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brainstorm/htsget-openapi-factored.yaml

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htsget-openapi-factored.yaml
Raw
htsget-openapi-factored.yaml
openapi: 3.0.0
servers:
- description: htsget genomics api
url: https://virtserver.swaggerhub.com/brainkod/htsget/1.1.1
info:
description: "This data retrieval API bridges from existing genomics bulk data transfers to a client/server model"
version: "1.1.1"
title: htsget
contact:
name: GA4GH
email: security-notification@ga4gh.org
license:
name: GPLv3
paths:
/reads/{id}:
get:
summary: Gets the reads from a pre-indexed id
operationId: searchReadId
description: |
Searches a pre-indexed object id.
parameters:
$ref: '#/components/schemas/commonRequestParameters'
- in: "query"
name: format
description: File format, BAM (default), CRAM.
example: "BAM"
required: false
schema:
type: string
- in: "query"
name: fields
description: A list of fields to include, such as QNAME, FLAG, RNAME, etc...
example: "fields=QNAME,RNAME"
required: false
schema:
enum:
- "QNAME"
- "FLAG"
- "RNAME"
- "POS"
- "MAPQ"
- "CIGAR"
- "RNEXT"
- "PNEXT"
- "TLEN"
- "SEQ"
- "QUAL"
type: string
responses:
'200':
description: results matching criteria
content:
application/json:
schema:
$ref: '#/components/schemas/readIdResponse'
'400':
description: something went wrong
content:
application/json:
schema:
$ref: '#/components/schemas/errorResponses'
'500':
description: Unexpected error
security:
- htsget_auth:
- read:genomic_reads
/variants/{id}:
get:
summary: Gets the variants from a pre-indexed id
operationId: searchVariantId
description: |
Searches a pre-indexed object id.
parameters:
$ref: '#/components/schemas/commonRequestParameters'
- in: "query"
name: format
description: File format, VCF (default), BCF.
example: "VCF"
required: false
schema:
type: string
- in: "query"
name: fields
description: A list of variant fields to include, such as INFO, SAMPLE, FORMAT, etc.
example: "fields=INFO,SAMPLE"
required: false
schema:
enum:
- "INFO"
- "SAMPLE"
- "FILTER"
- "FORMAT"
- "ALT"
type: string
responses:
'200':
description: results matching criteria
content:
application/json:
schema:
$ref: '#/components/schemas/variantIdResponse'
'400':
description: something went wrong
content:
application/json:
schema:
$ref: '#/components/schemas/errorResponses'
'500':
description: Unexpected error
security:
- htsget_auth:
- read:genomic_variants
components:
schemas:
readIdResponse:
$ref: '#/components/schemas/htsgetResponse'
variantIdResponse:
$ref: '#/components/schemas/htsgetResponse'
commonRequestParameters:
- in: "path"
name: id
description: identifier of the variant object
required: true
schema:
type: string
- in: "query"
name: referenceName
description: VReference sequence name
example: "chr1"
required: false
schema:
type: string
- in: "query"
name: start
description: The start position of the range on the reference, 0-based, inclusive.
example: "12312"
required: false
schema:
type: integer
format: int64
minimum: 0
- in: "query"
name: end
description: The end position of the range on the reference, 0-based exclusive.
example: "99999"
required: false
schema:
type: integer
format: int64
minimum: 0
- in: "query"
name: tags
description: A comma separated list of tags to include, by default all.
example: "cancer,melanoma"
required: false
schema:
type: string
- in: "query"
name: notags
description: A comma separated list of tags to exclude, default none.
