/brapi-r-v2

Test openapi generation of brapi R client

Primary LanguageR

R API client for openapi

The Breeding API (BrAPI) is a Standardized REST ful Web Service API Specification for communicating Plant Breeding Data. BrAPI allows for easy data sharing between databases and tools involved in plant breeding.

General Reference Documentation

URL Structure
Response Structure
Date/Time Encoding
Location Encoding
Error Handling
Search Services

BrAPI Core

The BrAPI Core module contains high level entities used for organization and management. This includes Programs, Trials, Studies, Locations, People, and Lists
V2.0
GitHub
SwaggerHub
Apiary

BrAPI Phenotyping

The BrAPI Phenotyping module contains entities related to phenotypic observations. This includes Observation Units, Observations, Observation Variables, Traits, Scales, Methods, and Images
V2.0
GitHub
SwaggerHub
Apiary

BrAPI Genotyping

The BrAPI Genotyping module contains entities related to genotyping analysis. This includes Samples, Markers, Variant Sets, Variants, Call Sets, Calls, References, Reads, and Vendor Orders
V2.0
GitHub
SwaggerHub
Apiary

BrAPI Germplasm

The BrAPI Germplasm module contains entities related to germplasm management. This includes Germplasm, Germplasm Attributes, Seed Lots, Crosses, Pedigree, and Progeny
V2.0
GitHub
SwaggerHub
Apiary
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Overview

This API client was generated by the OpenAPI Generator project. By using the OpenAPI spec from a remote server, you can easily generate an API client.

  • API version: 2.0
  • Package version: 1.0.0
  • Build package: org.openapitools.codegen.languages.RClientCodegen

Installation

Prerequisites

Install the dependencies

install.packages("jsonlite")
install.packages("httr")
install.packages("base64enc")

Build the package

git clone https://github.com/GIT_USER_ID/GIT_REPO_ID
cd GIT_REPO_ID
R CMD build .
R CMD check openapi_1.0.0.tar.gz --no-manual
R CMD INSTALL openapi_1.0.0.tar.gz

Install the package

install.packages("openapi")

To install directly from Github, use devtools:

install.packages("devtools")
library(devtools)
install_github("GIT_USER_ID/GIT_REPO_ID")

Usage

library(openapi)

