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brapi.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:
/calls:
get:
tags:
- Calls
summary: Get the list of implemented Calls
description: " Implementation Notes\nHaving a consistent structure for the path\
\ string of each call is very important for teams to be able to connect and\
\ find errors. Read more on Github.\nHere are the rules for the path of each\
\ call that should be returned\n\n\n\nEvery word in the call path should match\
\ the documentation exactly, both in spelling and capitalization. Note that\
\ path strings are all lower case, but path parameters are camel case.\n\n\
Each path should start relative to \"/\" and therefore should not include\
\ \"/\"\n\nNo leading or trailing slashes (\"/\") \n\nPath parameters are\
\ wrapped in curly braces (\"{}\"). The name of the path parameter should\
\ be spelled exactly as it is specified in the documentation.\n\n\n\n\nExamples\
\ GOOD \"call\": \"germplasm/{germplasmDbId}/markerprofiles\" BAD \"\
call\": \"germplasm/{id}/markerprofiles\" BAD \"call\": \"germplasm/{germplasmDbId}/markerProfiles\"\
\ BAD \"call\": \"germplasm/{germplasmdbid}/markerprofiles\" BAD \"\
call\": \"brapi/v1/germplasm/{germplasmDbId}/markerprofiles\" BAD \"call\"\
: \"/germplasm/{germplasmDbId}/markerprofiles/\" BAD \"call\": \"germplasm/<germplasmDbId>/markerprofiles\"\
\n\n\n\ntest-server.brapi.org/brapi/v1/calls"
parameters:
- name: datatype
in: query
description: DEPRECATED in v1.3 - see dataType (camel case)
required: false
deprecated: true
style: form
explode: true
schema:
type: string
- name: dataType
in: query
description: 'The data format supported by the call. Example: `json`'
required: false
style: form
explode: true
schema:
$ref: '#/components/schemas/WSMIMEDataTypes'
- name: page
in: query
description: Which result page is requested. The page indexing starts at 0
(the first page is 'page'= 0). Default is `0`.
required: false
style: form
explode: true
schema:
type: integer
example: "0"
- name: pageSize
in: query
description: The size of the pages to be returned. Default is `1000`.
required: false
style: form
explode: true
schema:
type: integer
example: 1000
- name: Authorization
in: header
description: "HTTP HEADER - Token used for Authorization \n\n<strong>Bearer\
\ {token_string} </strong>"
required: false
style: simple
explode: false
schema:
pattern: ^Bearer .*$
type: string
example: Bearer XXXX
responses:
200:
description: OK
content:
application/json:
schema:
$ref: '#/components/schemas/callsResponse'
example:
metadata:
datafiles: []
pagination:
currentPage: 0
pageSize: 2
totalCount: 103
totalPages: 52
status: []
result:
data:
- call: allelematrices
dataTypes:
- application/json
datatypes:
- application/json
methods:
- GET
versions:
- "1.0"
- "1.1"
- "1.2"
- "1.3"
- call: allelematrices-search
dataTypes:
- application/json
datatypes:
- application/json
methods:
- GET
- POST
versions:
- "1.2"
- "1.3"
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
/commoncropnames:
get:
tags:
- Crops
summary: Get the Common Crop Names
description: "List the common crop names for the crops available in a database\
\ server. \n\nThis call is **required** for multi-crop systems where data\
\ from multiple crops may be stored in the same database server. A distinct\
\ database server is defined by everything in the URL before \"/brapi/v1\"\
, including host name and base path. \n\nThis call is recommended for single\
\ crop systems to be compatible with multi-crop clients. For a single crop\
\ system the response should contain an array with exactly 1 element. \n\n\
The common crop name can be used as a search parameter for Programs, Studies,\
\ and Germplasm.\n\n\ntest-server.brapi.org/brapi/v1/commonCropNames"
parameters:
- 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/commonCropNamesResponse'
example:
metadata:
datafiles: []
pagination:
currentPage: 0
pageSize: 2
totalCount: 2
totalPages: 1
status: []
result:
data:
- Tomatillo
- Paw Paw
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
/crops:
get:
tags:
- Crops
- Deprecated
summary: List supported crops
description: |-
For multi crop systems this is a useful call to list all the supported crops.
