Commit 442c0601 authored by Daniel Teixeira's avatar Daniel Teixeira
Browse files

adding yaml

parent c4a9f897
swagger: '2.0'
info:
title: Beacon API
description: This document represents a proposal for the next version of the API for the GA4GH Beacon Project. The new API is intended to expose new functionalities motivated by potential uses cases contributed by the community.
version: '0.3'
schemes:
- https
basePath: /v03
produces:
- application/json
paths:
/info:
get:
summary: Beacon info endpoint
description: 'Returns the information about this beacon (name, description, API version, URL, etc...)'
responses:
'200':
description: A Beacon info page
schema:
$ref: '#/definitions/Beacon'
default:
description: Unexpected error
schema:
$ref: '#/definitions/BeaconError'
tags:
- Info
/query:
get:
summary: Beacon query endpoint
description: "To actually ask the beacon for questions like \"do you have any genomes with an 'A' at position 100,735 on chromosome 3?\" And the answer will be yes or no."
parameters:
- name: chrom
in: query
description: 'Chromosome name. Accepted values are 1-22, X, Y and MT.'
required: true
type: string
- name: pos
in: query
description: Coordinate within a chromosome (0-based)
required: true
type: number
- name: assembly
in: query
description: 'The version of the reference genome, NCBI notation.'
required: true
type: string
- name: alt
in: query
description: 'The bases that appear instead of the reference bases. The semantics correspond to the field ALT in VCF. Options are base Strings made up of A,C,G,T,N,* (case insensitive) or an angle-bracketed ID or a breakend replacement string.'
required: true
type: string
- name: ref
in: query
description: 'The reference bases for this variant, starting from `position`, in the genome described by the field `reference`. The semantics correspond to the field REF in VCF. One of A,C,G,T,N (case insensitive). Multiple bases are permitted.'
required: true
type: string
- name: datasetIds
in: query
description: 'Limit to a set of datasetIds at the target website. An ID is specific to the website that is queried and can be an accession ID, population or any other identifier'
required: false
type: array
items:
type: string
tags:
- Query
responses:
'200':
description: A beacon allele response
schema:
type: array
items:
$ref: '#/definitions/BeaconAlleleResponse'
default:
description: Unexpected error
schema:
$ref: '#/definitions/BeaconError'
definitions:
BeaconAlleleResponse:
type: object
properties:
beaconId:
type: string
description: Beacon identfier
exists:
type: boolean
description: indicates whether the variant has been observed.
alleleRequest:
type: object
items:
$ref: '#/definitions/BeaconAlleleRequest'
description: The request to the Beacon.
datasetAlleleResponses:
type: array
description: Datasets for which the variant is found.
items:
$ref: '#/definitions/DatasetAlleleResponse'
errorInfo:
type: object
items:
$ref: '#/definitions/BeaconError'
description: Error
BeaconAlleleRequest:
type: object
properties:
chrom:
type: string
description: 'Chromosome name. Accepted values are 1-22, X, Y and MT.'
pos:
type: number
description: Coordinate within a chromosome (0-based).
assembly:
type: string
description: 'The version of the reference genome, NCBI notation.'
alt:
type: string
description: 'The bases that appear instead of the reference bases. The semantics correspond to the field ALT in VCF. Options are base Strings made up of A,C,G,T,N,* (case insensitive) or an angle-bracketed ID or a breakend replacement string.'
ref:
type: string
description: 'The reference bases for this variant, starting from `position`, in the genome described by the field `reference`. The semantics correspond to the field REF in VCF. One of A,C,G,T,N (case insensitive). Multiple bases are permitted.'
datasetIds:
type: array
items:
type: string
description: 'Limit to a set of datasetIds at the target website. An ID is specific to the website that is queried and can be an accession ID, population or any other identifier.'
BeaconError:
type: object
properties:
status:
type: number
description: The error code.
reason:
type: string
description: The reason of the error.
message:
type: string
description: An error message.
DatasetAlleleResponse:
type: object
properties:
exists:
type: boolean
description: Can be used to indicate that this variant has been observed before and no other information.
frequency:
type: number
description: 'Frequency of the allele in the dataset, 0.0-1.0, inclusive.'
errorInfo:
type: array
items:
$ref: '#/definitions/BeaconError'
description: Beacon error.
variantCount:
type: number
description: Number of variants in the dataset.
callCount:
type: number
description: Number of called observations of this allele in the dataset.
sampleCount:
type: number
description: Number of observations of this allele in the dataset.
note:
type: string
description: Human-readable description of this variant.
externalUrl:
type: string
description: URL with more information about a variant.
info:
type: array
items:
type: string
description: General information about the query.
BeaconOrganization:
type: object
properties:
id:
type: string
description: Short unique identifier for the organization hosting the beacon.
name:
type: string
description: The organization name.
description:
type: string
description: The organization description.
address:
type: string
description: The address of the organization.
welcomeUrl:
type: string
description: URL of homepage with additional info about the organizazion
contactUrl:
type: string
description: Beacon contact person in the organization.
logoUrl:
type: string
description: URL with a logo shown.
info:
type: array
items:
type: string
description: General information about the organization.
Beacon:
type: object
properties:
id:
type: string
description: Short unique identifier for the beacon.
organization:
$ref: '#/definitions/BeaconOrganization'
description:
type: string
description: Longer human-readable description of the beacon.
datasets:
type: array
description: List of datasets served by the beacon.
items:
$ref: '#/definitions/BeaconDataset'
apiVersion:
type: string
description: Beacon API version.
welcomeUrl:
type: string
description: URL of homepage with additional info about the beacon.
sampleAlleleRequests:
type: array
description: Examples of allele requests.
items:
$ref: '#/definitions/BeaconAlleleRequest'
name:
type: string
description: The beacon name.
version:
type: string
description: The beacon version.
alternativeUrl:
type: string
description: Alternative URL.
created:
type: number
description: "The beacon's creation date."
updated:
type: number
description: "The beacon's last update date."
info:
description: General information about the beacon.
type: array
items:
type: string
BeaconDataset:
type: object
properties:
id:
type: string
description: Short unique identifier for the dataset.
assembly:
type: string
description: 'The version of the reference genome, NCBI notation.'
description:
type: string
description: "The dataset's description."
dataUse:
$ref: '#/definitions/DataUse'
name:
type: string
description: "The dataset's name."
created:
type: number
description: The dataset creation date.
updated:
type: number
description: "The dataset's last update date."
version:
type: string
description: The version of the dataset.
variantCount:
type: number
description: The number of variants in the dataset.
callCount:
type: number
description: The number of calls in the dataset.
sampleCount:
type: number
description: The number of samples in the dataset.
externalUrl:
type: string
description: The URL of a page with additional info about the dataset.
info:
description: General inoformation about the dataset.
type: array
items:
type: string
DataUse:
type: object
properties:
primaryCategory:
$ref: '#/definitions/DataUseCondition'
requirements:
description: List of data use requirements.
type: array
items:
$ref: '#/definitions/DataUseCondition'
secondaryCategories:
description: List of secondary data use conditions.
type: array
items:
$ref: '#/definitions/DataUseCondition'
DataUseCondition:
type: object
properties:
description:
type: string
description: Data use condition description.
code:
type: string
description: Data use condition code.
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