Documentation for API Endpoints

All URIs are relative to https://test-server.brapi.org/brapi/v2

Class Method HTTP request Description
CallSetsApi CallsetsCallSetDbIdCallsGet GET /callsets/{callSetDbId}/calls Gets a list of Calls associated with a CallSet.
CallSetsApi CallsetsCallSetDbIdGet GET /callsets/{callSetDbId} Gets a CallSet by ID.
CallSetsApi CallsetsGet GET /callsets Gets a filtered list of CallSet JSON objects.
CallSetsApi SearchCallsetsPost POST /search/callsets Gets a list of call sets matching the search criteria.
CallSetsApi SearchCallsetsSearchResultsDbIdGet GET /search/callsets/{searchResultsDbId} Gets a list of call sets matching the search criteria.
CallsApi CallsGet GET /calls Gets a filtered list of Calls
CallsApi SearchCallsPost POST /search/calls Submit a search request for Calls
CallsApi SearchCallsSearchResultsDbIdGet GET /search/calls/{searchResultsDbId} Returns a filtered list of Call JSON objects.
CommonCropNamesApi CommoncropnamesGet GET /commoncropnames Get the Common Crop Names
CrossesApi CrossesGet GET /crosses Get a filtered list of Cross entities
CrossesApi CrossesPost POST /crosses Create new Cross entities on this server
CrossesApi CrossesPut PUT /crosses Update existing Cross entities on this server
CrossesApi PlannedcrossesGet GET /plannedcrosses Get a filtered list of Planned Cross entities
CrossesApi PlannedcrossesPost POST /plannedcrosses Create new Planned Cross entities on this server
CrossesApi PlannedcrossesPut PUT /plannedcrosses Update existing Planned Cross entities on this server
CrossingProjectsApi CrossingprojectsCrossingProjectDbIdGet GET /crossingprojects/{crossingProjectDbId} Get a filtered list of Crossing Projects
CrossingProjectsApi CrossingprojectsCrossingProjectDbIdPut PUT /crossingprojects/{crossingProjectDbId} Update an existing Crossing Project
CrossingProjectsApi CrossingprojectsGet GET /crossingprojects Get a filtered list of Crossing Projects
CrossingProjectsApi CrossingprojectsPost POST /crossingprojects Create new Crossing Project entities on this server
EventsApi EventsGet GET /events Get the Events
GenomeMapsApi MapsGet GET /maps Get the Genomic Maps
GenomeMapsApi MapsMapDbIdGet GET /maps/{mapDbId} Get the details of a specific Genomic Map
GenomeMapsApi MapsMapDbIdLinkagegroupsGet GET /maps/{mapDbId}/linkagegroups Get the Linkage Groups of a specific Genomic Map
GenomeMapsApi MarkerpositionsGet GET /markerpositions Get marker position info
GenomeMapsApi SearchMarkerpositionsPost POST /search/markerpositions Get marker position info
GenomeMapsApi SearchMarkerpositionsSearchResultsDbIdGet GET /search/markerpositions/{searchResultsDbId} Get marker position info
GermplasmApi BreedingmethodsBreedingMethodDbIdGet GET /breedingmethods/{breedingMethodDbId} Get the details of a specific Breeding Method
GermplasmApi BreedingmethodsGet GET /breedingmethods Get the Breeding Methods
GermplasmApi GermplasmGermplasmDbIdGet GET /germplasm/{germplasmDbId} Get the details of a specific Germplasm
GermplasmApi GermplasmGermplasmDbIdMcpdGet GET /germplasm/{germplasmDbId}/mcpd Get the details of a specific Germplasm in MCPD format
GermplasmApi GermplasmGermplasmDbIdPedigreeGet GET /germplasm/{germplasmDbId}/pedigree Get the pedigree details of a specific Germplasm
GermplasmApi GermplasmGermplasmDbIdProgenyGet GET /germplasm/{germplasmDbId}/progeny Get the progeny details of a specific Germplasm
GermplasmApi GermplasmGermplasmDbIdPut PUT /germplasm/{germplasmDbId} Update the details of an existing Germplasm
GermplasmApi GermplasmGet GET /germplasm Get a filtered list of Germplasm
GermplasmApi GermplasmPost POST /germplasm Create new Germplasm entities on this server
GermplasmApi SearchGermplasmPost POST /search/germplasm Submit a search request for Germplasm
GermplasmApi SearchGermplasmSearchResultsDbIdGet GET /search/germplasm/{searchResultsDbId} Get the results of a Germplasm search request
GermplasmAttributeValuesApi AttributevaluesAttributeValueDbIdGet GET /attributevalues/{attributeValueDbId} Get the details for a specific Germplasm Attribute
GermplasmAttributeValuesApi AttributevaluesAttributeValueDbIdPut PUT /attributevalues/{attributeValueDbId} Update an existing Germplasm Attribute Value
GermplasmAttributeValuesApi AttributevaluesGet GET /attributevalues Get the Germplasm Attribute Values
GermplasmAttributeValuesApi AttributevaluesPost POST /attributevalues Create new Germplasm Attribute Values
GermplasmAttributeValuesApi SearchAttributevaluesPost POST /search/attributevalues Submit a search request for Germplasm Attribute Values
