R/biosample_api.R
In sdgamboa/omicidxClientR: R Package Client for OmicIDX
# OmicIDX
#
# The OmicIDX API documentation is available in three forms: - [RapiDoc](/docs) - [OpenAPI/Swagger Interactive](/swaggerdoc) - [ReDoc (more readable in some ways)](/redoc)
#
# The version of the OpenAPI document: 0.99.1
#
# Generated by: https://openapi-generator.tech
#' @docType class
#' @title Biosample operations
#' @description omicidxClientR.Biosample
#' @format An \code{R6Class} generator object
#' @field apiClient Handles the client-server communication.
#'
#' @section Methods:
#' \describe{
#' \strong{ BiosampleByAccessionBiosampleSamplesAccessionGet } \emph{ Biosample By Accession }
#'
#'
#' \itemize{
#' \item \emph{ @param } accession character
#' \item \emph{ @param } include.fields list( character )
#' \item \emph{ @param } exclude.fields list( character )
#' \item \emph{ @returnType } \link{AnyType} \cr
#'
#'
#' \item status code : 200 | Successful Response
#'
#' \item return type : AnyType
#' \item response headers :
#'
#' \tabular{ll}{
#' }
#' \item status code : 422 | Validation Error
#'
#' \item return type : HTTPValidationError
#' \item response headers :
#'
#' \tabular{ll}{
#' }
#' }
#'
#' \strong{ BiosamplesBiosampleSamplesGet } \emph{ Biosamples }
#'
#'
#' \itemize{
#' \item \emph{ @param } q character
#' \item \emph{ @param } size integer
#' \item \emph{ @param } cursor character
#' \item \emph{ @param } facet.size integer
#' \item \emph{ @param } include.fields list( character )
#' \item \emph{ @param } exclude.fields list( character )
#' \item \emph{ @param } facets list( character )
#' \item \emph{ @returnType } \link{ResponseModel} \cr
#'
#'
#' \item status code : 200 | Successful Response
#'
#' \item return type : ResponseModel
#' \item response headers :
#'
#' \tabular{ll}{
#' }
#' \item status code : 422 | Validation Error
#'
#' \item return type : HTTPValidationError
#' \item response headers :
#'
#' \tabular{ll}{
#' }
#' }
#'
#' \strong{ MappingBiosampleFieldsEntityGet } \emph{ Mapping }
#'
#'
#' \itemize{
#' \item \emph{ @param } entity character
#' \item \emph{ @returnType } \link{AnyType} \cr
#'
#'
#' \item status code : 200 | Successful Response
#'
#' \item return type : AnyType
#' \item response headers :
#'
#' \tabular{ll}{
#' }
#' \item status code : 422 | Validation Error
#'
#' \item return type : HTTPValidationError
#' \item response headers :
#'
#' \tabular{ll}{
#' }
#' }
#'
#' }
#'
#'
#' @examples
#' \dontrun{
#' #################### BiosampleByAccessionBiosampleSamplesAccessionGet ####################
#'
#' library(omicidxClientR)
#' var.accession <- 'accession_example' # character | An accession for lookup
#' var.include.fields <- {} # array[character] | Fields to include in results. The default is to all fields (*)
#' var.exclude.fields <- {} # array[character] | Fields to exclude from results. The default is to not exclude any fields.
#'
#' #Biosample By Accession
#' api.instance <- BiosampleApi$new()
#'
#' result <- api.instance$BiosampleByAccessionBiosampleSamplesAccessionGet(var.accession, include.fields=var.include.fields, exclude.fields=var.exclude.fields)
#'
#'
#' #################### BiosamplesBiosampleSamplesGet ####################
#'
#' library(omicidxClientR)
#' var.q <- 'cancer' # character | The query, using [lucene query syntax](https://lucene.apache.org/core/3_6_0/queryparsersyntax.html)
#' var.size <- 10 # integer |
#' var.cursor <- 'cursor_example' # character | The cursor is used to scroll through results. For a query with more results than `size`, the result will include `cursor` in the result json. Use that value here and re-issue the query. The next set or results will be returned. When no more results are available, the `cursor` will again be empty in the result json.
#' var.facet.size <- 10 # integer | The maximum number of records returned for each facet. This has no effect unless one or more facets are specified.
