his_emr_api_lab 1.1.19 → 1.1.22
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- checksums.yaml +4 -4
- metadata +8 -86
- data/MIT-LICENSE +0 -20
- data/README.md +0 -71
- data/Rakefile +0 -32
- data/app/controllers/lab/application_controller.rb +0 -6
- data/app/controllers/lab/labels_controller.rb +0 -17
- data/app/controllers/lab/orders_controller.rb +0 -38
- data/app/controllers/lab/reasons_for_test_controller.rb +0 -9
- data/app/controllers/lab/results_controller.rb +0 -19
- data/app/controllers/lab/specimen_types_controller.rb +0 -15
- data/app/controllers/lab/test_result_indicators_controller.rb +0 -9
- data/app/controllers/lab/test_types_controller.rb +0 -15
- data/app/controllers/lab/tests_controller.rb +0 -26
- data/app/jobs/lab/application_job.rb +0 -4
- data/app/jobs/lab/push_order_job.rb +0 -12
- data/app/jobs/lab/update_patient_orders_job.rb +0 -32
- data/app/jobs/lab/void_order_job.rb +0 -17
- data/app/mailers/lab/application_mailer.rb +0 -6
- data/app/models/lab/application_record.rb +0 -5
- data/app/models/lab/lab_accession_number_counter.rb +0 -13
- data/app/models/lab/lab_encounter.rb +0 -7
- data/app/models/lab/lab_order.rb +0 -54
- data/app/models/lab/lab_result.rb +0 -31
- data/app/models/lab/lab_test.rb +0 -19
- data/app/models/lab/lims_failed_import.rb +0 -4
- data/app/models/lab/lims_order_mapping.rb +0 -10
- data/app/serializers/lab/lab_order_serializer.rb +0 -55
- data/app/serializers/lab/result_serializer.rb +0 -36
- data/app/serializers/lab/test_serializer.rb +0 -29
- data/app/services/lab/accession_number_service.rb +0 -77
- data/app/services/lab/concepts_service.rb +0 -82
- data/app/services/lab/labelling_service/order_label.rb +0 -106
- data/app/services/lab/lims/api/blackhole_api.rb +0 -21
- data/app/services/lab/lims/api/couchdb_api.rb +0 -53
- data/app/services/lab/lims/api/mysql_api.rb +0 -316
- data/app/services/lab/lims/api/rest_api.rb +0 -413
- data/app/services/lab/lims/api/ws_api.rb +0 -121
- data/app/services/lab/lims/api_factory.rb +0 -19
- data/app/services/lab/lims/config.rb +0 -100
- data/app/services/lab/lims/exceptions.rb +0 -11
- data/app/services/lab/lims/migrator.rb +0 -216
- data/app/services/lab/lims/order_dto.rb +0 -105
- data/app/services/lab/lims/order_serializer.rb +0 -216
- data/app/services/lab/lims/pull_worker.rb +0 -289
- data/app/services/lab/lims/push_worker.rb +0 -144
- data/app/services/lab/lims/utils.rb +0 -91
- data/app/services/lab/lims/worker.rb +0 -86
- data/app/services/lab/metadata.rb +0 -24
- data/app/services/lab/orders_search_service.rb +0 -66
- data/app/services/lab/orders_service.rb +0 -212
- data/app/services/lab/results_service.rb +0 -122
- data/app/services/lab/tests_service.rb +0 -93
- data/config/routes.rb +0 -17
- data/db/migrate/20210126092910_create_lab_lab_accession_number_counters.rb +0 -12
- data/db/migrate/20210310115457_create_lab_lims_order_mappings.rb +0 -15
- data/db/migrate/20210323080140_change_lims_id_to_string_in_lims_order_mapping.rb +0 -15
- data/db/migrate/20210326195504_add_order_revision_to_lims_order_mapping.rb +0 -5
- data/db/migrate/20210407071728_create_lab_lims_failed_imports.rb +0 -19
- data/db/migrate/20210610095024_fix_numeric_results_value_type.rb +0 -20
- data/db/migrate/20210807111531_add_default_to_lims_order_mapping.rb +0 -7
- data/lib/auto12epl.rb +0 -201
- data/lib/couch_bum/couch_bum.rb +0 -92
- data/lib/generators/lab/install/USAGE +0 -9
- data/lib/generators/lab/install/install_generator.rb +0 -19
- data/lib/generators/lab/install/templates/rswag-ui-lab.rb +0 -5
- data/lib/generators/lab/install/templates/start_worker.rb +0 -32
- data/lib/generators/lab/install/templates/swagger.yaml +0 -714
- data/lib/his_emr_api_lab.rb +0 -5
- data/lib/lab/engine.rb +0 -15
- data/lib/lab/version.rb +0 -5
- data/lib/logger_multiplexor.rb +0 -38
- data/lib/tasks/lab_tasks.rake +0 -25
- data/lib/tasks/loaders/data/reasons-for-test.csv +0 -7
- data/lib/tasks/loaders/data/test-measures.csv +0 -225
- data/lib/tasks/loaders/data/tests.csv +0 -161
- data/lib/tasks/loaders/loader_mixin.rb +0 -53
- data/lib/tasks/loaders/metadata_loader.rb +0 -26
- data/lib/tasks/loaders/reasons_for_test_loader.rb +0 -23
- data/lib/tasks/loaders/specimens_loader.rb +0 -65
