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/generators/lab/install/templates/swagger.yaml DELETED
@@ -1,714 +0,0 @@
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- ---
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- openapi: 3.0.1
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- info:
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- title: API V1
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- version: v1
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- paths:
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- "/api/v1/lab/orders":
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- post:
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- summary: Create order
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- tags:
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- - Orders
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- description: |
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- Create a lab order for a test.
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-
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- Broadly a lab order consists of a test type and a number of specimens.
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- To each specimen is assigned a tracking number which can be used
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- to query the status and results of the specimen.
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- parameters: []
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- security:
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- - api_key: []
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- responses:
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- '201':
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- description: Created
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- content:
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- application/json:
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- schema:
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- type: array
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- items:
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- type: object
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- properties:
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- id:
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- type: integer
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- patient_id:
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- type: integer
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- encounter_id:
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- type: integer
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- order_date:
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- type: string
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- format: datetime
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- accession_number:
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- type: string
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- specimen:
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- type: object
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- properties:
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- concept_id:
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- type: integer
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- name:
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- type: string
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- required:
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- - concept_id
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- - name
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- requesting_clinician:
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- type: string
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- nullable: true
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- target_lab:
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- type: string
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- reason_for_test:
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- type: object
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- properties:
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- concept_id:
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- type: integer
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- name:
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- type: string
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- required:
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- - concept_id
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- - name
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- tests:
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- type: array
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- items:
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- type: object
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- properties:
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- id:
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- type: integer
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- concept_id:
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- type: integer
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- name:
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- type: string
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- result:
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- type: object
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- nullable: true
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- properties:
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- id:
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- type: integer
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- value:
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- type: string
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- nullable: true
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- date:
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- type: string
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- format: datetime
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- nullable: true
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- required:
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- - id
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- - value
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- - date
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- required:
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- - id
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- - concept_id
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- - name
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- required:
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- - id
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- - specimen
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- - reason_for_test
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- - accession_number
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- - patient_id
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- - order_date
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- requestBody:
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- content:
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- application/json:
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- schema:
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- type: object
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- properties:
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- orders:
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- type: array
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- items:
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- properties:
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- encounter_id:
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- type: integer
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- specimen:
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- type: object
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- properties:
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- concept_id:
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- type: integer
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- description: Specimen type concept ID (see GET /lab/test_types)
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- tests:
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- type: array
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- items:
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- type: object
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- properties:
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- concept_id:
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- type: integer
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- description: Test type concept ID (see GET /lab/test_types)
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- requesting_clinician:
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- type: string
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- description: Fullname of the clinician requesting the test
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- (defaults to orderer)
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- target_lab:
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- type: string
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- reason_for_test_id:
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- type: string
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- description: One of routine, targeted, or confirmatory
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- required:
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- - encounter_id
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- - tests
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- - target_lab
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- - reason_for_test_id
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- get:
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- summary: Retrieve lab orders
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- tags:
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- - Orders
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- description: Search/retrieve for lab orders.
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- security:
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- - api_key: []
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- parameters:
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- - name: patient_id
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- in: query
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- required: false
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- description: Filter orders using patient_id
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- schema:
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- type: integer
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- - name: accession_number
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- in: query
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- required: false
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- description: Filter orders using sample accession number
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- schema:
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- type: integer
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- - name: date
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- in: query
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- required: false
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- description: Select results falling on a specific date
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- schema:
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- type: date
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- - name: status
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- in: query
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- required: false
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- description: 'Filter by sample status: ordered, drawn'
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- schema:
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- type: string
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- - name: end_date
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- in: query
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- required: false
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- description: Select all results before this date
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- schema:
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- type: date
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- responses:
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- '200':
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- description: Success
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- content:
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- application/json:
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- schema:
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- type: array
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- items:
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- type: object
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- properties:
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- id:
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- type: integer
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- patient_id:
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- type: integer
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- encounter_id:
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- type: integer
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- order_date:
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- type: string
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- format: datetime
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- accession_number:
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- type: string
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- specimen:
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- type: object
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- properties:
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- concept_id:
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- type: integer
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- name:
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- type: string
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- required:
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- - concept_id
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- - name
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- requesting_clinician:
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- type: string
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- nullable: true
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- target_lab:
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- type: string
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- reason_for_test:
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- type: object
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- properties:
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- concept_id:
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- type: integer
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- name:
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- type: string
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- required:
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- - concept_id
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- - name
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- tests:
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- type: array
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- items:
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- type: object
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- properties:
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- id:
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- type: integer
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- concept_id:
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- type: integer
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- name:
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- type: string
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- result:
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- type: object
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- nullable: true
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- properties:
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- id:
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- type: integer
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- value:
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- type: string
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- nullable: true
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- date:
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- type: string
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- format: datetime
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- nullable: true
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- required:
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- - id
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- - value
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- - date
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- required:
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- - id
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- - concept_id
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- - name
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- required:
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- - id
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- - specimen
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- - reason_for_test
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- - accession_number
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- - patient_id
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- - order_date
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- "/api/v1/lab/orders/{order_id}":
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- put:
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- summary: Update order
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- tags:
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- - Orders
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- description: Update an existing order
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- security:
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- - api_key: []
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- parameters:
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- - name: order_id
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- in: path
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- required: true
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- schema:
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- type: integer
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- responses:
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- '200':
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- description: Ok
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- content:
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- application/json:
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- schema:
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- type: object
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- properties:
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- type: object
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- properties:
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- id:
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- type: integer
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- patient_id:
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- type: integer
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- encounter_id:
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- type: integer
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- order_date:
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- type: string
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- format: datetime
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- accession_number:
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- type: string
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- specimen:
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- type: object
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- properties:
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- concept_id:
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- type: integer
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- name:
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- type: string
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- required:
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- - concept_id
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- - name
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- requesting_clinician:
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- type: string
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- nullable: true
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- target_lab:
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- type: string
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- reason_for_test:
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- type: object
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- properties:
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- concept_id:
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- type: integer
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- name:
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- type: string
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- required:
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- - concept_id
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- - name
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- tests:
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- type: array
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- items:
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- type: object
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- properties:
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- id:
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- type: integer
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- concept_id:
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- type: integer
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- name:
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- type: string
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- result:
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- type: object
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- nullable: true
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- properties:
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- id:
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- type: integer
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- value:
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- type: string
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- nullable: true
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- date:
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- type: string
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- format: datetime
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- nullable: true
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- required:
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- - id
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- - value
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- - date
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- required:
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- - id
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- - concept_id
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- - name
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- required:
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- - id
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- - specimen
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- - reason_for_test
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- - accession_number
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- - patient_id
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- - order_date
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- requestBody:
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- content:
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- application/json:
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- schema:
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- type: object
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- properties:
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- specimen:
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- type: object
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- properties:
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- concept_id:
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- type: integer
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- required:
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- - concept_id
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- delete:
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- summary: Void lab order
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- tags:
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- - Orders
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- description: |
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- Void a lab order and all it's associated records
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-
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- This action voids an order, all it's linked tests and results.
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- security:
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- - api_key: []
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- parameters:
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- - name: order_id
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- in: path
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- required: true
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- schema:
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- type: integer
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- - name: reason
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- in: query
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- required: true
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- schema:
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- type: string
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- responses:
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- '204':
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- description: No Content
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- "/api/v1/lab/reasons_for_test":
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- get:
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- summary: Reasons for test
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- description: Retrieve default reasons for test concept set
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- tags:
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- - Concepts
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- security:
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- - api_key: []
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- responses:
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- '200':
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- description: Success
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- content:
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- application/json:
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- schema:
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- type: array
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- items:
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- type: object
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- properties:
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- concept_id:
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- type: integer
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- name:
426
- type: string
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- example: Routine
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- required:
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- - concept_id
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- - name
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- "/api/v1/lab/tests/{test_id}/results":
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- post:
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- summary: Add results to order