#' var.include.fields <- {} # array[character] | Fields to include in results. The default is to all fields (*)
#' var.exclude.fields <- {} # array[character] | Fields to exclude from results. The default is to not exclude any fields.
#' var.facets <- {} # array[character] | A list of strings identifying fields for faceted search results. Simple term faceting is used here, meaning that fields that are short text and repeated across records will be binned and counted.
#'
#' #Biosamples
#' api.instance <- BiosampleApi$new()
#'
#' result <- api.instance$BiosamplesBiosampleSamplesGet(q=var.q, size=var.size, cursor=var.cursor, facet.size=var.facet.size, include.fields=var.include.fields, exclude.fields=var.exclude.fields, facets=var.facets)
#'
#'
#' #################### MappingBiosampleFieldsEntityGet ####################
#'
#' library(omicidxClientR)
#' var.entity <- 'entity_example' # character |
#'
#' #Mapping
#' api.instance <- BiosampleApi$new()
#'
#' result <- api.instance$MappingBiosampleFieldsEntityGet(var.entity)
#'
#'
#' }
#' @importFrom R6 R6Class
#' @importFrom base64enc base64encode
#' @export
BiosampleApi <- R6::R6Class(
'BiosampleApi',
public = list(
apiClient = NULL,
initialize = function(apiClient){
if (!missing(apiClient)) {
self$apiClient <- apiClient
}
else {
self$apiClient <- ApiClient$new()
}
},
BiosampleByAccessionBiosampleSamplesAccessionGet = function(accession, include.fields={}, exclude.fields={}, ...){
apiResponse <- self$BiosampleByAccessionBiosampleSamplesAccessionGetWithHttpInfo(accession, include.fields, exclude.fields, ...)
resp <- apiResponse$response
if (httr::status_code(resp) >= 200 && httr::status_code(resp) <= 299) {
apiResponse$content
} else if (httr::status_code(resp) >= 300 && httr::status_code(resp) <= 399) {
apiResponse
} else if (httr::status_code(resp) >= 400 && httr::status_code(resp) <= 499) {
apiResponse
} else if (httr::status_code(resp) >= 500 && httr::status_code(resp) <= 599) {
apiResponse
}
},
BiosampleByAccessionBiosampleSamplesAccessionGetWithHttpInfo = function(accession, include.fields={}, exclude.fields={}, ...){
args <- list(...)
queryParams <- list()
headerParams <- c()
if (missing(`accession`)) {
stop("Missing required parameter `accession`.")
}
queryParams['include_fields'] <- include.fields
queryParams['exclude_fields'] <- exclude.fields
body <- NULL
urlPath <- "/biosample/samples/{accession}"
if (!missing(`accession`)) {
urlPath <- gsub(paste0("\\{", "accession", "\\}"), URLencode(as.character(`accession`), reserved = TRUE), urlPath)
}
resp <- self$apiClient$CallApi(url = paste0(self$apiClient$basePath, urlPath),
method = "GET",
queryParams = queryParams,
headerParams = headerParams,
body = body,
...)
if (httr::status_code(resp) >= 200 && httr::status_code(resp) <= 299) {
deserializedRespObj <- tryCatch(
self$apiClient$deserialize(resp, "AnyType", loadNamespace("omicidxClientR")),
error = function(e){
stop("Failed to deserialize response")
}
)
ApiResponse$new(deserializedRespObj, resp)
} else if (httr::status_code(resp) >= 300 && httr::status_code(resp) <= 399) {
ApiResponse$new(paste("Server returned " , httr::status_code(resp) , " response status code."), resp)
} else if (httr::status_code(resp) >= 400 && httr::status_code(resp) <= 499) {
ApiResponse$new("API client error", resp)
} else if (httr::status_code(resp) >= 500 && httr::status_code(resp) <= 599) {
ApiResponse$new("API server error", resp)
}
},
BiosamplesBiosampleSamplesGet = function(q=NULL, size=10, cursor=NULL, facet.size=10, include.fields={}, exclude.fields={}, facets={}, ...){
apiResponse <- self$BiosamplesBiosampleSamplesGetWithHttpInfo(q, size, cursor, facet.size, include.fields, exclude.fields, facets, ...)