test-server.brapi.org/brapi/v1/crops
parameters:
- 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/cropsResponse'
example:
metadata:
datafiles: []
pagination:
currentPage: 2
pageSize: 1000
totalCount: 2
totalPages: 1
status: []
result:
data: []
deprecated: true
/events:
get:
summary: Get the Events
description: Get list of events (backported from BrAPI Phenotyping v2.0)
parameters:
- description: Filter based on study unique identifier in which the events occured
in: query
name: studyDbId
required: false
schema:
type: string
- description: Filter based on an ObservationUnit unique identifier in which the events occured
in: query
name: observationUnitDbId
required: false
schema:
type: string
- description: Filter based on an Event DbId
in: query
name: eventDbId
required: false
schema:
type: string
- description: Filter based on an Event Type
in: query
name: eventType
required: false
schema:
type: string
- description: Filter based on an Date Range
in: query
name: dateRangeStart
required: false
schema:
type: string
format: date-time
- description: Filter based on an Date Range
in: query
name: dateRangeEnd
required: false
schema:
type: string
format: date-time
- $ref: '#/components/parameters/page'
- $ref: '#/components/parameters/pageSize'
- $ref: '#/components/parameters/authorizationHeader'
responses:
'200':
content:
application/json:
schema:
properties:
'@context':
$ref: '#/components/schemas/Context'
metadata:
$ref: '#/components/schemas/metadata'
result:
properties:
data:
items:
$ref: '#/components/schemas/Event'
type: array
required:
- data
type: object
required:
- metadata
- result
title: eventsResponse
type: object
description: OK
headers: {}
'400':
$ref: '#/components/responses/400BadRequest'
'401':
$ref: '#/components/responses/401Unauthorized'
'403':
$ref: '#/components/responses/403Forbidden'
tags:
- Events
/germplasm:
get:
tags:
- Germplasm
summary: Get the Germplasm
description: "Addresses these needs\n\n- General germplasm search mechanism\
\ that accepts POST for complex queries \n\n- Possibility to search germplasm\
\ by more parameters than those allowed by the existing germplasm search \n\
\n- Possibility to get MCPD details by PUID rather than dbId"
parameters:
- name: germplasmPUI
in: query
description: Permanent unique identifier (DOI, URI, etc.)
required: false
style: form
explode: true
schema:
type: string
- name: germplasmDbId
in: query
description: Internal database identifier
required: false
style: form
explode: true
schema:
type: string
- name: germplasmName
in: query
description: Name of the germplasm
required: false
style: form
explode: true
schema:
type: string
- name: commonCropName
in: query
description: The common crop name related to this germplasm
required: false
style: form
explode: true
schema:
type: string
- name: page
in: query
description: Which result page is requested. The page indexing starts at 0
(the first page is 'page'= 0). Default is `0`.
required: false
style: form
explode: true
schema:
type: integer
example: "0"
- name: pageSize
in: query
description: The size of the pages to be returned. Default is `1000`.
required: false
style: form
explode: true
schema:
type: integer
example: 1000
- name: Authorization
in: header
description: "HTTP HEADER - Token used for Authorization \n\n<strong>Bearer\
\ {token_string} </strong>"
required: false
style: simple
explode: false
schema:
pattern: ^Bearer .*$
type: string
example: Bearer XXXX
responses:
200:
description: OK
content:
application/json:
schema:
$ref: '#/components/schemas/germplasmResponse'
example:
metadata:
datafiles: []
pagination:
currentPage: 0
pageSize: 2
totalCount: 2
totalPages: 1
status: []
result:
data:
- accessionNumber: A000003
acquisitionDate: 2001-01-01
biologicalStatusOfAccessionCode: 500
breedingMethodDbId: bm1
commonCropName: G000003
countryOfOriginCode: COUNTRY1
defaultDisplayName: G000003
documentationURL: https://brapi.org
donors: []
genus: Fructus
germplasmDbId: "3"
germplasmGenus: Fructus
germplasmName: Name003
germplasmPUI: http://pui.per/accession/A000003
germplasmSpecies: novus
instituteCode: PER001
instituteName: INST1
pedigree: A000001/A000002
seedSource: A000001/A000002
species: novus
speciesAuthority: L
subtaxa: subtaxa
subtaxaAuthority: N
synonyms:
- variety 1
taxonIds:
- sourceName: ncbiTaxon
taxonId: "2340"
- sourceName: ciradTaxon
taxonId: E312
typeOfGermplasmStorageCode: []
- accessionNumber: A000004
acquisitionDate: 2001-01-01
biologicalStatusOfAccessionCode: 500
breedingMethodDbId: bm1
commonCropName: G000004
countryOfOriginCode: COUNTRY1
defaultDisplayName: G000004
documentationURL: https://brapi.org
donors: []
genus: Fructus
germplasmDbId: "4"
germplasmGenus: Fructus
germplasmName: Name004
germplasmPUI: http://pui.per/accession/A000004
germplasmSpecies: novus
instituteCode: PER001
instituteName: INST1
pedigree: A000001/A000003
seedSource: open pollination
species: novus
speciesAuthority: L
subtaxa: subtaxa
subtaxaAuthority: N
synonyms:
- variety 4
taxonIds:
- sourceName: ncbiTaxon
taxonId: "2340"
- sourceName: ciradTaxon
taxonId: E312
typeOfGermplasmStorageCode: []
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
/locations:
get:
tags:
- Locations
summary: Get the Locations
description: |-
Implemented by: Germinate
Get a list of locations.