- data/lib/tasks/loaders/test_result_indicators_loader.rb +0 -54
@@ -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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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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name:
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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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name:
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tests:
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properties:
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id:
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concept_id:
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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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- date
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required:
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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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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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name:
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type: string
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required:
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- concept_id
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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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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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required:
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required:
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-
- id
|
363
|
-
- specimen
|
364
|
-
- reason_for_test
|
365
|
-
- accession_number
|
366
|
-
- patient_id
|
367
|
-
- order_date
|
368
|
-
requestBody:
|
369
|
-
content:
|
370
|
-
application/json:
|
371
|
-
schema:
|
372
|
-
type: object
|
373
|
-
properties:
|
374
|
-
specimen:
|
375
|
-
type: object
|
376
|
-
properties:
|
377
|
-
concept_id:
|
378
|
-
type: integer
|
379
|
-
required:
|
380
|
-
- concept_id
|
381
|
-
delete:
|
382
|
-
summary: Void lab order
|
383
|
-
tags:
|
384
|
-
- Orders
|
385
|
-
description: |
|
386
|
-
Void a lab order and all it's associated records
|
387
|
-
|
388
|
-
This action voids an order, all it's linked tests and results.
|
389
|
-
security:
|
390
|
-
- api_key: []
|
391
|
-
parameters:
|
392
|
-
- name: order_id
|
393
|
-
in: path
|
394
|
-
required: true
|
395
|
-
schema:
|
396
|
-
type: integer
|
397
|
-
- name: reason
|
398
|
-
in: query
|
399
|
-
required: true
|
400
|
-
schema:
|
401
|
-
type: string
|
402
|
-
responses:
|
403
|
-
'204':
|
404
|
-
description: No Content
|
405
|
-
"/api/v1/lab/reasons_for_test":
|
406
|
-
get:
|
407
|
-
summary: Reasons for test
|
408
|
-
description: Retrieve default reasons for test concept set
|
409
|
-
tags:
|
410
|
-
- Concepts
|
411
|
-
security:
|
412
|
-
- api_key: []
|
413
|
-
responses:
|
414
|
-
'200':
|
415
|
-
description: Success
|
416
|
-
content:
|
417
|
-
application/json:
|
418
|
-
schema:
|
419
|
-
type: array
|
420
|
-
items:
|
421
|
-
type: object
|
422
|
-
properties:
|
423
|
-
concept_id:
|
424
|
-
type: integer
|
425
|
-
name:
|
426
|
-
type: string
|
427
|
-
example: Routine
|
428
|
-
required:
|
429
|
-
- concept_id
|
430
|
-
- name
|
431
|
-
"/api/v1/lab/tests/{test_id}/results":
|
432
|
-
post:
|
433
|
-
summary: Add results to order
|
434
|
-
tags:
|
435
|
-
- Results
|
436
|
-
description: Attach results to specimens on order
|
437
|
-
parameters:
|
438
|
-
- name: test_id
|
439
|
-
in: path
|
440
|
-
required: true
|
441
|
-
schema:
|
442
|
-
type: integer
|
443
|
-
security:
|
444
|
-
- api_key: []
|
445
|
-
responses:
|
446
|
-
'201':
|
447
|
-
description: Created
|
448
|
-
requestBody:
|
449
|
-
content:
|
450
|
-
application/json:
|
451
|
-
schema:
|
452
|
-
type: object
|
453
|
-
properties:
|
454
|
-
encounter_id:
|
455
|
-
type: integer
|
456
|
-
provider_id:
|
457
|
-
type: integer
|
458
|
-
date:
|
459
|
-
type: string
|
460
|
-
measures:
|
461
|
-
type: array
|
462
|
-
items:
|
463
|
-
type: object
