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brapi_complete.yaml
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brapi_complete.yaml
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openapi: 3.0.0
info:
title: BrAPI
description: |-
The Breeding API (BrAPI) is a Standardized RESTful Web Service API Specification for communicating Plant Breeding Data. BrAPI allows for easy data sharing between databases and tools involved in plant breeding.
<strong>General Reference Documentation</strong>
<a href="https://github.com/plantbreeding/API/blob/master/Specification/GeneralInfo/URL_Structure.md">URL Structure</a>
<a href="https://github.com/plantbreeding/API/blob/master/Specification/GeneralInfo/Response_Structure.md">Response Structure</a>
<a href="https://github.com/plantbreeding/API/blob/master/Specification/GeneralInfo/Date_Time_Encoding.md">Date/Time Encoding</a>
<a href="https://github.com/plantbreeding/API/blob/master/Specification/GeneralInfo/Location_Encoding.md">Location Encoding</a>
<a href="https://github.com/plantbreeding/API/blob/master/Specification/GeneralInfo/Error_Handling.md">Error Handling</a>
<a href="https://github.com/plantbreeding/API/blob/master/Specification/GeneralInfo/Search_Services.md">Search Services</a>
<a href="https://github.com/plantbreeding/API/blob/master/Specification/GeneralInfo/Asychronous_Processing.md">Asynchronous Processing</a>
version: "1.3"
servers:
- url: http://localhost:5000/brapi/v1
#security:
#- AuthorizationToken: []
tags:
- name: Calls
description: Check the available calls on a server
externalDocs:
description: Docs
url: https://wiki.brapi.org/
- name: Crops
description: Information about Crops
externalDocs:
description: Docs
url: https://wiki.brapi.org/
- name: Programs
description: Information about Programs
externalDocs:
description: Docs
url: https://wiki.brapi.org/
- name: Locations
description: Information about Locations
externalDocs:
description: Docs
url: https://wiki.brapi.org/
- name: Trials
description: Information about Trials
externalDocs:
description: Docs
url: https://wiki.brapi.org/
- name: Studies
description: Information about Studies
externalDocs:
description: Docs
url: https://wiki.brapi.org/
- name: Observations
description: Information about Observations
externalDocs:
description: Docs
url: https://wiki.brapi.org/
- name: Observation Variables
description: API to retrieve list and details of observation variables. An observation
variable is composed by the unique combination of one Trait, one Method and one
Scale.
externalDocs:
description: Docs
url: https://wiki.brapi.org/
- name: Phenotypes
description: Information about Phenotypes
externalDocs:
description: Docs
url: https://wiki.brapi.org/
- name: Germplasm
description: Information about Germplasm
externalDocs:
description: Docs
url: https://wiki.brapi.org/
- name: Germplasm Attributes
description: Information about Germplasm Attributes
externalDocs:
description: Docs
url: https://wiki.brapi.org/
- name: Markers
description: Information about Markers
externalDocs:
description: Docs
url: https://wiki.brapi.org/
- name: Marker Profiles
description: Information about Marker Profiles
externalDocs:
description: Docs
url: https://wiki.brapi.org/
- name: Genome Maps
description: Information about Genome Maps
externalDocs:
description: Docs
url: https://wiki.brapi.org/
- name: Samples
description: Information about Samples
externalDocs:
description: Docs
url: https://wiki.brapi.org/
- name: Vendor
description: |-
This interface is specific to facilities that performs an external analysis, such as genotyping facilities. The interface should be implemented by that facility's server. The breeding database is the client of this interface.