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- tags:
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- - Results
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- description: Attach results to specimens on order
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- parameters:
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- - name: test_id
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- in: path
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- required: true
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- schema:
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- type: integer
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- security:
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- - api_key: []
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- responses:
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- '201':
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- description: Created
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- requestBody:
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- content:
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- application/json:
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- schema:
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- type: object
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- properties:
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- encounter_id:
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- type: integer
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- provider_id:
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- type: integer
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- date:
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- type: string
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- measures:
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- type: array
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- items:
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- type: object
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- properties:
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- indicator:
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- type: object
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- properties:
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- concept_id:
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- type: integer
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- description: Concept ID of a test result indicator for
471
- this test (see GET /test_result_indicators)
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- required:
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- - concept_id
474
- value:
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- type: string
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- example: LDL
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- value_modifier:
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- type: string
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- example: "="
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- value_type:
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- type: string
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- enum:
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- - text
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- - boolean
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- - numeric
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- - coded
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- description: Determines under what column the value is to
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- be saved under in the obs table (defaults to text)
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- example: text
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- required:
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- - indicator
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- - value
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- required:
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- - measures
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- "/api/v1/lab/specimen_types":
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- get:
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- summary: Specimen types
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- tags:
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- - Concepts
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- description: Retrieve all specimen types
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- security:
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- - api_key: []
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- parameters:
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- - name: test_type
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- in: query
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- required: false
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- description: Select specimen types having this test type only
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- schema:
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- type: string
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- responses:
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- '200':
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- description: Success
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- content:
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- application/json:
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- schema:
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- type: array
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- items:
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- type: object
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- properties:
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- concept_id:
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- type: integer
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- name:
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- type: string
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- required:
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- - concept_id
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- - name
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- "/api/v1/lab/test_result_indicators":
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- get:
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- summary: Test Result Indicators
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- tags:
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- - Concepts
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- description: Retrieve all result indicators for a given test
533
- security:
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- - api_key: []
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- parameters:
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- - name: test_type_id
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- in: query
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- required: true
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- description: Concept ID for the desired test
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- schema:
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- type: integer
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- responses:
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- '200':
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- description: Ok
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- content:
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- application/json:
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- schema:
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- type: array
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- items:
550
- type: object
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- properties:
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- concept_id:
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- type: integer
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- name:
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- type: string
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- required:
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- - concept_id
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- - name
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- "/api/v1/lab/test_types":
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- get:
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- summary: Test types
562
- tags:
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- - Concepts
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- description: Retrieve all test types
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- security:
566
- - api_key: []
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- parameters:
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- - name: specimen_type
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- in: query
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- required: false
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- description: Select test types having this specimen type only
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- schema:
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- type: string
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- responses:
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- '200':
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- description: Success
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- content:
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- application/json:
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- schema:
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- type: array
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- items:
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- type: object
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- properties:
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- concept_id:
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- type: integer
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- name:
587
- type: string
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- required:
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- - concept_id
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- - name
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- "/api/v1/lab/tests":
592
- get:
593
- summary: Search for tests
594
- tags:
595
- - Tests
596
- description: 'Search for tests by accession number, date and other parameters.
597
-
598
- '
599
- parameters:
600
- - name: accession_number
601
- in: query
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- required: false
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- schema:
604
- type: string
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- - name: test_type_id
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- in: query
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- required: false
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- schema:
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- type: integer
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- - name: specimen_type_id
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- in: query
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- required: false
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- schema:
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- type: integer
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- - name: patient_id
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- in: query
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- required: false
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- schema:
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- type: integer
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- - name: order_date
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- in: query
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- required: false
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- schema:
624
- type: boolean
625
- responses:
626
- '200':
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- description: Okay
628
- content:
629
- application/json:
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- schema:
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- type: array
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- items:
633
- type: object
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- properties:
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- id:
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- type: integer
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- concept_id:
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- type: integer
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- name:
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- type: string
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- order:
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- order_id:
643
- type: string
644
- accession_number:
645
- type: string
646
- post:
647
- summary: Add tests to an existing order
648
- tags:
649
- - Tests
650
- description: |
651
- Add tests to an existing order.
652
-
653
- An order can be created without specifying tests.
654
- This endpoint allows one to add tests to that order.
655
- parameters: []
656
- security:
657
- - api_key: []
658
- responses:
659
- '201':
660
- description: Created
661
- content:
662
- application/json:
663
- schema:
664
- type: array
665
- items:
666
- type: object
667
- properties:
668
- id:
669
- type: integer
670
- concept_id:
671
- type: integer
672
- name:
673
- type: string
674
- order:
675
- order_id:
676
- type: string
677
- accession_number:
678
- type: string
679
- requestBody:
680
- content:
681
- application/json:
682
- schema:
683
- type: object
684
- properties:
685
- order_id:
686
- type: integer
687
- tests:
688
- type: array
689
- items:
690
- type: object
691
- properties:
692
- concept_id:
693
- type: integer
694
- description: Test type concept ID
695
- required:
696
- - concept_id
697
- required:
698
- - order_id
699
- - tests
700
- servers:
701
- - url: http://{defaultHost}
702
- variables:
703
- defaultHost:
704
- default: localhost:3000
705
- components:
706
- securitySchemes:
707
- api_key:
708
- type: apiKey
709
- name: Authorization
710
- in: header
711
- bearer:
712
- type: bearer
713
- name: Authorization
714
- in: header
data/lib/his_emr_api_lab.rb DELETED
@@ -1,5 +0,0 @@
1
- require 'lab/engine'
2
-
3
- module Lab
4
- # Your code goes here...
5
- end