Gencove pipeline API
The pipeline API from Gencove — 5 operation(s) for pipeline.
OpenAPI Specification
openapi: 3.0.3
info:
title: Gencove Back array pipeline API
version: v2
contact:
email: support@gencove.com
license:
name: Proprietary
description: API for Gencove REST service. Visit <a href='https://enterprise.gencove.com/'>enterprise.gencove.com</a> and <a href='https://docs.gencove.com/'>docs.gencove.com</a> for more information. <br><hr><p>To work with Insomnia, you can generate a Gencove API key by <a target='_blank' href='https://web.gencove.com/account?filter=api-keys'>clicking here</a>. Once you have the API key and have imported the project in Insomnia as a <i>Request Collection</i>, enter the key in Insomnia under <i>Manage Environment</i>.</p><a href='https://insomnia.rest/run/?label=back_api2&uri=https%3A%2F%2Fv2-api-files-prod.s3.amazonaws.com%2Fpublic%2Finsomnia%2Finsomnia_gencove_prod.json' target='_blank'>Run in Insomnia</a><hr>
servers:
- url: https://api.gencove.com
tags:
- name: pipeline
paths:
/api/v2/pipeline/:
get:
operationId: pipeline_list
description: Retrieve list of user projects.
parameters:
- name: limit
required: false
in: query
description: Number of results to return per page.
schema:
type: integer
- name: offset
required: false
in: query
description: The initial index from which to return the results.
schema:
type: integer
- in: query
name: sort_by
schema:
type: string
enum:
- created
description: Sort results
- in: query
name: sort_order
schema:
type: string
enum:
- asc
- desc
description: Sort direction
tags:
- pipeline
security:
- JWT: []
- API key: []
responses:
'200':
content:
application/json:
schema:
$ref: '#/components/schemas/PaginatedPipelineListList'
description: ''
/api/v2/pipeline-capabilities/:
get:
operationId: pipeline_capabilities_list
description: List pipeline capabilities
parameters:
- name: limit
required: false
in: query
description: Number of results to return per page.
schema:
type: integer
- name: offset
required: false
in: query
description: The initial index from which to return the results.
schema:
type: integer
- in: query
name: search
schema:
type: string
description: Search pipeline capabilities by id
tags:
- pipeline
security:
- JWT: []
- API key: []
responses:
'200':
content:
application/json:
schema:
$ref: '#/components/schemas/PaginatedPipelineCapabilitiesList'
description: ''
/api/v2/pipeline-capabilities/{pipeline_capabilities_id}:
get:
operationId: pipeline_capabilities_retrieve
description: Fetch single pipeline capabilities details
parameters:
- in: path
name: pipeline_capabilities_id
schema:
type: string
format: uuid
required: true
tags:
- pipeline
security:
- JWT: []
- API key: []
responses:
'200':
content:
application/json:
schema:
$ref: '#/components/schemas/PipelineCapabilities'
description: ''
/api/v2/pipeline-latest/:
get:
operationId: pipeline_latest_retrieve
description: 'Returns latest (newest) Pipeline instance.
retrieve: Fetch single newest pipeline details including it''s capabilities'
tags:
- pipeline
security:
- JWT: []
- API key: []
responses:
'200':
content:
application/json:
schema:
$ref: '#/components/schemas/PipelineDetail'
description: ''
/api/v2/pipeline/{pipeline_id}:
get:
operationId: pipeline_retrieve
description: Fetch single pipeline details including it's capabilities
parameters:
- in: path
name: pipeline_id
schema:
type: string
format: uuid
required: true
tags:
- pipeline
security:
- JWT: []
- API key: []
responses:
'200':
content:
application/json:
schema:
$ref: '#/components/schemas/PipelineDetail'
description: ''
components:
schemas:
PipelineCapabilities:
type: object
properties:
id:
type: string
format: uuid
readOnly: true
name:
type: string
description: Name from pipeline config
maxLength: 254
key:
type: string
description: Key from pipeline config
maxLength: 254
private:
type: boolean
description: True if private
merge_vcfs_enabled:
type: boolean
description: Set to True if MergeVCFs can be run
supported_project_modifications:
nullable: true
description: List of project modification objects supported by the pipeline. Only the modifications listed under 'key' can be used. Note that 'value' is only used by the front-end to determine whether the check box should be set to True or False by default.
modifications_enabled:
type: string
readOnly: true
species:
type: string
readOnly: true
description: Species
pipeline_category:
nullable: true
description: 'Category of the pipeline capability
* `Human Genomics` - human genomics
* `Agriculture Animals & Plant Genomics` - animals plants
* `Companion Animals` - companion animals
* `Other` - other'
oneOf:
- $ref: '#/components/schemas/PipelineCategoryEnum'
- $ref: '#/components/schemas/BlankEnum'
- $ref: '#/components/schemas/NullEnum'
description_markdown:
type: string
readOnly: true
description: 'Description markdown of a pipeline capability. '
datasets:
type: string
readOnly: true
description: Dataset descriptions.
steps:
type: string
readOnly: true
description: Pipeline capability steps that are enabled.
required:
- datasets
- description_markdown
- id
- key
- modifications_enabled
- name
- species
- steps
PaginatedPipelineCapabilitiesList:
type: object
required:
- results
properties:
meta:
type: object
properties:
count:
type: integer
next:
type: string
format: uri
nullable: true
previous:
type: string
format: uri
nullable: true
required:
- count
results:
type: array
items:
$ref: '#/components/schemas/PipelineCapabilities'
NullEnum:
enum:
- null
PipelineDetail:
type: object
properties:
id:
type: string
format: uuid
readOnly: true
version:
type: string
maxLength: 100
capabilities:
type: array
items:
$ref: '#/components/schemas/PipelineCapabilities'
required:
- capabilities
- id
- version
PipelineCategoryEnum:
enum:
- Human Genomics
- Agriculture Animals & Plant Genomics
- Companion Animals
- Other
type: string
description: '* `Human Genomics` - human genomics
* `Agriculture Animals & Plant Genomics` - animals plants
* `Companion Animals` - companion animals
* `Other` - other'
BlankEnum:
enum:
- ''
PipelineList:
type: object
properties:
id:
type: string
format: uuid
readOnly: true
version:
type: string
maxLength: 100
required:
- id
- version
PaginatedPipelineListList:
type: object
required:
- results
properties:
meta:
type: object
properties:
count:
type: integer
next:
type: string
format: uri
nullable: true
previous:
type: string
format: uri
nullable: true
required:
- count
results:
type: array
items:
$ref: '#/components/schemas/PipelineList'
securitySchemes:
API key:
type: apiKey
description: 'Authorization header content formated as: `Api-Key <API-key>`
You can obtain new API key through Gencove''s web UI or `user-api-key` endpoint'
in: header
name: Authorization
JWT:
type: apiKey
description: 'Authorization header content formated as: `Bearer <json-web-token>`
You can obtain access token using `jwt-create` endpoint.'
in: header
name: Authorization