resp <- apiResponse$response
if (httr::status_code(resp) >= 200 && httr::status_code(resp) <= 299) {
apiResponse$content
} else if (httr::status_code(resp) >= 300 && httr::status_code(resp) <= 399) {
apiResponse
} else if (httr::status_code(resp) >= 400 && httr::status_code(resp) <= 499) {
apiResponse
} else if (httr::status_code(resp) >= 500 && httr::status_code(resp) <= 599) {
apiResponse
}
},
BiosamplesBiosampleSamplesGetWithHttpInfo = function(q=NULL, size=10, cursor=NULL, facet.size=10, include.fields={}, exclude.fields={}, facets={}, ...){
args <- list(...)
queryParams <- list()
headerParams <- c()
queryParams['q'] <- q
queryParams['size'] <- size
queryParams['cursor'] <- cursor
queryParams['facet_size'] <- facet.size
queryParams['include_fields'] <- include.fields
queryParams['exclude_fields'] <- exclude.fields
queryParams['facets'] <- facets
body <- NULL
urlPath <- "/biosample/samples"
resp <- self$apiClient$CallApi(url = paste0(self$apiClient$basePath, urlPath),
method = "GET",
queryParams = queryParams,
headerParams = headerParams,
body = body,
...)
if (httr::status_code(resp) >= 200 && httr::status_code(resp) <= 299) {
deserializedRespObj <- tryCatch(
self$apiClient$deserialize(resp, "ResponseModel", loadNamespace("omicidxClientR")),
error = function(e){
stop("Failed to deserialize response")
}
)
ApiResponse$new(deserializedRespObj, resp)
} else if (httr::status_code(resp) >= 300 && httr::status_code(resp) <= 399) {
ApiResponse$new(paste("Server returned " , httr::status_code(resp) , " response status code."), resp)
} else if (httr::status_code(resp) >= 400 && httr::status_code(resp) <= 499) {
ApiResponse$new("API client error", resp)
} else if (httr::status_code(resp) >= 500 && httr::status_code(resp) <= 599) {
ApiResponse$new("API server error", resp)
}
},
MappingBiosampleFieldsEntityGet = function(entity, ...){
apiResponse <- self$MappingBiosampleFieldsEntityGetWithHttpInfo(entity, ...)
resp <- apiResponse$response
if (httr::status_code(resp) >= 200 && httr::status_code(resp) <= 299) {
apiResponse$content
} else if (httr::status_code(resp) >= 300 && httr::status_code(resp) <= 399) {
apiResponse
} else if (httr::status_code(resp) >= 400 && httr::status_code(resp) <= 499) {
apiResponse
} else if (httr::status_code(resp) >= 500 && httr::status_code(resp) <= 599) {
apiResponse
}
},
MappingBiosampleFieldsEntityGetWithHttpInfo = function(entity, ...){
args <- list(...)
queryParams <- list()
headerParams <- c()
if (missing(`entity`)) {
stop("Missing required parameter `entity`.")
}
body <- NULL
urlPath <- "/biosample/fields/{entity}"
if (!missing(`entity`)) {
urlPath <- gsub(paste0("\\{", "entity", "\\}"), URLencode(as.character(`entity`), reserved = TRUE), urlPath)
}
resp <- self$apiClient$CallApi(url = paste0(self$apiClient$basePath, urlPath),
method = "GET",
queryParams = queryParams,
headerParams = headerParams,
body = body,
...)
if (httr::status_code(resp) >= 200 && httr::status_code(resp) <= 299) {
deserializedRespObj <- tryCatch(
self$apiClient$deserialize(resp, "AnyType", loadNamespace("omicidxClientR")),
error = function(e){
stop("Failed to deserialize response")
}
)
ApiResponse$new(deserializedRespObj, resp)
} else if (httr::status_code(resp) >= 300 && httr::status_code(resp) <= 399) {
ApiResponse$new(paste("Server returned " , httr::status_code(resp) , " response status code."), resp)
} else if (httr::status_code(resp) >= 400 && httr::status_code(resp) <= 499) {
ApiResponse$new("API client error", resp)
} else if (httr::status_code(resp) >= 500 && httr::status_code(resp) <= 599) {
ApiResponse$new("API server error", resp)
}
}
)
)
sdgamboa/omicidxClientR documentation built on Dec. 22, 2021, 11:12 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
# OmicIDX
#
# The OmicIDX API documentation is available in three forms: - [RapiDoc](/docs) - [OpenAPI/Swagger Interactive](/swaggerdoc) - [ReDoc (more readable in some ways)](/redoc)
#
# The version of the OpenAPI document: 0.99.1
#
# Generated by: https://openapi-generator.tech
#' @docType class
#' @title Biosample operations
#' @description omicidxClientR.Biosample
#' @format An \code{R6Class} generator object
#' @field apiClient Handles the client-server communication.