* The `countryCode` is as per [ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3) spec.
* `altitude` is in meters.
**Note**: Consider revising to describe polygon lat/lan points and check if adopting http://geojson.org/ is worth doing for v1.
parameters:
- name: locationType
in: query
description: Filter by location type specified.
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/locationsResponse'
example:
metadata:
datafiles: []
pagination:
currentPage: 0
pageSize: 2
totalCount: 17
totalPages: 9
status: []
result:
data:
- abbreviation: L1
abreviation: L1
additionalInfo:
adm1: Junin
adm2: Chanchamayo
adm3: San Ramon
annualMeanTemperature: "23"
annualTotalPrecipitation: "360"
cont: South America
creg: LAC
local: San Ramon
altitude: 828
countryCode: PER
countryName: Peru
documentationURL: https://brapi.org
instituteAddress: 71 Pilgrim Avenue Chevy Chase MD 20815
instituteAdress: 71 Pilgrim Avenue Chevy Chase MD 20815
instituteName: Plant Science Institute
latitude: -11.1274995803833
locationDbId: "1"
locationName: Location 1
locationType: Storage location
longitude: -75.35639190673828
name: Location 1
- abbreviation: L2
abreviation: L2
additionalInfo: {}
altitude: 964
countryCode: PER
countryName: Peru
documentationURL: https://brapi.org
instituteAddress: 71 Pilgrim Avenue Chevy Chase MD 20815
instituteAdress: 71 Pilgrim Avenue Chevy Chase MD 20815
instituteName: Plant Science Institute
latitude: -11.161160469055176
locationDbId: "2"
locationName: Location 2
locationType: Breeding location
longitude: -75.34171295166016
name: Location 2
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
/locations/{locationDbId}:
get:
tags:
- Locations
summary: Get the details of a specific Location
description: |-
Get details for a location.
- The `countryCode` is as per [ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3) spec.
- `altitude` is in meters.
parameters:
- name: locationDbId
in: path
description: The internal DB id for a location
required: true
style: simple
explode: false
schema:
type: string
- 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/locationResponse'
example:
metadata:
datafiles: []
pagination:
currentPage: 0
pageSize: 0
totalCount: 0
totalPages: 0
status: []
result:
abbreviation: L1
abreviation: L1
additionalInfo:
adm1: Junin
adm2: Chanchamayo
adm3: San Ramon
annualMeanTemperature: "23"
annualTotalPrecipitation: "360"
cont: South America
creg: LAC
local: San Ramon
altitude: 828
countryCode: PER
countryName: Peru
documentationURL: https://brapi.org
instituteAddress: 71 Pilgrim Avenue Chevy Chase MD 20815
instituteAdress: 71 Pilgrim Avenue Chevy Chase MD 20815
instituteName: Plant Science Institute
latitude: -11.1274995803833
locationDbId: "1"
locationName: Location 1
locationType: Storage location
longitude: -75.35639190673828
name: Location 1
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
404:
description: Not Found
content:
application/json:
schema:
type: string
example: ERROR - 2018-10-08T20:15:11Z - The requested object DbId is
not found
/observationunits:
get:
tags:
- Observations
summary: Get the Observation Units
description: Get a set of observation units
parameters:
- name: germplasmDbId
in: query
description: The unique ID of a germplasm (accession) to filter on
required: false
style: form
explode: true
schema:
type: string
- name: observationVariableDbId
in: query
description: The unique ID of an observation variable
required: false
style: form
explode: true
schema:
type: string
- name: studyDbId
in: query
description: The unique ID of a studies to filter on
required: false
style: form
explode: true
schema:
type: string
- name: locationDbId
in: query
description: The unique ID of a location where these observations were collected
required: false
style: form
explode: true
schema:
type: string
- name: trialDbId
in: query
description: The unique ID of a trial to filter on
required: false
style: form
explode: true
schema:
type: string
- name: programDbId
in: query
description: The unique ID of a program to filter on
required: false
style: form
explode: true
schema:
type: string
- name: seasonDbId
in: query
description: The year or Phenotyping campaign of a multi-annual study (trees,
grape, ...)
required: false
style: form
explode: true
schema:
type: string
- name: observationUnitDbId
in: query
description: unique ID of an observationUnit to filter on
required: false
style: form
explode: true
schema:
type: string
- name: observationLevel
in: query
description: The type of the observationUnit. Returns only the observation
unit of the specified type; the parent levels ID can be accessed through
observationUnitStructure.
required: false
style: form