GermplasmAttributeValuesApi SearchAttributevaluesSearchResultsDbIdGet GET /search/attributevalues/{searchResultsDbId} Get the results of a Germplasm Attribute Values search request
GermplasmAttributesApi AttributesAttributeDbIdGet GET /attributes/{attributeDbId} Get the details for a specific Germplasm Attribute
GermplasmAttributesApi AttributesAttributeDbIdPut PUT /attributes/{attributeDbId} Update an existing Germplasm Attribute
GermplasmAttributesApi AttributesCategoriesGet GET /attributes/categories Get the Categories of Germplasm Attributes
GermplasmAttributesApi AttributesGet GET /attributes Get the Germplasm Attributes
GermplasmAttributesApi AttributesPost POST /attributes Create new Germplasm Attributes
GermplasmAttributesApi SearchAttributesPost POST /search/attributes Submit a search request for Germplasm Attributes
GermplasmAttributesApi SearchAttributesSearchResultsDbIdGet GET /search/attributes/{searchResultsDbId} Get the results of a Germplasm Attributes search request
ImagesApi ImagesGet GET /images Get the image meta data summaries
ImagesApi ImagesImageDbIdGet GET /images/{imageDbId} Get the an image meta data summary
ImagesApi ImagesImageDbIdImagecontentPut PUT /images/{imageDbId}/imagecontent Update an image with the image file content
ImagesApi ImagesImageDbIdPut PUT /images/{imageDbId} Update an image meta data
ImagesApi ImagesPost POST /images Create new image meta data objects
ImagesApi SearchImagesPost POST /search/images Submit a search request for Images
ImagesApi SearchImagesSearchResultsDbIdGet GET /search/images/{searchResultsDbId} Get the results of an Images search request
ListsApi ListsGet GET /lists Get filtered set of generic lists
ListsApi ListsListDbIdGet GET /lists/{listDbId} Get the details of a specific List
ListsApi ListsListDbIdItemsPost POST /lists/{listDbId}/items Add Items to a specific List
ListsApi ListsListDbIdPut PUT /lists/{listDbId} Update an existing generic list
ListsApi ListsPost POST /lists Create New List Objects
ListsApi SearchListsPost POST /search/lists Submit a search request for Lists
ListsApi SearchListsSearchResultsDbIdGet GET /search/lists/{searchResultsDbId} Get the results of a List search request
LocationsApi LocationsGet GET /locations Get a filtered list of Locations
LocationsApi LocationsLocationDbIdGet GET /locations/{locationDbId} Get the details of a specific Location
LocationsApi LocationsLocationDbIdPut PUT /locations/{locationDbId} Update the details for an existing Location
LocationsApi LocationsPost POST /locations Create new Locations
LocationsApi SearchLocationsPost POST /search/locations Submit a search request for Locations
LocationsApi SearchLocationsSearchResultsDbIdGet GET /search/locations/{searchResultsDbId} Get the results of a Locations search request
MethodsApi MethodsGet GET /methods Get the Methods
MethodsApi MethodsMethodDbIdGet GET /methods/{methodDbId} Get the details for a specific Method
MethodsApi MethodsMethodDbIdPut PUT /methods/{methodDbId} Update an existing Method
MethodsApi MethodsPost POST /methods Add new Methods
ObservationUnitsApi ObservationlevelsGet GET /observationlevels Get the Observation Levels
ObservationUnitsApi ObservationunitsGet GET /observationunits Get a filtered set of Observation Units
ObservationUnitsApi ObservationunitsObservationUnitDbIdGet GET /observationunits/{observationUnitDbId} Get the details of a specific Observation Unit
ObservationUnitsApi ObservationunitsObservationUnitDbIdPut PUT /observationunits/{observationUnitDbId} Update an existing Observation Units
ObservationUnitsApi ObservationunitsPost POST /observationunits Add new Observation Units
ObservationUnitsApi ObservationunitsPut PUT /observationunits Update a set of Observation Units
ObservationUnitsApi ObservationunitsTableGet GET /observationunits/table Get a list of Observations in a table format
ObservationUnitsApi SearchObservationunitsPost POST /search/observationunits Submit a search request for Observation Units
ObservationUnitsApi SearchObservationunitsSearchResultsDbIdGet GET /search/observationunits/{searchResultsDbId} Observation Unit Search
ObservationVariablesApi SearchVariablesPost POST /search/variables Submit a search request for Observation Variables
ObservationVariablesApi SearchVariablesSearchResultsDbIdGet GET /search/variables/{searchResultsDbId} Get the results of a Observation Variable search request
ObservationVariablesApi VariablesGet GET /variables Get the Observation Variables