#'
#' @section Methods:
#' \describe{
#' \strong{ BiosampleByAccessionBiosampleSamplesAccessionGet } \emph{ Biosample By Accession }
#'
#'
#' \itemize{
#' \item \emph{ @param } accession character
#' \item \emph{ @param } include.fields list( character )
#' \item \emph{ @param } exclude.fields list( character )
#' \item \emph{ @returnType } \link{AnyType} \cr
#'
#'
#' \item status code : 200 | Successful Response
#'
#' \item return type : AnyType
#' \item response headers :
#'
#' \tabular{ll}{
#' }
#' \item status code : 422 | Validation Error
#'
#' \item return type : HTTPValidationError
#' \item response headers :
#'
#' \tabular{ll}{
#' }
#' }
#'
#' \strong{ BiosamplesBiosampleSamplesGet } \emph{ Biosamples }
#'
#'
#' \itemize{
#' \item \emph{ @param } q character
#' \item \emph{ @param } size integer
#' \item \emph{ @param } cursor character
#' \item \emph{ @param } facet.size integer
#' \item \emph{ @param } include.fields list( character )
#' \item \emph{ @param } exclude.fields list( character )
#' \item \emph{ @param } facets list( character )
#' \item \emph{ @returnType } \link{ResponseModel} \cr
#'
#'
#' \item status code : 200 | Successful Response
#'
#' \item return type : ResponseModel
#' \item response headers :
#'
#' \tabular{ll}{
#' }
#' \item status code : 422 | Validation Error
#'
#' \item return type : HTTPValidationError
#' \item response headers :
#'
#' \tabular{ll}{
#' }
#' }
#'
#' \strong{ MappingBiosampleFieldsEntityGet } \emph{ Mapping }
#'
#'
#' \itemize{
#' \item \emph{ @param } entity character
#' \item \emph{ @returnType } \link{AnyType} \cr
#'
#'
#' \item status code : 200 | Successful Response
#'
#' \item return type : AnyType
#' \item response headers :
#'
#' \tabular{ll}{
#' }
#' \item status code : 422 | Validation Error
#'
#' \item return type : HTTPValidationError
#' \item response headers :
#'
#' \tabular{ll}{
#' }
#' }
#'
#' }
#'
#'
#' @examples
#' \dontrun{
#' #################### BiosampleByAccessionBiosampleSamplesAccessionGet ####################
#'
#' library(omicidxClientR)
#' var.accession <- 'accession_example' # character | An accession for lookup
#' var.include.fields <- {} # array[character] | Fields to include in results. The default is to all fields (*)
#' var.exclude.fields <- {} # array[character] | Fields to exclude from results. The default is to not exclude any fields.
#'
#' #Biosample By Accession
#' api.instance <- BiosampleApi$new()
#'
#' result <- api.instance$BiosampleByAccessionBiosampleSamplesAccessionGet(var.accession, include.fields=var.include.fields, exclude.fields=var.exclude.fields)
#'
#'
#' #################### BiosamplesBiosampleSamplesGet ####################
#'
#' library(omicidxClientR)
#' var.q <- 'cancer' # character | The query, using [lucene query syntax](https://lucene.apache.org/core/3_6_0/queryparsersyntax.html)
#' var.size <- 10 # integer |
#' var.cursor <- 'cursor_example' # character | The cursor is used to scroll through results. For a query with more results than `size`, the result will include `cursor` in the result json. Use that value here and re-issue the query. The next set or results will be returned. When no more results are available, the `cursor` will again be empty in the result json.
#' var.facet.size <- 10 # integer | The maximum number of records returned for each facet. This has no effect unless one or more facets are specified.
