15
  14. data/app/controllers/lab/tests_controller.rb +0 -26
  15. data/app/jobs/lab/application_job.rb +0 -4
  16. data/app/jobs/lab/push_order_job.rb +0 -12
  17. data/app/jobs/lab/update_patient_orders_job.rb +0 -32
  18. data/app/jobs/lab/void_order_job.rb +0 -17
  19. data/app/mailers/lab/application_mailer.rb +0 -6
  20. data/app/models/lab/application_record.rb +0 -5
  21. data/app/models/lab/lab_accession_number_counter.rb +0 -13
  22. data/app/models/lab/lab_encounter.rb +0 -7
  23. data/app/models/lab/lab_order.rb +0 -58
  24. data/app/models/lab/lab_result.rb +0 -31
  25. data/app/models/lab/lab_test.rb +0 -19
  26. data/app/models/lab/lims_failed_import.rb +0 -4
  27. data/app/models/lab/lims_order_mapping.rb +0 -10
  28. data/app/serializers/lab/lab_order_serializer.rb +0 -55
  29. data/app/serializers/lab/result_serializer.rb +0 -36
  30. data/app/serializers/lab/test_serializer.rb +0 -29
  31. data/app/services/lab/accession_number_service.rb +0 -77
  32. data/app/services/lab/concepts_service.rb +0 -82
  33. data/app/services/lab/labelling_service/order_label.rb +0 -106
  34. data/app/services/lab/lims/api/blackhole_api.rb +0 -21
  35. data/app/services/lab/lims/api/couchdb_api.rb +0 -53
  36. data/app/services/lab/lims/api/mysql_api.rb +0 -316
  37. data/app/services/lab/lims/api/rest_api.rb +0 -416
  38. data/app/services/lab/lims/api/ws_api.rb +0 -121
  39. data/app/services/lab/lims/api_factory.rb +0 -19
  40. data/app/services/lab/lims/config.rb +0 -100
  41. data/app/services/lab/lims/exceptions.rb +0 -11
  42. data/app/services/lab/lims/migrator.rb +0 -216
  43. data/app/services/lab/lims/order_dto.rb +0 -105
  44. data/app/services/lab/lims/order_serializer.rb +0 -244
  45. data/app/services/lab/lims/pull_worker.rb +0 -289
  46. data/app/services/lab/lims/push_worker.rb +0 -149
  47. data/app/services/lab/lims/utils.rb +0 -91
  48. data/app/services/lab/lims/worker.rb +0 -86
  49. data/app/services/lab/metadata.rb +0 -24
  50. data/app/services/lab/orders_search_service.rb +0 -66
  51. data/app/services/lab/orders_service.rb +0 -212
  52. data/app/services/lab/results_service.rb +0 -147
  53. data/app/services/lab/tests_service.rb +0 -93
  54. data/config/routes.rb +0 -17
  55. data/db/migrate/20210126092910_create_lab_lab_accession_number_counters.rb +0 -12
  56. data/db/migrate/20210310115457_create_lab_lims_order_mappings.rb +0 -15
  57. data/db/migrate/20210323080140_change_lims_id_to_string_in_lims_order_mapping.rb +0 -15
  58. data/db/migrate/20210326195504_add_order_revision_to_lims_order_mapping.rb +0 -5
  59. data/db/migrate/20210407071728_create_lab_lims_failed_imports.rb +0 -19
  60. data/db/migrate/20210610095024_fix_numeric_results_value_type.rb +0 -20
  61. data/db/migrate/20210807111531_add_default_to_lims_order_mapping.rb +0 -7
  62. data/lib/auto12epl.rb +0 -201
  63. data/lib/couch_bum/couch_bum.rb +0 -92
  64. data/lib/generators/lab/install/USAGE +0 -9
  65. data/lib/generators/lab/install/install_generator.rb +0 -19
  66. data/lib/generators/lab/install/templates/rswag-ui-lab.rb +0 -5
  67. data/lib/generators/lab/install/templates/start_worker.rb +0 -32
  68. data/lib/generators/lab/install/templates/swagger.yaml +0 -714
  69. data/lib/his_emr_api_lab.rb +0 -5
  70. data/lib/lab/engine.rb +0 -15
  71. data/lib/lab/version.rb +0 -5
  72. data/lib/logger_multiplexor.rb +0 -38
  73. data/lib/tasks/lab_tasks.rake +0 -25
  74. data/lib/tasks/loaders/data/reasons-for-test.csv +0 -7
  75. data/lib/tasks/loaders/data/test-measures.csv +0 -225
  76. data/lib/tasks/loaders/data/tests.csv +0 -161
  77. data/lib/tasks/loaders/loader_mixin.rb +0 -53
  78. data/lib/tasks/loaders/metadata_loader.rb +0 -26
  79. data/lib/tasks/loaders/reasons_for_test_loader.rb +0 -23
  80. data/lib/tasks/loaders/specimens_loader.rb +0 -65
  81. data/lib/tasks/loaders/test_result_indicators_loader.rb +0 -54
data/lib/tasks/loaders/test_result_indicators_loader.rb DELETED
@@ -1,54 +0,0 @@
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- # frozen_string_literal: true
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-
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- require 'csv'
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- require_relative './loader_mixin'
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-
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- module Lab
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- module Loaders
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- ##
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- # Load specimens and their tests into the database
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- module TestResultIndicatorsLoader
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- class << self
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- include LoaderMixin
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-
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- def load
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- puts "------- Loading measures ------------"
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- CSV.open(data_path('test-measures.csv'), headers: :first_row) do |csv|
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- csv.each_with_object({}) do |row, test_measures|
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- test_name = row['test_name']
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- measure_name = row['measure_name']
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-
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- ActiveRecord::Base.transaction do
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- measure_concept = find_or_create_concept(measure_name)
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- add_measure_to_test(test_name, measure_concept)
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- end
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-
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- puts "Created measure #{test_name} <--< #{measure_name}"
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- rescue StandardError => e
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- puts "Error: #{measure_name}: #{e}"
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- end
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- end
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- end
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-
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- def create_test_type(name)
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- concept_id = find_or_create_concept(name, is_set: true).concept_id
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-
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- create_concept_set(concept_set: test_type_concept_id, concept_id: concept_id)
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- rescue StandardError => e
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- raise "Failed to create test type `#{name}`: #{e}"
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- end
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-
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- def add_measure_to_test(test_name, measure_concept)
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- [
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- add_concept_to_set(set_concept_id: find_or_create_concept(Lab::Metadata::TEST_RESULT_INDICATOR_CONCEPT_NAME).concept_id,
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- concept_id: measure_concept.concept_id),
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- add_concept_to_set(set_concept_id: measure_concept.concept_id,
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- concept_id: find_or_create_concept(test_name).concept_id)
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- ]
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- rescue StandardError => e
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- raise "Failed to create measure for test `#{name}`: #{e}"
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- end
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- end
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- end
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- end
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- end