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APISpecification.yaml
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APISpecification.yaml
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openapi: 3.0.0
info:
title: Tools api
version: 0.0.1
paths:
/api/tools/vep/config:
get:
parameters:
- name: genome_id
in: query
required: true
schema:
type: string
responses:
'200':
description: The request has succeeded.
content:
application/json:
schema:
$ref: '#/components/schemas/VepConfigResponse'
/api/tools/vep/submissions:
post:
requestBody:
content:
multipart/form-data:
schema:
type: object
properties:
genome_id:
type: string
input_file:
type: string
format: binary
parameters:
type: string
description: |
Stringified JSON of parameters, such as '{"transcript_set":"blah","symbol":true,"biotype":true}'
responses:
'200':
description: Successful operaiton.
content:
application/json:
schema:
$ref: '#/components/schemas/VepFormSubmissionCreatedResponse'
/api/tools/vep/submissions/{id}/results:
get:
description: Returns results of VEP analysis
parameters:
- name: id
in: path
required: true
schema:
type: string
- name: page
in: query
required: false
schema:
type: number
default: 1
- name: per_page
in: query
required: false
schema:
type: number
default: 100
responses:
'200':
description: Successful operaiton.
content:
application/json:
schema:
$ref: '#/components/schemas/VepResultsResponse'
components:
schemas:
AlternativeVariantAllele:
type: object
required:
- allele_sequence
- allele_type
- predicted_molecular_consequences
properties:
allele_sequence:
type: string
allele_type:
type: string
representative_population_allele_frequency:
type: number
nullable: true
predicted_molecular_consequences:
type: array
items:
anyOf:
- $ref: '#/components/schemas/PredictedTranscriptConsequence'
- $ref: '#/components/schemas/PredictedIntergenicConsequence'
BooleanConfigOption:
type: object
required:
- label
- description
- type
- default_value
properties:
label:
type: string
description:
type: string
nullable: true
type:
type: string
enum:
- boolean
default_value:
type: boolean
PaginationMetadata:
type: object
required:
- page
- per_page
- total
properties:
page:
type: number
per_page:
type: number
total:
type: number
PredictedIntergenicConsequence:
type: object
required:
- feature_type
- consequences
properties:
feature_type:
nullable: true
description: The value of this field is always null. The presence of null in this field will serve as a marker that this is a consequence of an intergenic variant.
consequences:
type: array
items:
type: string
description: The only expected member of this array will be the string 'intergenic_variant'
PredictedTranscriptConsequence:
type: object
required:
- feature_type
- stable_id
- gene_stable_id
- symbol
- biotype
- is_canonical
- consequences
- strand
properties:
feature_type:
type: string
enum:
- transcript
stable_id:
type: string
description: transcript stable id, versioned
gene_stable_id:
type: string
description: gene stable id, versioned
symbol:
type: string
nullable: true
biotype:
type: string
is_canonical:
type: boolean
consequences:
type: array
items:
type: string
strand:
type: string
enum:
- forward
- reverse
ReferenceVariantAllele:
type: object
required:
- allele_sequence
properties:
allele_sequence:
type: string
SelectConfigOption:
type: object
required:
- label
- description
- type
- options
- default_value
properties:
label:
type: string
description:
type: string
nullable: true
type:
type: string
enum:
- select
options:
type: array
items:
type: object
properties:
label:
type: string
value:
type: string
required:
- label
- value
default_value:
type: string
Variant:
type: object
required:
- name
- allele_type
- location
- reference_allele
- alternative_alleles
properties:
name:
type: string
nullable: true
description: User's name for the variant; optional
allele_type:
type: string
location:
type: object
properties:
region_name:
type: string
start:
type: number
end:
type: number
required:
- region_name
- start
- end
reference_allele:
$ref: '#/components/schemas/ReferenceVariantAllele'
alternative_alleles:
type: array
items:
$ref: '#/components/schemas/AlternativeVariantAllele'
VepConfigResponse:
type: object
required:
- parameters
properties:
parameters:
type: array
items:
anyOf:
- $ref: '#/components/schemas/BooleanConfigOption'
- $ref: '#/components/schemas/SelectConfigOption'
VepResultsResponse:
type: object
required:
- metadata
- variants
properties:
metadata:
type: object
properties:
pagination:
$ref: '#/components/schemas/PaginationMetadata'
required:
- pagination
variants:
type: array
items:
$ref: '#/components/schemas/Variant'
VepFormSubmissionCreatedResponse:
type: object
required:
- submission_id
properties:
submission_id:
type: string