One Codex Assemblies API
The Assemblies API from One Codex — 3 operation(s) for assemblies.
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 Assemblies API
version: v1
servers:
- url: https://app.onecodex.com
security:
- apiKeyAuth: []
tags:
- name: Assemblies
paths:
/api/v1/assemblies:
get:
operationId: get_assemblies_instances
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:
properties:
$uri:
example: /api/v1/assemblies/0d77065796f8d173
pattern: ^/api/v1/assemblies/[a-f0-9]{16}$
readOnly: true
title: $Uri
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
filename:
anyOf:
- type: string
- type: 'null'
title: Filename
genome:
anyOf:
- properties:
$ref:
example: /api/v1/genomes/a1b2c3d4e5f67890
format: uri
pattern: ^/api/v1/genomes/[a-f0-9]{16}$
type: string
type: object
- type: 'null'
input_samples:
anyOf:
- items:
properties:
$ref:
example: /api/v1/samples/a1b2c3d4e5f67890
format: uri
pattern: ^/api/v1/samples/[a-f0-9]{16}$
type: string
title: samples
type: object
type: array
- type: 'null'
title: Input Samples
job:
anyOf:
- properties:
$ref:
example: /api/v1/jobs/a1b2c3d4e5f67890
format: uri
pattern: ^/api/v1/jobs/[a-f0-9]{16}$
type: string
title: jobs
type: object
- type: 'null'
title: Job
owner:
properties:
$ref:
example: /api/v1/users/a1b2c3d4e5f67890
format: uri
pattern: ^/api/v1/users/[a-f0-9]{16}$
type: string
title: users
type: object
primary_annotation_set:
anyOf:
- properties:
$ref:
example: /api/v1/annotation_sets/a1b2c3d4e5f67890
format: uri
pattern: ^/api/v1/annotation_sets/[a-f0-9]{16}$
type: string
type: object
- type: 'null'
size:
anyOf:
- type: integer
- type: 'null'
title: Size
visibility:
description: 'Enum for the v1 API `visibility` attribute.
Note: this is legacy and only exists for backwards-compatibility in the public v1 API.'
enum:
- public
- shared
- private
- importing
- awaiting data
title: ApiV1Visibility
type: string
required:
- $uri
- created_at
- filename
- genome
- input_samples
- job
- owner
- primary_annotation_set
- size
- visibility
title: assemblies
type: object
type: array
description: OK
summary: GET assemblies instances
tags:
- Assemblies
/api/v1/assemblies/{id}:
get:
operationId: get_assemblies_self
parameters:
- in: path
name: id
required: true
schema:
type: string
responses:
'200':
content:
application/json:
schema:
properties:
$uri:
example: /api/v1/assemblies/0d77065796f8d173
pattern: ^/api/v1/assemblies/[a-f0-9]{16}$
readOnly: true
title: $Uri
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
filename:
anyOf:
- type: string
- type: 'null'
title: Filename
genome:
anyOf:
- properties:
$ref:
example: /api/v1/genomes/a1b2c3d4e5f67890
format: uri
pattern: ^/api/v1/genomes/[a-f0-9]{16}$
type: string
type: object
- type: 'null'
input_samples:
anyOf:
- items:
properties:
$ref:
example: /api/v1/samples/a1b2c3d4e5f67890
format: uri
pattern: ^/api/v1/samples/[a-f0-9]{16}$
type: string
title: samples
type: object
type: array
- type: 'null'
title: Input Samples
job:
anyOf:
- properties:
$ref:
example: /api/v1/jobs/a1b2c3d4e5f67890
format: uri
pattern: ^/api/v1/jobs/[a-f0-9]{16}$
type: string
title: jobs
type: object
- type: 'null'
title: Job
owner:
properties:
$ref:
example: /api/v1/users/a1b2c3d4e5f67890
format: uri
pattern: ^/api/v1/users/[a-f0-9]{16}$
type: string
title: users
type: object
primary_annotation_set:
anyOf:
- properties:
$ref:
example: /api/v1/annotation_sets/a1b2c3d4e5f67890
format: uri
pattern: ^/api/v1/annotation_sets/[a-f0-9]{16}$
type: string
type: object
- type: 'null'
size:
anyOf:
- type: integer
- type: 'null'
title: Size
visibility:
description: 'Enum for the v1 API `visibility` attribute.
Note: this is legacy and only exists for backwards-compatibility in the public v1 API.'
enum:
- public
- shared
- private
- importing
- awaiting data
title: ApiV1Visibility
type: string
required:
- $uri
- created_at
- filename
- genome
- input_samples
- job
- owner
- primary_annotation_set
- size
- visibility
title: assemblies
type: object
description: OK
summary: GET assemblies
tags:
- Assemblies
/api/v1/assemblies/{id}/download_uri:
post:
operationId: post_assemblies_download_uri
parameters:
- in: path
name: id
required: true
schema:
type: string
requestBody:
content:
application/json:
schema:
properties:
original_format:
default: false
title: Original Format
type: boolean
title: AssemblyDownloadUriRequestSchema
type: object
required: true
responses:
'200':
content:
application/json:
schema:
properties:
download_uri:
title: Download Uri
type: string
expires_in_hours:
title: Expires In Hours
type: integer
save_as_filename:
title: Save As Filename
type: string
required:
- download_uri
- expires_in_hours
- save_as_filename
title: AssemblyDownloadUriSchema
type: object
description: OK
summary: POST assemblies download_uri
tags:
- Assemblies
components:
securitySchemes:
apiKeyAuth:
in: header
name: X-API-Key
type: apiKey