Note that to use these calls, you likely have to use the authentication call prior to connecting (see Authentication best practices).
externalDocs:
description: Docs
url: https://wiki.brapi.org/
- name: Lists
description: Create and manipulate generic lists
externalDocs:
description: Docs
url: https://wiki.brapi.org/
- name: Images
description: Create and manipulate image data
externalDocs:
description: Docs
url: https://wiki.brapi.org/
- name: People
description: Create and manipulate information about people
externalDocs:
description: Docs
url: https://wiki.brapi.org/
- name: Search Services
description: The available Search Services for finding data
externalDocs:
description: Docs
url: https://wiki.brapi.org/
- name: Authentication
description: Authenticacte your requests
externalDocs:
description: Docs
url: https://wiki.brapi.org/
- name: Deprecated
description: Deprecated Calls
externalDocs:
description: Docs
url: https://wiki.brapi.org/
paths:
/allelematrices:
get:
tags:
- Marker Profiles
summary: Get the Allele Matrix summaries
description: |-
This resource is used for reading and writing genomic matrices
GET provides a list of available matrices, optionally filtered by study;
parameters:
- name: studyDbId
in: query
description: restricts the list of matrices to a specific study.
required: true
style: form
explode: true
schema:
type: string
- name: page
in: query
description: Which result page is requested. The page indexing starts at 0
(the first page is 'page'= 0). Default is `0`.
required: false
style: form
explode: true
schema:
type: integer
example: "0"
- name: pageSize
in: query
description: The size of the pages to be returned. Default is `1000`.
required: false
style: form
explode: true
schema:
type: integer
example: 1000
- name: Authorization
in: header
description: "HTTP HEADER - Token used for Authorization \n\n<strong>Bearer\
\ {token_string} </strong>"
required: false
style: simple
explode: false
schema:
pattern: ^Bearer .*$
type: string
example: Bearer XXXX
responses:
200:
description: OK
content:
application/json:
schema:
$ref: '#/components/schemas/alleleMatrixDetailsResponse'
example:
metadata:
datafiles: []
pagination:
currentPage: 0
pageSize: 2
totalCount: 1
totalPages: 1
status: []
result:
data:
- description: example matrix
lastUpdated: 2018-05-03T11:03:56-04:00
matrixDbId: mat1
matrixName: Example Matrix
name: Example Matrix
studyDbId: "1001"
400:
description: Bad Request
content:
application/json:
schema:
type: string
example: |-
ERROR - 2018-10-08T20:15:11Z - Malformed JSON Request Object
ERROR - 2018-10-08T20:15:11Z - Invalid query parameter
ERROR - 2018-10-08T20:15:11Z - Required parameter is missing
401:
description: Unauthorized
content:
application/json:
schema:
type: string
example: ERROR - 2018-10-08T20:15:11Z - Missing or expired authorization
token
403:
description: Forbidden
content:
application/json:
schema:
type: string
example: ERROR - 2018-10-08T20:15:11Z - User does not have permission
to perform this action
/allelematrices-search:
get:
tags:
- Marker Profiles
summary: Get the a Matrix of Allele data
description: |-
See Search Services for additional implementation details.
This uses a more efficient data structure and pagination for large number of markers.
See Search Services for additional implementation details.
Use GET when parameter size is less than 2K bytes.
This method may support asynchronous processing.
parameters:
- name: markerprofileDbId
in: query
description: DEPRECATED in v1.3 - see "markerProfileDbId" (camel case)
required: false
style: form
explode: true
schema:
type: array
items:
type: string
- name: markerProfileDbId
in: query
description: The marker Profile db ids. Not Required if 'markerDbId' or 'matrixDbId'
is present.
required: false
style: form
explode: true
schema:
type: array
items:
type: string
- name: markerDbId
in: query
description: ids of the markers. if none are specified, results are returned
for all markers in the database. Not Required if 'markerProfileDbId' or
'matrixDbId' is present.
required: false
style: form
explode: true
schema:
type: array
items:
type: string
- name: matrixDbId
in: query
required: false
style: form
explode: true
schema:
type: array
items:
type: string
- name: format
in: query
description: format for the datafile to be downloaded. tsv and csv currently
supported; flapjack may be supported.
required: false
style: form
explode: true
schema:
type: string
- name: expandHomozygotes
in: query
description: Should homozygotes NOT be collapsed into a single occurrence?
required: false
style: form
explode: true
schema:
type: boolean
- name: unknownString
in: query
description: The string to use as a representation for missing data or the
reserved word "empty_string".
