#' ba_germplasm_pedigree
#'
#' Retrieve germplasm pedigree by internal germplasm database identifier
#'
#' @param con list, brapi connection object
#' @param germplasmDbId character, the internal database identifier for a
#' germplasm of which the germplasm pedigree is to be
#' retrieved e.g. "9932"; \strong{REQUIRED ARGUMENT} with
#' default: ""
#' @param notation character, text representation of the pedigree e.g. "purdy";
#' default: ""
#' @param includeSiblings logical, indicating whether to include, specified as
#' TRUE, a siblings array or not, specified as FALSE;
#' default: NA
#' @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 germplasm
#' pedigree.
#'
#' @note Tested against: test-server
#' @note BrAPI Version: 1.2
#' @note BrAPI Status: active
#'
#' @author Reinhard Simon, Maikel Verouden
#' @references \href{https://github.com/plantbreeding/API/blob/V1.2/Specification/Germplasm/Germplasm_Pedigree_GET.md}{github}
#'
#' @family germplasm
#' @family brapicore
#'
#' @example inst/examples/ex-ba_germplasm_pedigree.R
#'
#' @import httr
#' @export
ba_germplasm_pedigree <- function(con = NULL,
germplasmDbId = "",
notation = "",
includeSiblings = NA,
rclass = c("tibble", "data.frame",
"list", "json")) {
ba_check(con = con, verbose = FALSE)
check_character(germplasmDbId)
stopifnot(is.logical(includeSiblings))
check_req(germplasmDbId)
rclass <- match_req(rclass)
brp <- get_brapi(con = con) %>% paste0("germplasm/", germplasmDbId, "/pedigree")
callurl <- get_endpoint(brp,
notation = notation,
includeSiblings = includeSiblings)
try({
resp <- brapiGET(url = callurl, con = con)
cont <- httr::content(x = resp, as = "text", encoding = "UTF-8")
out <- NULL
ms2tbl <- function(res) {
lst <- jsonlite::fromJSON(txt = res)
dat <- jsonlite::toJSON(x = lst$result)
res3 <- jsonlite::fromJSON(txt = dat, simplifyDataFrame = TRUE)
for (i in 1:length(res3)) {
if (length(res3[[i]]) == 0) res[[i]] <- ''
}
# Set null length list-type elements to ''
for (i in 1:length(res3)) {
if (length(res3[[i]]) == 0) res3[[i]] <- ""
}
if (length(res3$siblings) > 1) {
siblings <- res3$siblings
names(siblings) <- paste0('siblings.', names(siblings))
res3$siblings <- NULL
res3 <- tibble::as.tibble(res3)
res3 <- cbind(res3, siblings)
siblings <- NULL
}
attr(res3, "metadata") <- lst$metadata
return(res3)
}
if (rclass %in% c("json", "list")) {
out <- dat2tbl(res = cont, rclass = rclass)
}
if (rclass == "tibble")
out <- ms2tbl(res = cont) %>% tibble::as_tibble()
if (rclass == "data.frame") {
out <- ms2tbl(res = cont) %>%
tibble::as_tibble() %>%
as.data.frame()
}
class(out) <- c(class(out), "ba_germplasm_pedigree")
show_metadata(resp)
return(out)
})
}
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