ObservationVariablesApi VariablesObservationVariableDbIdGet GET /variables/{observationVariableDbId} Get the details for a specific Observation Variable
ObservationVariablesApi VariablesObservationVariableDbIdPut PUT /variables/{observationVariableDbId} Update an existing Observation Variable
ObservationVariablesApi VariablesPost POST /variables Add new Observation Variables
ObservationsApi ObservationsGet GET /observations Get a filtered set of Observations
ObservationsApi ObservationsObservationDbIdGet GET /observations/{observationDbId} Get the details of a specific Observations
ObservationsApi ObservationsObservationDbIdPut PUT /observations/{observationDbId} Update an existing Observation
ObservationsApi ObservationsPost POST /observations Add new Observation entities
ObservationsApi ObservationsPut PUT /observations Update multiple Observation entities
ObservationsApi ObservationsTableGet GET /observations/table Get a list of Observations in a table format
ObservationsApi SearchObservationsPost POST /search/observations Submit a search request for a set of Observations
ObservationsApi SearchObservationsSearchResultsDbIdGet GET /search/observations/{searchResultsDbId} Returns a list of Observations based on search criteria.
OntologiesApi OntologiesGet GET /ontologies Get the Ontologies
PeopleApi PeopleGet GET /people Get filtered list of People
PeopleApi PeoplePersonDbIdGet GET /people/{personDbId} Get the details for a specific Person
PeopleApi PeoplePersonDbIdPut PUT /people/{personDbId} Update an existing Person
PeopleApi PeoplePost POST /people Create new People
PeopleApi SearchPeoplePost POST /search/people Submit a search request for People
PeopleApi SearchPeopleSearchResultsDbIdGet GET /search/people/{searchResultsDbId} Get the results of a People search request
ProgramsApi ProgramsGet GET /programs Get a filtered list of breeding Programs
ProgramsApi ProgramsPost POST /programs Add new breeding Programs to the database
ProgramsApi ProgramsProgramDbIdGet GET /programs/{programDbId} Get a breeding Program by Id
ProgramsApi ProgramsProgramDbIdPut PUT /programs/{programDbId} Update an existing Program
ProgramsApi SearchProgramsPost POST /search/programs Submit a search request for Programs
ProgramsApi SearchProgramsSearchResultsDbIdGet GET /search/programs/{searchResultsDbId} Get the results of a Programs search request
ReferenceSetsApi ReferencesetsGet GET /referencesets Gets a list of ReferenceSets.
ReferenceSetsApi ReferencesetsReferenceSetDbIdGet GET /referencesets/{referenceSetDbId} Gets a ReferenceSet by ID.
ReferenceSetsApi SearchReferencesetsPost POST /search/referencesets Gets a list of ReferenceSet matching the search criteria.
ReferenceSetsApi SearchReferencesetsSearchResultsDbIdGet GET /search/referencesets/{searchResultsDbId} Gets a list of ReferenceSet matching the search criteria.
ReferencesApi ReferencesGet GET /references Gets a filtered list of Reference objects.
ReferencesApi ReferencesReferenceDbIdBasesGet GET /references/{referenceDbId}/bases Lists Reference bases by ID and optional range.
ReferencesApi ReferencesReferenceDbIdGet GET /references/{referenceDbId} Gets a Reference by ID.
ReferencesApi SearchReferencesPost POST /search/references Gets a list of Reference matching the search criteria.
ReferencesApi SearchReferencesSearchResultsDbIdGet GET /search/references/{searchResultsDbId} Gets a list of Reference matching the search criteria.
SamplesApi SamplesGet GET /samples Get the Samples
SamplesApi SamplesPost POST /samples Add new Samples
SamplesApi SamplesSampleDbIdGet GET /samples/{sampleDbId} Get the details of a specific Sample
SamplesApi SamplesSampleDbIdPut PUT /samples/{sampleDbId} Update the details of an existing Sample
SamplesApi SearchSamplesPost POST /search/samples Submit a search request for Samples
SamplesApi SearchSamplesSearchResultsDbIdGet GET /search/samples/{searchResultsDbId} Get the results of a Samples search request
ScalesApi ScalesGet GET /scales Get the Scales
ScalesApi ScalesPost POST /scales Add new Scales
ScalesApi ScalesScaleDbIdGet GET /scales/{scaleDbId} Get the details of a specific Scale
ScalesApi ScalesScaleDbIdPut PUT /scales/{scaleDbId} Update an existing Scale
SeasonsApi SeasonsGet GET /seasons Get the Seasons
SeasonsApi SeasonsPost POST /seasons POST new Seasons
SeasonsApi SeasonsSeasonDbIdGet GET /seasons/{seasonDbId} Get the a single Season
SeasonsApi SeasonsSeasonDbIdPut PUT /seasons/{seasonDbId} Update existing Seasons