example: "normal,skin"
required: false
schema:
type: string
htsgetResponse:
type: object
properties:
htsget:
type: object
required:
- format
- urls
properties:
format:
type: string
example:
"BAM"
urls:
$ref: '#/components/schemas/htsgetUrlsHeaders'
md5:
type: string
example: "8a6049fad4943ff4c6de5c22df97d001"
htsgetUrlsHeaders:
type: array
example:
- url: "data:application/vnd.ga4gh.bam;base64,QkFNAQ=="
- url: "data:application/vnd.ga4gh.vcf;base64,QkFNAQ=="
headers:
"Authorization": "Bearer xxxxx"
"Range": "bytes=65536-1003750"
items:
$ref: '#/components/schemas/urlsItems'
urlsItems:
type: object
required:
- url
properties:
url:
type: string
headers:
type: object
# HTTP 400 errors
errorResponses:
oneOf:
- $ref: '#/components/schemas/UnsupportedFormat'
- $ref: '#/components/schemas/InvalidInput'
- $ref: '#/components/schemas/InvalidRange'
UnsupportedFormat:
description: The requested file format is not supported by the server
InvalidInput:
description: The request parameters do not adhere to the specification
InvalidRange:
description: The requested range cannot be satisfied
securitySchemes:
htsget_auth:
type: oauth2
flows:
authorizationCode:
authorizationUrl: https://example.com/api/oauth/dialog
tokenUrl: https://example.com/api/oauth/token
scopes:
read:genomic_reads: read access to genomic reads
read:genomic_variants: read access to genomic variants
Raw
htsget-openapi-nonfactored.yaml
openapi: 3.0.0
servers:
- description: htsget genomics api
url: https://virtserver.swaggerhub.com/brainkod/htsget/1.1.1
info:
description: "This data retrieval API bridges from existing genomics bulk data transfers to a client/server model"
version: "1.1.1"
title: htsget
contact:
name: GA4GH
email: security-notification@ga4gh.org
license:
name: GPLv3
paths:
/reads/{id}:
get:
summary: Gets the reads from a pre-indexed id
operationId: searchReadId
description: |
Searches a pre-indexed object id.
parameters:
- in: "path"
name: id
description: identifier of the read object
required: true
schema:
type: string
- in: "query"
name: format
description: File format, BAM (default), CRAM.
example: "BAM"
required: false
schema:
type: string
- in: "query"
name: referenceName
description: VReference sequence name
example: "chr1"
required: false
schema:
type: string
- in: "query"
name: start
description: The start position of the range on the reference, 0-based, inclusive.
example: "12312"
required: false
schema:
type: integer
format: int64
minimum: 0
- in: "query"
name: end
description: The end position of the range on the reference, 0-based exclusive.
example: "99999"
required: false
schema:
type: integer
format: int64
minimum: 0
- in: "query"
name: fields
description: A list of fields to include, such as QNAME, FLAG, RNAME, etc...
example: "fields=QNAME,RNAME"
required: false
schema:
enum:
- "QNAME"
- "FLAG"
- "RNAME"
- "POS"
- "MAPQ"
- "CIGAR"
- "RNEXT"
- "PNEXT"
- "TLEN"
- "SEQ"
- "QUAL"
type: string
- in: "query"
name: tags
description: A comma separated list of tags to include, by default all.
example: "cancer,melanoma"
required: false
schema:
type: string
- in: "query"
name: notags
description: A comma separated list of tags to exclude, default none.
example: "normal,healthy"
required: false
schema:
type: string
responses:
'200':
description: results matching criteria
content:
application/json:
schema:
$ref: '#/components/schemas/readIdResponse'
'400':
description: something went wrong
content:
application/json:
schema:
$ref: '#/components/schemas/errorResponses'
'500':
description: Unexpected error
security:
- htsget_auth:
- read:genomic_reads
/variants/{id}:
get:
summary: Gets the variants from a pre-indexed id
operationId: searchVariantId
description: |
Searches a pre-indexed object id.
parameters:
- in: "path"
name: id
description: identifier of the variant object
required: true
schema:
type: string
- in: "query"
name: format
description: File format, VCF (default), BCF.
example: "VCF"
required: false
schema:
type: string
- in: "query"
name: referenceName
description: VReference sequence name
example: "chr1"
required: false
schema:
type: string
- in: "query"
name: start
description: The start position of the range on the reference, 0-based, inclusive.
example: "12312"
required: false
schema:
type: integer
format: int64
minimum: 0
- in: "query"
name: end
description: The end position of the range on the reference, 0-based exclusive.
example: "99999"
required: false
schema:
type: integer
format: int64
minimum: 0
- in: "query"
name: fields
description: A list of variant fields to include, such as INFO, SAMPLE, FORMAT, etc.
example: "fields=INFO,SAMPLE"
required: false
schema:
enum:
- "INFO"
- "SAMPLE"
- "FILTER"
- "FORMAT"
- "ALT"
type: string
- in: "query"
name: tags
description: A comma separated list of tags to include, by default all.
example: "cancer,melanoma"
required: false
schema:
type: string
- in: "query"
name: notags
description: A comma separated list of tags to exclude, default none.