required: false
style: form
explode: true
schema:
type: string
- name: sepPhased
in: query
description: The string to use as a separator for phased allele calls or the
reserved word "empty_string".
required: false
style: form
explode: true
schema:
type: string
- name: sepUnphased
in: query
description: The string to use as a separator for unphased allele calls or
the reserved word "empty_string".
required: false
style: form
explode: true
schema:
type: string
- name: page
in: query
description: Which result page is requested. The page indexing starts at 0
(the first page is 'page'= 0). Default is `0`.
required: false
style: form
explode: true
schema:
type: integer
example: "0"
- name: pageSize
in: query
description: The size of the pages to be returned. Default is `1000`.
required: false
style: form
explode: true
schema:
type: integer
example: 1000
- name: Authorization
in: header
description: "HTTP HEADER - Token used for Authorization \n\n<strong>Bearer\
\ {token_string} </strong>"
required: false
style: simple
explode: false
schema:
pattern: ^Bearer .*$
type: string
example: Bearer XXXX
responses:
200:
description: OK
content:
application/json:
schema:
$ref: '#/components/schemas/alleleMatrixValuesResponse'
example:
metadata:
datafiles: []
pagination:
currentPage: 0
pageSize: 2
totalCount: 280
totalPages: 140
status: []
result:
data:
- - mr01
- P1
- A
- - mr02
- P1
- C
400:
description: Bad Request
content:
application/json:
schema:
type: string
example: |-
ERROR - 2018-10-08T20:15:11Z - Malformed JSON Request Object
ERROR - 2018-10-08T20:15:11Z - Invalid query parameter
ERROR - 2018-10-08T20:15:11Z - Required parameter is missing
401:
description: Unauthorized
content:
application/json:
schema:
type: string
example: ERROR - 2018-10-08T20:15:11Z - Missing or expired authorization
token
403:
description: Forbidden
content:
application/json:
schema:
type: string
example: ERROR - 2018-10-08T20:15:11Z - User does not have permission
to perform this action
post:
tags:
- Marker Profiles
summary: Submit a request to get a Matrix of Allele data
description: |-
See Search Services for additional implementation details.
This uses a more efficient data structure and pagination for large number of markers.
Use POST when parameter size is greater than 2K bytes.
- If no format is specified, this call returns the data in JSON form.
- If a format (other than JSON) is specified and the server supports this format, it will return the link to the exported data file in the "datafiles" field of the "metadata".
- If more than one format is requested at a time, the server will throw a "501 Not Implemented" error.
The format of the tsv response can be found on GitHub (https://github.com/plantbreeding/Documentation/wiki/BrAPI-TSV-Expected-Formats)'
parameters:
- name: Authorization
in: header
description: "HTTP HEADER - Token used for Authorization \n\n<strong>Bearer\
\ {token_string} </strong>"
required: false
style: simple
explode: false
schema:
pattern: ^Bearer .*$
type: string
example: Bearer XXXX
requestBody:
description: The marker profile db ids. Not Required if 'markerDbId' or 'matrixDbId'
is present.