|
464
|
-
properties:
|
465
|
-
indicator:
|
466
|
-
type: object
|
467
|
-
properties:
|
468
|
-
concept_id:
|
469
|
-
type: integer
|
470
|
-
description: Concept ID of a test result indicator for
|
471
|
-
this test (see GET /test_result_indicators)
|
472
|
-
required:
|
473
|
-
- concept_id
|
474
|
-
value:
|
475
|
-
type: string
|
476
|
-
example: LDL
|
477
|
-
value_modifier:
|
478
|
-
type: string
|
479
|
-
example: "="
|
480
|
-
value_type:
|
481
|
-
type: string
|
482
|
-
enum:
|
483
|
-
- text
|
484
|
-
- boolean
|
485
|
-
- numeric
|
486
|
-
- coded
|
487
|
-
description: Determines under what column the value is to
|
488
|
-
be saved under in the obs table (defaults to text)
|
489
|
-
example: text
|
490
|
-
required:
|
491
|
-
- indicator
|
492
|
-
- value
|
493
|
-
required:
|
494
|
-
- measures
|
495
|
-
"/api/v1/lab/specimen_types":
|
496
|
-
get:
|
497
|
-
summary: Specimen types
|
498
|
-
tags:
|
499
|
-
- Concepts
|
500
|
-
description: Retrieve all specimen types
|
501
|
-
security:
|
502
|
-
- api_key: []
|
503
|
-
parameters:
|
504
|
-
- name: test_type
|
505
|
-
in: query
|
506
|
-
required: false
|
507
|
-
description: Select specimen types having this test type only
|
508
|
-
schema:
|
509
|
-
type: string
|
510
|
-
responses:
|
511
|
-
'200':
|
512
|
-
description: Success
|
513
|
-
content:
|
514
|
-
application/json:
|
515
|
-
schema:
|
516
|
-
type: array
|
517
|
-
items:
|
518
|
-
type: object
|
519
|
-
properties:
|
520
|
-
concept_id:
|
521
|
-
type: integer
|
522
|
-
name:
|
523
|
-
type: string
|
524
|
-
required:
|
525
|
-
- concept_id
|
526
|
-
- name
|
527
|
-
"/api/v1/lab/test_result_indicators":
|
528
|
-
get:
|
529
|
-
summary: Test Result Indicators
|
530
|
-
tags:
|
531
|
-
- Concepts
|
532
|
-
description: Retrieve all result indicators for a given test
|
533
|
-
security:
|
534
|
-
- api_key: []
|
535
|
-
parameters:
|
536
|
-
- name: test_type_id
|
537
|
-
in: query
|
538
|
-
required: true
|
539
|
-
description: Concept ID for the desired test
|
540
|
-
schema:
|
541
|
-
type: integer
|
542
|
-
responses:
|
543
|
-
'200':
|
544
|
-
description: Ok
|
545
|
-
content:
|
546
|
-
application/json:
|
547
|
-
schema:
|
548
|
-
type: array
|
549
|
-
items:
|
550
|
-
type: object
|
551
|
-
properties:
|
552
|
-
concept_id:
|
553
|
-
type: integer
|
554
|
-
name:
|
555
|
-
type: string
|
556
|
-
required:
|
557
|
-
- concept_id
|
558
|
-
- name
|
559
|
-
"/api/v1/lab/test_types":
|
560
|
-
get:
|
561
|
-
summary: Test types
|
562
|
-
tags:
|
563
|
-
- Concepts
|
564
|
-
description: Retrieve all test types
|
565
|
-
security:
|
566
|
-
- api_key: []
|
567
|
-
parameters:
|
568
|
-
- name: specimen_type
|
569
|
-
in: query
|
570
|
-
required: false
|
571
|
-
description: Select test types having this specimen type only
|
572
|
-
schema:
|
573
|
-
type: string
|
574
|
-
responses:
|
575
|
-
'200':
|
576
|
-
description: Success
|
577
|
-
content:
|
578
|
-
application/json:
|
579
|
-
schema:
|
580
|
-
type: array
|
581
|
-
items:
|
582
|
-
type: object
|
583
|
-
properties:
|
584
|
-
concept_id:
|
585
|
-
type: integer
|
586
|
-
name:
|
587
|
-
type: string
|
588
|
-
required:
|
589
|
-
- concept_id
|
590
|
-
- name
|
591
|
-
"/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
|
602
|
-
required: false
|
603
|
-
schema:
|
604
|
-
type: string
|
605
|
-
- name: test_type_id
|
606
|
-
in: query
|
607
|
-
required: false
|
608
|
-
schema:
|
609
|
-
type: integer
|
610
|
-
- name: specimen_type_id
|
611
|
-
in: query
|
612
|
-
required: false
|
613
|
-
schema:
|
614
|
-
type: integer
|
615
|
-
- name: patient_id
|
616
|
-
in: query
|
617
|
-
required: false
|
618
|
-
schema:
|
619
|
-
type: integer
|
620
|
-
- name: order_date
|
621
|
-
in: query
|
622
|
-
required: false
|
623
|
-
schema:
|
624
|
-
type: boolean
|
625
|
-
responses:
|
626
|
-
'200':
|
627
|
-
description: Okay
|
628
|
-
content:
|
629
|
-
application/json:
|
630
|
-
schema:
|
631
|
-
type: array
|
632
|
-
items:
|
633
|
-
type: object
|
634
|
-
properties:
|
635
|
-
id:
|
636
|
-
type: integer
|
637
|
-
concept_id:
|
638
|
-
type: integer
|
639
|
-
name:
|
640
|
-
type: string
|
641
|
-
order:
|
642
|
-
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
|