example: "normal,skin"
required: false
schema:
type: string
responses:
'200':
description: results matching criteria
content:
application/json:
schema:
$ref: '#/components/schemas/variantIdResponse'
'400':
description: something went wrong
content:
application/json:
schema:
$ref: '#/components/schemas/errorResponses'
'500':
description: Unexpected error
security:
- htsget_auth:
- read:genomic_variants
components:
schemas:
readIdResponse:
$ref: '#/components/schemas/htsgetResponse'
variantIdResponse:
$ref: '#/components/schemas/htsgetResponse'
htsgetResponse:
type: object
properties:
htsget:
type: object
required:
- format
- urls
properties:
format:
type: string
example:
"BAM"
urls:
$ref: '#/components/schemas/htsgetUrlsHeaders'
md5:
type: string
example: "8a6049fad4943ff4c6de5c22df97d001"
htsgetUrlsHeaders:
type: array
example:
- url: "data:application/vnd.ga4gh.bam;base64,QkFNAQ=="
- url: "data:application/vnd.ga4gh.vcf;base64,QkFNAQ=="
headers:
"Authorization": "Bearer xxxxx"
"Range": "bytes=65536-1003750"
items:
$ref: '#/components/schemas/urlsItems'
urlsItems:
type: object
required:
- url
properties:
url:
type: string
headers:
type: object
# HTTP 400 errors
errorResponses:
oneOf:
- $ref: '#/components/schemas/UnsupportedFormat'
- $ref: '#/components/schemas/InvalidInput'
- $ref: '#/components/schemas/InvalidRange'
UnsupportedFormat:
description: The requested file format is not supported by the server
InvalidInput:
description: The request parameters do not adhere to the specification
InvalidRange:
description: The requested range cannot be satisfied
securitySchemes:
htsget_auth:
type: oauth2
flows:
authorizationCode:
authorizationUrl: https://example.com/api/oauth/dialog
tokenUrl: https://example.com/api/oauth/token
scopes:
read:genomic_reads: read access to genomic reads
read:genomic_variants: read access to genomic variants
Raw
htsget-response-refactoring-ref-errors.yaml
openapi: 3.0.2
servers:
- description: WIP WIP WIP htsget genomics api WIP WIP WIP
url: https://virtserver.swaggerhub.com/brainkod/htsget/1.2.0
info:
description: "This data retrieval API bridges from existing genomics bulk data transfers to a client/server model"
version: "1.2.0"
title: htsget
contact:
name: GA4GH
email: security-notification@ga4gh.org
paths:
/reads/{id}:
get:
summary: Gets the reads from a pre-indexed id
operationId: searchReadId
description: |
Searches a pre-indexed object id.
parameters:
- in: "path"
name: id
description: identifier of the read object
required: true
schema:
type: string
- in: "query"
name: format
description: File format, BAM (default), CRAM.
example: "BAM"
required: false
schema:
type: string
- in: "query"
name: referenceName
description: Reference sequence name
example: "chr1"
required: false
schema:
type: string
- in: "query"
name: start
description: The start position of the range on the reference, 0-based, inclusive.
example: "12312"
required: false
schema:
type: integer
format: int64
minimum: 0
- in: "query"
name: end
description: The end position of the range on the reference, 0-based exclusive.
example: "99999"
required: false
schema:
type: integer
format: int64
minimum: 0
- in: "query"
name: fields
description: A list of fields to include, such as QNAME, FLAG, RNAME, etc...
example: "fields=QNAME,RNAME"
required: false
schema:
enum:
- "QNAME"
- "FLAG"
- "RNAME"
- "POS"
- "MAPQ"
- "CIGAR"
- "RNEXT"
- "PNEXT"
- "TLEN"
- "SEQ"
- "QUAL"
type: string
- in: "query"
name: tags
description: A comma separated list of tags to include, by default all.
example: "cancer,melanoma"
required: false
schema:
type: string
- in: "query"
name: notags
description: A comma separated list of tags to exclude, default none.
