#' ba_germplasm_search
#'
#' Retrieve germplasm information as result of a GET search.
#'
#' @param con list, brapi connection object
#' @param germplasmPUI character, search for germplasm information using a
#' Permanent Unique Identifier (DOI, URI, etc.); default: ""
#' @param germplasmDbId character, search for germplasm information using an
#' internal germplasm database identifier; default: ""
#' @param germplasmName character, search for germplasm information using the
#' name of the germplasm; default: ""
#' @param commonCropName character, search for germplasm information using the
#' common crop name related to the germplasm; default: ""
#' @param pageSize integer, items per page to be returned; default: 1000
#' @param page integer, the requested page to be returned; default: 0 (1st page)
#' @param rclass character, class of the object to be returned; default: "tibble"
#' , possible other values: "data.frame"/"list"/"json"
#'
#' @return An object of class as defined by rclass containing the germaplasm
#' information result of the search.
#'
#' @note Tested against: test-server, BMS
#' @note BrAPI Version: 1.0, 1.1, 1.2
#' @note BrAPI Status: active
#'
#' @author Reinhard Simon, Maikel Verouden
#' @references \href{https://github.com/plantbreeding/API/blob/V1.2/Specification/Germplasm/GermplasmSearch_GET.md}{github}
#'
#' @family brapicore
#' @family genotyping
#' @family germplasm
#'
#' @example inst/examples/ex-ba_germplasm_search.R
#'
#' @import httr
#' @import progress
#' @importFrom magrittr '%>%'
#' @export
ba_germplasm_search <- function(con = NULL,
germplasmPUI = "",
germplasmDbId = "",
germplasmName = "",
commonCropName = "",
pageSize = 1000,
page = 0,
rclass = c("tibble", "data.frame", "list", "json")) {
ba_check(con = con, verbose = FALSE, brapi_calls = "germplasm-search")
check_character(germplasmPUI, germplasmDbId, germplasmName, commonCropName)
rclass <- match.arg(rclass)
brp <- get_brapi(con = con) %>% paste0("germplasm-search")
callurl <- get_endpoint(brp,
germplasmPUI = germplasmPUI,
germplasmDbId = germplasmDbId,
germplasmName = germplasmName,
commonCropName = commonCropName,
pageSize = pageSize,
page = page)
get_data <- function(cont, typ = "1") {
out <- dat2tbl(res = cont, rclass = rclass)
if (rclass == "data.frame") {
out <- gp2tbl(cont, typ)
}
if (rclass == "tibble") {
out <- gp2tbl(cont, typ) %>% tibble::as_tibble()
}
out
}
out <- try({
resp <- brapiGET(url = callurl, con = con)
cont <- httr::content(x = resp, as = "text", encoding = "UTF-8")
get_data(cont)
})
# }
nms <- names(out)
if (all(stringr::str_detect(nms, "data."))) {
names(out) <- stringr::str_replace_all(nms, "data.", "")
}
class(out) <- c(class(out), "ba_germplasm_search")
show_metadata(resp)
return(out)
}
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