#' var.include.fields <- {} # array[character] | Fields to include in results. The default is to all fields (*)
#' var.exclude.fields <- {} # array[character] | Fields to exclude from results. The default is to not exclude any fields.
#' var.facets <- {} # array[character] | A list of strings identifying fields for faceted search results. Simple term faceting is used here, meaning that fields that are short text and repeated across records will be binned and counted.
#'
#' #Biosamples
#' api.instance <- BiosampleApi$new()
#'
#' result <- api.instance$BiosamplesBiosampleSamplesGet(q=var.q, size=var.size, cursor=var.cursor, facet.size=var.facet.size, include.fields=var.include.fields, exclude.fields=var.exclude.fields, facets=var.facets)
#'
#'
#' #################### MappingBiosampleFieldsEntityGet ####################
#'
#' library(omicidxClientR)
#' var.entity <- 'entity_example' # character |
#'
#' #Mapping
#' api.instance <- BiosampleApi$new()
#'
#' result <- api.instance$MappingBiosampleFieldsEntityGet(var.entity)
#'
#'
#' }
#' @importFrom R6 R6Class
#' @importFrom base64enc base64encode
#' @export
BiosampleApi <- R6::R6Class(
'BiosampleApi',
public = list(
apiClient = NULL,
initialize = function(apiClient){
if (!missing(apiClient)) {
self$apiClient <- apiClient
}
else {
self$apiClient <- ApiClient$new()
}
},
BiosampleByAccessionBiosampleSamplesAccessionGet = function(accession, include.fields={}, exclude.fields={}, ...){
apiResponse <- self$BiosampleByAccessionBiosampleSamplesAccessionGetWithHttpInfo(accession, include.fields, exclude.fields, ...)
resp <- apiResponse$response
if (httr::status_code(resp) >= 200 && httr::status_code(resp) <= 299) {
apiResponse$content
} else if (httr::status_code(resp) >= 300 && httr::status_code(resp) <= 399) {
apiResponse
} else if (httr::status_code(resp) >= 400 && httr::status_code(resp) <= 499) {
apiResponse
} else if (httr::status_code(resp) >= 500 && httr::status_code(resp) <= 599) {
apiResponse
}
},
BiosampleByAccessionBiosampleSamplesAccessionGetWithHttpInfo = function(accession, include.fields={}, exclude.fields={}, ...){
args <- list(...)
queryParams <- list()
headerParams <- c()
if (missing(`accession`)) {
stop("Missing required parameter `accession`.")
}
queryParams['include_fields'] <- include.fields
queryParams['exclude_fields'] <- exclude.fields
body <- NULL
urlPath <- "/biosample/samples/{accession}"
if (!missing(`accession`)) {
urlPath <- gsub(paste0("\\{", "accession", "\\}"), URLencode(as.character(`accession`), reserved = TRUE), urlPath)
}
resp <- self$apiClient$CallApi(url = paste0(self$apiClient$basePath, urlPath),
method = "GET",
queryParams = queryParams,
headerParams = headerParams,
body = body,
...)
if (httr::status_code(resp) >= 200 && httr::status_code(resp) <= 299) {
deserializedRespObj <- tryCatch(
self$apiClient$deserialize(resp, "AnyType", loadNamespace("omicidxClientR")),
error = function(e){
stop("Failed to deserialize response")
}
)
ApiResponse$new(deserializedRespObj, resp)
} else if (httr::status_code(resp) >= 300 && httr::status_code(resp) <= 399) {
ApiResponse$new(paste("Server returned " , httr::status_code(resp) , " response status code."), resp)
} else if (httr::status_code(resp) >= 400 && httr::status_code(resp) <= 499) {
ApiResponse$new("API client error", resp)
} else if (httr::status_code(resp) >= 500 && httr::status_code(resp) <= 599) {
ApiResponse$new("API server error", resp)
}
},
BiosamplesBiosampleSamplesGet = function(q=NULL, size=10, cursor=NULL, facet.size=10, include.fields={}, exclude.fields={}, facets={}, ...){
apiResponse <- self$BiosamplesBiosampleSamplesGetWithHttpInfo(q, size, cursor, facet.size, include.fields, exclude.fields, facets, ...)
