#' ba_germplasmattributes_details
#'
#' attibutes call.
#'
#' @param con brapi connection object
#' @param rclass character; default: tibble; or else: json, list, data.frame.
#' @param germplasmDbId character; default: ''.
#' @param attributeList character vector; default: ''.
#' @param page integer; default: 0.
#' @param pageSize integer; default: 10.
#'
#' @return rclass as set by parameter.
#' @example inst/examples/ex-ba_germplasmattributes_details.R
#' @import httr
#' @author Reinhard Simon
#' @references \href{https://github.com/plantbreeding/API/blob/master/Specification/GermplasmAttributes/GermplasmAttributeValuesByGermplasmDbId.md}{github}
#' @family germplasmattributes
#' @family genotyping
#' @export
ba_germplasmattributes_details <- function(con = NULL,
germplasmDbId = "",
attributeList = "",
page = 0,
pageSize = 10,
rclass = "tibble") {
.Deprecated('ba_germplasm_attributes')
ba_check(con = con, verbose = FALSE)
stopifnot(is.character(germplasmDbId))
stopifnot(germplasmDbId != "")
stopifnot(is.character(attributeList))
check_paging(pageSize = pageSize, page = page)
check_rclass(rclass = rclass)
# fetch the url of the brapi implementation of the database
brp <- get_brapi(con = con)
# generate the specific brapi call url
pattributeList <- ifelse(attributeList != "", paste("attributeList=", attributeList, collapse = ",", sep=""), "")
germplasm_attributes_list <- paste0(brp,
"germplasm/",
germplasmDbId,
"/attributes/?",
pattributeList,
"&page=",
page,
"&pageSize=",
pageSize)
try({
res <- brapiGET(url = germplasm_attributes_list, con = con)
res2 <- httr::content(x = res, as = "text", encoding = "UTF-8")
ms2tbl <- function(res) {
lst <- tryCatch(
jsonlite::fromJSON(txt = res2)
)
assertthat::assert_that("data" %in% names(lst$result),
msg = "The json return object lacks a data element.")
dat <- jsonlite::toJSON(x = lst$result$data)
df <- jsonlite::fromJSON(txt = dat, simplifyDataFrame = TRUE,
flatten = TRUE)[[1]]
# assertthat::validate_that(nrow(df) > 0,
# msg = "The json return object lacks a data element.")
return(df)
}
if (rclass %in% c("json", "list")) {
out <- dat2tbl(res = res2, rclass = rclass)
}
if (rclass == "data.frame") {
out <- ms2tbl(res = res2)%>% tibble::as_tibble() %>% as.data.frame()
}
if (rclass == "tibble") {
out <- ms2tbl(res = res2) %>% tibble::as_tibble()
}
class(out) <- c(class(out), "ba_germplasmattributes_details")
show_metadata(res)
return(out)
})
}
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