example: "normal,healthy"
required: false
schema:
type: string
# Cannot reuse those since responses does not accept $ref directly, yet:
# https://github.com/OAI/OpenAPI-Specification/issues/1586
responses:
'200':
$ref: '#/components/schemas/success'
'400':
$ref: '#/components/schemas/errors/Unspecified'
'401':
$ref: '#/components/schemas/errors/AuthInvalid'
'403':
$ref: '#/components/schemas/errors/AuthAccessDenied'
'404':
$ref: '#/components/schemas/errors/NotFound'
'500':
$ref: '#/components/schemas/errors/InternalServer'
default:
$ref: '#/components/schemas/errors/InternalServer'
security:
- htsget_auth:
- read:genomic_reads
/variants/{id}:
get:
summary: Gets the variants from a pre-indexed id
operationId: searchVariantId
description: Searches a pre-indexed object id.
parameters:
- in: "path"
name: id
description: identifier of the variant object
required: true
schema:
type: string
- in: "query"
name: format
description: File format, VCF (default), BCF.
example: "VCF"
required: false
schema:
type: string
- in: "query"
name: referenceName
description: Reference sequence name
example: "chr1"
required: false
schema:
type: string
- in: "query"
name: start
description: The start position of the range on the reference, 0-based, inclusive.
example: "12312"
required: false
schema:
type: integer
format: int64
minimum: 0
- in: "query"
name: end
description: The end position of the range on the reference, 0-based exclusive.
example: "99999"
required: false
schema:
type: integer
format: int64
minimum: 0
- in: "query"
name: tags
description: A comma separated list of tags to include, by default all.
example: "cancer,melanoma"
required: false
schema:
type: string
- in: "query"
name: notags
description: A comma separated list of tags to exclude, default none.
example: "normal,skin"
required: false
schema:
type: string
responses:
'200':
$ref: '#/components/schemas/success'
'400':
$ref: '#/components/schemas/errors/Unspecified'
'401':
$ref: '#/components/schemas/errors/AuthInvalid'
'403':
$ref: '#/components/schemas/errors/AuthAccessDenied'
'404':
$ref: '#/components/schemas/errors/NotFound'
'500':
$ref: '#/components/schemas/errors/InternalServer'
default:
$ref: '#/components/schemas/errors/InternalServer'
security:
- htsget_auth:
- read:genomic_variants
components:
schemas:
IdResponse:
$ref: '#/components/schemas/htsgetResponse'
htsgetResponse:
type: object
properties:
htsget:
type: object
required:
- format
- urls
properties:
format:
type: string
example:
"BAM"
urls:
$ref: '#/components/schemas/htsgetUrlsHeaders'
md5:
type: string
example: "8a6049fad4943ff4c6de5c22df97d001"
htsgetUrlsHeaders:
type: array
example:
- url: "data:application/vnd.ga4gh.vcf;base64,QkFNAQ=="
- url: "https://htsget.blocksrv.example/sample1234/run1.bam"
headers:
"Authorization": "Bearer xxxxx"
"Range": "bytes=65536-1003750"
items:
$ref: '#/components/schemas/urlsItems'
urlsItems:
type: object
required:
- url
properties:
url:
type: string
headers:
type: object
success:
description: results matching criteria
content:
application/json:
schema:
$ref: '#/components/schemas/IdResponse'
example:
{
"htsget" : {
"format" : "BAM",
"urls" : [
{
"url" : "https://htsget.blocksrv.example/sample1234/run1.bam",
"headers" : {
"Authorization" : "Bearer xxxx",
"Range" : "bytes=2744831-9375732"
},
"class" : "body"
}
]
}
}
errors:
UnsupportedFormat:
description: The requested file format is not supported by the server
InvalidInput:
description: The request parameters do not adhere to the specification
InvalidRange:
description: The requested range cannot be satisfied
AuthInvalid:
description: Authorization provided is invalid
AuthAccessDenied:
description: Authorization is required to access the resource
NotFound:
description: Authorization is required to access the resource
InternalServer:
description: Internal Server Error
Unspecified:
description: Something went wrong
content:
application/json:
schema:
oneOf:
- $ref: '#/components/schemas/errors/UnsupportedFormat'
- $ref: '#/components/schemas/errors/InvalidInput'
- $ref: '#/components/schemas/errors/InvalidRange'
securitySchemes:
htsget_auth:
type: oauth2
flows:
authorizationCode:
authorizationUrl: https://example.com/api/oauth/dialog
tokenUrl: https://example.com/api/oauth/token
scopes:
read:genomic_reads: read access to genomic reads
read:genomic_variants: read access to genomic variants
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