resp <- apiResponse$response
if (httr::status_code(resp) >= 200 && httr::status_code(resp) <= 299) {
apiResponse$content
} else if (httr::status_code(resp) >= 300 && httr::status_code(resp) <= 399) {
apiResponse
} else if (httr::status_code(resp) >= 400 && httr::status_code(resp) <= 499) {
apiResponse
} else if (httr::status_code(resp) >= 500 && httr::status_code(resp) <= 599) {
apiResponse
}
},
BiosamplesBiosampleSamplesGetWithHttpInfo = function(q=NULL, size=10, cursor=NULL, facet.size=10, include.fields={}, exclude.fields={}, facets={}, ...){
args <- list(...)
queryParams <- list()
headerParams <- c()
queryParams['q'] <- q
queryParams['size'] <- size
queryParams['cursor'] <- cursor
queryParams['facet_size'] <- facet.size
queryParams['include_fields'] <- include.fields
queryParams['exclude_fields'] <- exclude.fields
queryParams['facets'] <- facets
body <- NULL
urlPath <- "/biosample/samples"
resp <- self$apiClient$CallApi(url = paste0(self$apiClient$basePath, urlPath),
method = "GET",
queryParams = queryParams,
headerParams = headerParams,
body = body,
...)
if (httr::status_code(resp) >= 200 && httr::status_code(resp) <= 299) {
deserializedRespObj <- tryCatch(
self$apiClient$deserialize(resp, "ResponseModel", loadNamespace("omicidxClientR")),
error = function(e){
stop("Failed to deserialize response")
}
)
ApiResponse$new(deserializedRespObj, resp)
} else if (httr::status_code(resp) >= 300 && httr::status_code(resp) <= 399) {
ApiResponse$new(paste("Server returned " , httr::status_code(resp) , " response status code."), resp)
} else if (httr::status_code(resp) >= 400 && httr::status_code(resp) <= 499) {
ApiResponse$new("API client error", resp)
} else if (httr::status_code(resp) >= 500 && httr::status_code(resp) <= 599) {
ApiResponse$new("API server error", resp)
}
},
MappingBiosampleFieldsEntityGet = function(entity, ...){
apiResponse <- self$MappingBiosampleFieldsEntityGetWithHttpInfo(entity, ...)
resp <- apiResponse$response
if (httr::status_code(resp) >= 200 && httr::status_code(resp) <= 299) {
apiResponse$content
} else if (httr::status_code(resp) >= 300 && httr::status_code(resp) <= 399) {
apiResponse
} else if (httr::status_code(resp) >= 400 && httr::status_code(resp) <= 499) {
apiResponse
} else if (httr::status_code(resp) >= 500 && httr::status_code(resp) <= 599) {
apiResponse
}
},
MappingBiosampleFieldsEntityGetWithHttpInfo = function(entity, ...){
args <- list(...)
queryParams <- list()
headerParams <- c()
if (missing(`entity`)) {
stop("Missing required parameter `entity`.")
}
body <- NULL
urlPath <- "/biosample/fields/{entity}"
if (!missing(`entity`)) {
urlPath <- gsub(paste0("\\{", "entity", "\\}"), URLencode(as.character(`entity`), reserved = TRUE), urlPath)
}
resp <- self$apiClient$CallApi(url = paste0(self$apiClient$basePath, urlPath),
method = "GET",
queryParams = queryParams,
headerParams = headerParams,
body = body,
...)
if (httr::status_code(resp) >= 200 && httr::status_code(resp) <= 299) {
deserializedRespObj <- tryCatch(
self$apiClient$deserialize(resp, "AnyType", loadNamespace("omicidxClientR")),
error = function(e){
stop("Failed to deserialize response")
}
)
ApiResponse$new(deserializedRespObj, resp)
} else if (httr::status_code(resp) >= 300 && httr::status_code(resp) <= 399) {
ApiResponse$new(paste("Server returned " , httr::status_code(resp) , " response status code."), resp)
} else if (httr::status_code(resp) >= 400 && httr::status_code(resp) <= 499) {
ApiResponse$new("API client error", resp)
} else if (httr::status_code(resp) >= 500 && httr::status_code(resp) <= 599) {
ApiResponse$new("API server error", resp)
}
}
)
)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.