One Codex Sequencing API
The Sequencing API from One Codex — 4 operation(s) for sequencing.
OpenAPI Specification
openapi: 3.1.0
info:
description: The One Codex API (v1) -- programmatic access to One Codex's suite of microbial genomics data storage, analysis, and query tools.
title: One Codex API (v1) Account Sequencing API
version: v1
servers:
- url: https://app.onecodex.com
security:
- apiKeyAuth: []
tags:
- name: Sequencing
paths:
/api/v1/sequencing/batches:
get:
operationId: get_sequencing_instances_batches
parameters:
- description: Page number. Defaults to 1. See Pagination for more details.
in: query
name: page
required: false
schema:
default: 1
format: int32
type: integer
- description: Number of requested paginated records. Defaults to 50. See Pagination for more details.
in: query
name: per_page
required: false
schema:
default: 50
format: int32
type: integer
- description: 'Optional Mongo-style JSON sort clause, e.g., `sort={"created_at": true}` to sort by created_at (descending)'
in: query
name: sort
required: false
schema:
anyOf:
- type: string
- type: 'null'
default: null
- description: 'Optional Mongo-style JSON filter clause, e.g., `where={"$uri": {"$eq": "/api/v1/samples/0ee172af60e84f61"}}`'
in: query
name: where
required: false
schema:
anyOf:
- type: string
- type: 'null'
default: null
responses:
'200':
content:
application/json:
schema:
items:
$ref: '#/components/schemas/sequencing_batches'
type: array
description: OK
summary: GET sequencing instances_batches
tags:
- Sequencing
/api/v1/sequencing/batches/register:
post:
operationId: post_sequencing_instances_batches_register
requestBody:
content:
application/json:
schema:
properties:
batch_name:
description: A human-readable name for the sequencing batch.
maxLength: 100
minLength: 1
title: Batch Name
type: string
return_tracking_numbers:
description: One or more tracking numbers associated with the sample shipment(s) to the lab.
items:
type: string
maxItems: 100
minItems: 1
title: Return Tracking Numbers
type: array
uniqueItems: true
samples:
description: The tube barcodes, specimen type, and sequencing depth for each sample to be sequenced.
items:
properties:
sequencing_depth:
enum:
- Standard
- Deep
title: SequencingDepth
type: string
specimen_type:
enum:
- Human stool
- Microbial cell culture
title: SpecimenType
type: string
tube_barcode:
title: Tube Barcode
type: string
required:
- sequencing_depth
- specimen_type
- tube_barcode
title: _RegisterSampleSchema
type: object
maxItems: 5000
minItems: 1
title: Samples
type: array
required:
- batch_name
- return_tracking_numbers
- samples
title: SequencingBatchRegisterSchema
type: object
required: true
responses:
'200':
content:
application/json:
schema:
properties:
batch:
$ref: '#/components/schemas/sequencing_batches'
description: The sequencing batch object that was created.
samples:
description: The sample object associated with the tube barcode. This will be in an `awaiting_data` state until the lab has finished processing the physical sample.
items:
properties:
sample:
description: The sample object associated with the tube barcode. Note this may be in a pending upload state if the lab has not finished processing the physical sample.
properties:
$ref:
example: /api/v1/samples/a1b2c3d4e5f67890
format: uri
pattern: ^/api/v1/samples/[a-f0-9]{16}$
type: string
type: object
tube_barcode:
description: The tube barcode for the sample sent to the lab.
title: Tube Barcode
type: string
required:
- sample
- tube_barcode
title: _TubeAndSampleSchema
type: object
title: Samples
type: array
required:
- batch
- samples
title: SequencingBatchRegisterResponse
type: object
description: OK
summary: POST sequencing instances_batches_register
tags:
- Sequencing
/api/v1/sequencing/batches/{id}:
get:
operationId: get_sequencing_batches
parameters:
- in: path
name: id
required: true
schema:
type: string
responses:
'200':
content:
application/json:
schema:
$ref: '#/components/schemas/sequencing_batches'
description: OK
summary: GET sequencing batches
tags:
- Sequencing
/api/v1/sequencing/batches/{id}/samples:
get:
operationId: get_sequencing_batches_samples
parameters:
- in: path
name: id
required: true
schema:
type: string
responses:
'200':
content:
application/json:
schema:
items:
properties:
sample:
description: The sample object associated with the tube barcode. Note this may be in a pending upload state if the lab has not finished processing the physical sample.
properties:
$ref:
example: /api/v1/samples/a1b2c3d4e5f67890
format: uri
pattern: ^/api/v1/samples/[a-f0-9]{16}$
type: string
type: object
tube_barcode:
description: The tube barcode for the sample sent to the lab.
title: Tube Barcode
type: string
required:
- sample
- tube_barcode
title: SequencingBatchSamplesResponse
type: object
type: array
description: OK
summary: GET sequencing batches_samples
tags:
- Sequencing
components:
schemas:
sequencing_batches:
properties:
$uri:
example: /api/v1/sequencing/batches/0d77065796f8d173
pattern: ^/api/v1/sequencing/batches/[a-f0-9]{16}$
readOnly: true
title: $Uri
type: string
batch_number:
description: A unique batch number.
title: Batch Number
type: string
created_at:
description: Timestamp for when the object was created on the One Codex platform, encoded as a [RFC 3339](https://www.ietf.org/rfc/rfc3339.txt) timestamp.
format: date-time
title: Created At
type: string
name:
anyOf:
- type: string
- type: 'null'
description: A human-readable name for the sequencing batch.
title: Name
owner:
description: The user that created the sequencing batch.
properties:
$ref:
example: /api/v1/users/a1b2c3d4e5f67890
format: uri
pattern: ^/api/v1/users/[a-f0-9]{16}$
type: string
title: users
type: object
status:
description: The current status of the sequencing batch.
enum:
- registered
- shipped_to_lab
- received_at_lab
- extracting
- preparing_library
- sequencing
- quality_control
- done
- canceled
title: Status
type: string
required:
- $uri
- batch_number
- created_at
- name
- owner
- status
title: sequencing/batches
type: object
securitySchemes:
apiKeyAuth:
in: header
name: X-API-Key
type: apiKey