content:
application/json:
schema:
$ref: '#/components/schemas/alleleMatrixSearchRequest'
required: true
responses:
200:
description: OK
content:
application/json:
schema:
$ref: '#/components/schemas/alleleMatrixValuesResponse'
example:
metadata:
asynchStatus:
asynchId: ""
endTime: 2018-12-05
percentComplete: 100
startTime: 2018-12-05
status: FINISHED
datafiles: []
pagination:
currentPage: 0
pageSize: 2
totalCount: 280
totalPages: 140
status: []
result:
data:
- - mr01
- P1
- A
- - mr02
- P1
- C
application/tsv:
example:
metadata:
datafiles:
- https://my-fancy-server/files/allelematrix-1234.tsv
pagination:
currentPage: 0
pageSize: 0
totalCount: 0
totalPages: 0
status: []
result:
data: []
400:
description: Bad Request
content:
application/json:
schema:
type: string
example: |-
ERROR - 2018-10-08T20:15:11Z - Malformed JSON Request Object
ERROR - 2018-10-08T20:15:11Z - Invalid query parameter
ERROR - 2018-10-08T20:15:11Z - Required parameter is missing
401:
description: Unauthorized
content:
application/json:
schema:
type: string
example: ERROR - 2018-10-08T20:15:11Z - Missing or expired authorization
token
403:
description: Forbidden
content:
application/json:
schema:
type: string
example: ERROR - 2018-10-08T20:15:11Z - User does not have permission
to perform this action
/allelematrix-search:
get:
tags:
- Marker Profiles
- Deprecated
summary: Scores through GET
description: "Status: ACCEPTED.\n\nImplemented by: Germinate (POST only), Cassavabase\n\
\nUsed by: Flapjack (POST only)\n\nSee Search Services for additional implementation\
\ details.\n\nThis uses a more efficient data structure and pagination for\
\ large number of markers.\n\nSee Search Services for additional implementation\
\ details.\n\n\n\nThis uses a more efficient data structure and pagination\
\ for large number of markers. \n\n\n\nUse GET when parameter size is less\
\ than 2K bytes.\nThis method may support asynchronous processing."
parameters:
- name: markerprofileDbId
in: query
description: The marker profile db ids. Not Required if 'markerDbId' or 'matrixDbId'
is present.
required: false
style: form
explode: true
schema:
type: array
items:
type: string
- name: markerDbId
in: query
description: ids of the markers. if none are specified, results are returned
for all markers in the database. Not Required if 'markerprofileDbId' or
'matrixDbId' is present.
required: false
style: form
explode: true
schema:
type: array
items:
type: string
- name: matrixDbId
in: query
required: false
style: form
explode: true
schema:
type: array
items:
type: string
- name: format
in: query
description: format for the datafile to be downloaded. tsv and csv currently
supported; flapjack may be supported.
required: false
style: form
explode: true
schema:
type: string
- name: expandHomozygotes
in: query
description: Should homozygotes NOT be collapsed into a single occurrence?
required: false
style: form
explode: true
schema:
type: boolean
- name: unknownString
in: query
description: The string to use as a representation for missing data or the
reserved word "empty_string".
required: false
style: form
explode: true
schema:
type: string
- name: sepPhased
in: query
description: The string to use as a separator for phased allele calls or the
reserved word "empty_string".
required: false
style: form
explode: true
schema:
type: string
- name: sepUnphased
in: query
description: The string to use as a separator for unphased allele calls or
the reserved word "empty_string".
required: false
style: form
explode: true
schema:
type: string
- name: page
in: query
description: Which result page is requested. The page indexing starts at 0
(the first page is 'page'= 0). Default is `0`.
required: false
style: form
explode: true
schema:
type: integer
example: "0"
- name: pageSize
in: query
description: The size of the pages to be returned. Default is `1000`.
required: false
style: form
explode: true
schema:
type: integer
example: 1000
responses:
200:
description: OK
content:
application/json:
schema:
$ref: '#/components/schemas/alleleMatrixValuesResponse_1'
example:
metadata:
asynchStatus:
asynchId: ""
endTime: 2018-12-05
percentComplete: 100
startTime: 2018-12-05
status: FINISHED
datafiles: []
pagination:
currentPage: 0
pageSize: 2
totalCount: 280
totalPages: 140
status: []
result:
data:
- - mr01
- P1
- A
- - mr02
- P1
- C
deprecated: true
post:
tags:
- Marker Profiles
- Deprecated
summary: Scores through POST
description: |-
Status: ACCEPTED.
Implemented by: Germinate (POST only), Cassavabase
Used by: Flapjack (POST only)
See Search Services for additional implementation details.
This uses a more efficient data structure and pagination for large number of markers.
Use POST when parameter size is greater than 2K bytes.
- If no format is specified, this call returns the data in JSON form.
- If a format (other than JSON) is specified and the server supports this format, it will return the link to the exported data file in the "datafiles" field of the "metadata".
- If more than one format is requested at a time, the server will throw a "501 Not Implemented" error.
