One Codex Genomes API
The Genomes API from One Codex — 2 operation(s) for genomes.
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 Genomes API
version: v1
servers:
- url: https://app.onecodex.com
security:
- apiKeyAuth: []
tags:
- name: Genomes
paths:
/api/v1/genomes:
get:
operationId: get_genomes_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:
$uri:
example: /api/v1/genomes/0d77065796f8d173
pattern: ^/api/v1/genomes/[a-f0-9]{16}$
readOnly: true
title: $Uri
type: string
assemblies:
items:
properties:
$ref:
example: /api/v1/assemblies/a1b2c3d4e5f67890
format: uri
pattern: ^/api/v1/assemblies/[a-f0-9]{16}$
type: string
title: assemblies
type: object
title: Assemblies
type: array
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
description:
anyOf:
- type: string
- type: 'null'
title: Description
name:
anyOf:
- type: string
- type: 'null'
title: Name
primary_assembly:
anyOf:
- properties:
$ref:
example: /api/v1/assemblies/a1b2c3d4e5f67890
format: uri
pattern: ^/api/v1/assemblies/[a-f0-9]{16}$
type: string
title: assemblies
type: object
- type: 'null'
title: Primary Assembly
tags:
items:
properties:
$ref:
example: /api/v1/tags/a1b2c3d4e5f67890
format: uri
pattern: ^/api/v1/tags/[a-f0-9]{16}$
type: string
title: tags
type: object
title: Tags
type: array
taxon:
properties:
$ref:
example: /api/v1/taxa/a1b2c3d4e5f67890
format: uri
pattern: ^/api/v1/taxa/[a-f0-9]{16}$
type: string
title: taxa
type: object
required:
- $uri
- assemblies
- created_at
- description
- name
- primary_assembly
- tags
- taxon
title: genomes
type: object
type: array
description: OK
summary: GET genomes instances
tags:
- Genomes
/api/v1/genomes/{id}:
get:
operationId: get_genomes_self
parameters:
- in: path
name: id
required: true
schema:
type: string
responses:
'200':
content:
application/json:
schema:
properties:
$uri:
example: /api/v1/genomes/0d77065796f8d173
pattern: ^/api/v1/genomes/[a-f0-9]{16}$
readOnly: true
title: $Uri
type: string
assemblies:
items:
properties:
$ref:
example: /api/v1/assemblies/a1b2c3d4e5f67890
format: uri
pattern: ^/api/v1/assemblies/[a-f0-9]{16}$
type: string
title: assemblies
type: object
title: Assemblies
type: array
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
description:
anyOf:
- type: string
- type: 'null'
title: Description
name:
anyOf:
- type: string
- type: 'null'
title: Name
primary_assembly:
anyOf:
- properties:
$ref:
example: /api/v1/assemblies/a1b2c3d4e5f67890
format: uri
pattern: ^/api/v1/assemblies/[a-f0-9]{16}$
type: string
title: assemblies
type: object
- type: 'null'
title: Primary Assembly
tags:
items:
properties:
$ref:
example: /api/v1/tags/a1b2c3d4e5f67890
format: uri
pattern: ^/api/v1/tags/[a-f0-9]{16}$
type: string
title: tags
type: object
title: Tags
type: array
taxon:
properties:
$ref:
example: /api/v1/taxa/a1b2c3d4e5f67890
format: uri
pattern: ^/api/v1/taxa/[a-f0-9]{16}$
type: string
title: taxa
type: object
required:
- $uri
- assemblies
- created_at
- description
- name
- primary_assembly
- tags
- taxon
title: genomes
type: object
description: OK
summary: GET genomes
tags:
- Genomes
components:
securitySchemes:
apiKeyAuth:
in: header
name: X-API-Key
type: apiKey