SeedLotsApi SeedlotsGet GET /seedlots Get a filtered list of Seed Lot descriptions
SeedLotsApi SeedlotsPost POST /seedlots Add new Seed Lot descriptions to a server
SeedLotsApi SeedlotsSeedLotDbIdGet GET /seedlots/{seedLotDbId} Get a specific Seed Lot
SeedLotsApi SeedlotsSeedLotDbIdPut PUT /seedlots/{seedLotDbId} Update an existing Seed Lot
SeedLotsApi SeedlotsSeedLotDbIdTransactionsGet GET /seedlots/{seedLotDbId}/transactions Get all Transactions related to a specific Seed Lot
SeedLotsApi SeedlotsTransactionsGet GET /seedlots/transactions Get a filtered list of Seed Lot Transactions
SeedLotsApi SeedlotsTransactionsPost POST /seedlots/transactions Add new Seed Lot Transaction to be recorded
ServerInfoApi ServerinfoGet GET /serverinfo Get the list of implemented Calls
StudiesApi SearchStudiesPost POST /search/studies Submit a search request for Studies
StudiesApi SearchStudiesSearchResultsDbIdGet GET /search/studies/{searchResultsDbId} Get the results of a Studies search request
StudiesApi StudiesGet GET /studies Get a filtered list of Studies
StudiesApi StudiesPost POST /studies Create new Studies.
StudiesApi StudiesStudyDbIdGet GET /studies/{studyDbId} Get the details for a specific Study
StudiesApi StudiesStudyDbIdPut PUT /studies/{studyDbId} Update an existing Study
StudiesApi StudytypesGet GET /studytypes Get the Study Types
TraitsApi TraitsGet GET /traits Get the Traits
TraitsApi TraitsPost POST /traits Add new Traits
TraitsApi TraitsTraitDbIdGet GET /traits/{traitDbId} Get the details of a specific Trait
TraitsApi TraitsTraitDbIdPut PUT /traits/{traitDbId} Update an existing Trait
TrialsApi SearchTrialsPost POST /search/trials Submit a search request for Trials
TrialsApi SearchTrialsSearchResultsDbIdGet GET /search/trials/{searchResultsDbId} Get the results of a Trials search request
TrialsApi TrialsGet GET /trials Get a filtered list of Trials
TrialsApi TrialsPost POST /trials Create new trials
TrialsApi TrialsTrialDbIdGet GET /trials/{trialDbId} Get the details of a specific Trial
TrialsApi TrialsTrialDbIdPut PUT /trials/{trialDbId} Update the details of an existing Trial
VariantSetsApi SearchVariantsetsPost POST /search/variantsets Gets a list of VariantSet matching the search criteria.
VariantSetsApi SearchVariantsetsSearchResultsDbIdGet GET /search/variantsets/{searchResultsDbId} Gets a list of VariantSet matching the search criteria.
VariantSetsApi VariantsetsExtractPost POST /variantsets/extract Create new VariantSet based on search results
VariantSetsApi VariantsetsGet GET /variantsets Gets a filtered list of VariantSets.
VariantSetsApi VariantsetsVariantSetDbIdCallsGet GET /variantsets/{variantSetDbId}/calls Gets a list of Calls associated with a VariantSet.
VariantSetsApi VariantsetsVariantSetDbIdCallsetsGet GET /variantsets/{variantSetDbId}/callsets Gets a list of CallSets associated with a VariantSet.
VariantSetsApi VariantsetsVariantSetDbIdGet GET /variantsets/{variantSetDbId} Gets a VariantSet by ID.
VariantSetsApi VariantsetsVariantSetDbIdVariantsGet GET /variantsets/{variantSetDbId}/variants Gets a Variants for a given VariantSet.
VariantsApi SearchVariantsPost POST /search/variants Gets a list of Variant matching the search criteria.
VariantsApi SearchVariantsSearchResultsDbIdGet GET /search/variants/{searchResultsDbId} Gets a list of Variant matching the search criteria.
VariantsApi VariantsGet GET /variants Gets a filtered list of Variants.
VariantsApi VariantsVariantDbIdCallsGet GET /variants/{variantDbId}/calls Gets a list of Calls associated with a Variant.
VariantsApi VariantsVariantDbIdGet GET /variants/{variantDbId} Gets a Variant by ID.
VendorApi VendorOrdersGet GET /vendor/orders List current available orders
VendorApi VendorOrdersOrderIdPlatesGet GET /vendor/orders/{orderId}/plates Get the Plates for a specific Order
VendorApi VendorOrdersOrderIdResultsGet GET /vendor/orders/{orderId}/results Get the results of a specific Order
VendorApi VendorOrdersOrderIdStatusGet GET /vendor/orders/{orderId}/status Get the status of a specific Order
VendorApi VendorOrdersPost POST /vendor/orders Submit New Order
VendorApi VendorPlatesPost POST /vendor/plates Submit a new set of Sample data
VendorApi VendorPlatesSubmissionIdGet GET /vendor/plates/{submissionId} Get the data for a submitted set of plates
VendorApi VendorSpecificationsGet GET /vendor/specifications Get the Vendor Specifications

Documentation for Models

Documentation for Authorization

AuthorizationToken

  • Type: HTTP basic authentication

Author