The format of the tsv response can be found on GitHub (https://github.com/plantbreeding/Documentation/wiki/BrAPI-TSV-Expected-Formats)
requestBody:
description: The markerprofile db ids. Not Required if 'markerDbId' or 'matrixDbId'
is present.
content:
application/json:
schema:
$ref: '#/components/schemas/alleleMatrixSearchRequest'
required: true
responses:
200:
description: OK
content:
application/json:
schema:
$ref: '#/components/schemas/alleleMatrixValuesResponse_1'
example:
metadata:
datafiles: []
pagination:
currentPage: 0
pageSize: 1000
totalCount: 280
totalPages: 1
status: []
result:
data:
- - mr01
- P1
- A
- - mr02
- P1
- C
- - mr03
- P1
- A
- - mr04
- P1
- G
- - mr05
- P1
- C
- - mr06
- P1
- A
- - mr07
- P1
- G
- - mr08
- P1
- G
- - mr09
- P1
- T
- - mr10
- P1
- C
- - mr11
- P1
- G
- - mr12
- P1
- C
- - mr13
- P1
- A
- - mr14
- P1
- G
- - mr15
- P1
- T
- - mr16
- P1
- C
- - mr17
- P1
- A
- - mr18
- P1
- G
- - mr19
- P1
- T
- - mr20
- P1
- T
- - mr01
- P2
- C
- - mr02
- P2
- C
- - mr03
- P2
- C
- - mr04
- P2
- C
- - mr05
- P2
- C
- - mr06
- P2
- G
- - mr07
- P2
- G
- - mr08
- P2
- A
- - mr09
- P2
- A
- - mr10
- P2
- C
- - mr11
- P2
- C
- - mr12
- P2
- A
- - mr13
- P2
- A
- - mr14
- P2
- T
- - mr15
- P2
- T
- - mr16
- P2
- T
- - mr17
- P2
- G
- - mr18
- P2
- G
- - mr19
- P2
- A
- - mr20
- P2
- T
- - mr01
- F1-02
- A/C
- - mr02
- F1-02
- C
- - mr03
- F1-02
- '-'
- - mr04
- F1-02
- '-'
- - mr05
- F1-02
- '-'
- - mr06
- F1-02
- '-'
- - mr07
- F1-02
- '-'
- - mr08
- F1-02
- '-'
- - mr09
- F1-02
- '-'
- - mr10
- F1-02
- '-'
- - mr11
- F1-02
- '-'
- - mr12
- F1-02
- '-'
- - mr13
- F1-02
- '-'
- - mr14
- F1-02
- G/T
- - mr15
- F1-02
- T
- - mr16
- F1-02
- C/T
- - mr17
- F1-02
- A/G
- - mr18
- F1-02
- G
- - mr19
- F1-02
- T/A
- - mr20
- F1-02
- T
- - mr01
- F1-03
- A/C
- - mr02
- F1-03
- C
- - mr03
- F1-03
- A/C
- - mr04
- F1-03
- G/C
- - mr05
- F1-03
- C
- - mr06
- F1-03
- A/G
- - mr07
- F1-03
- G
- - mr08
- F1-03
- G/A
- - mr09
- F1-03
- T/A
- - mr10
- F1-03
- C
- - mr11
- F1-03
- C/G
- - mr12
- F1-03
- A/C
- - mr13
- F1-03
- A
- - mr14
- F1-03
- G/T
- - mr15
- F1-03
- T
- - mr16
- F1-03
- C/T
- - mr17
- F1-03
- A/G
- - mr18
- F1-03
- G
- - mr19
- F1-03
- T/A
- - mr20
- F1-03
- T
- - mr01
- F1-04
- A
- - mr02
- F1-04
- C
- - mr03
- F1-04
- A
- - mr04
- F1-04
- G
- - mr05
- F1-04
- C
- - mr06
- F1-04
- A
- - mr07
- F1-04
- G
- - mr08
- F1-04
- G
- - mr09
- F1-04
- T
- - mr10
- F1-04
- C
- - mr11
- F1-04
- G
- - mr12
- F1-04
- C
- - mr13
- F1-04
- A
- - mr14