R/prevGBIFdownload.R

In occCite: Querying and Managing Large Biodiversity Occurrence Datasets

#' @title Download previously-prepared GBIF data sets
#'
#' @description Searches the list of a user's most recent 1000 downloads
#' on the GBIF servers and returns the data set key for the most recently
#' prepared download.
#'
#' @param taxonKey A taxon key as returned from `rgbif::name_suggest()`.
#'
#' @param GBIFLogin An object of class \code{\link{GBIFLogin}} to log in to
#' GBIF to begin the download.
#'
#' @return A GBIF download key, if one is available
#'
#' @examples
#' \dontrun{
#' GBIFLogin <- GBIFLoginManager(
#'   user = "theWoman",
#'   email = "ireneAdler@@laScala.org",
#'   pwd = "sh3r"
#' )
#' taxKey <- rgbif::name_suggest(
#'   q = "Protea cynaroides",
#'   rank = "species"
#' )$key[1]
#' prevGBIFdownload(
#'   taxonKey = taxKey,
#'   GBIFLogin = myGBIFLogin
#' )
#' }
#'
#' @export
#'
prevGBIFdownload <- function(taxonKey, GBIFLogin) {
  tryCatch(
    expr = dl <- rgbif::occ_download_list(
      user = GBIFLogin@username,
      pwd = GBIFLogin@pwd,
      limit = 1000
    ),
    error = function(e) {
      message(paste("GBIF unreachable; please try again later. \n"))
    }
  )

  if (!exists("dl")) {
    return(invisible(NULL))
  }

  recKey <- NULL
  retmat <- NULL
  for (i in 1:dim(dl$results)[1]) {
    if (!is.na(dl$results$request.predicate.key[i]) &
      dl$results$request.predicate.key[i] == "TAXON_KEY") {
      recKey <- dl$results$request.predicate.value[i]
    } else if (any(na.omit(dl$results$
      request.predicate.predicates[[i]]$key == "TAXON_KEY"))) {
      recKey <- dl$results$request.predicate.predicates[[i]][
        dl$results$request.predicate.predicates[[i]]$key == "TAXON_KEY",
      ]$value
    }
    if (any(grepl(pattern = taxonKey, recKey))) {
      retmat <- rbind(retmat, dl$results[i, ])
    }
  }
  if (is.null(retmat)) {
    return(NULL)
  } else {
    return(retmat[retmat$modified == rev(sort(retmat$modified))[1], ]$key)
  }
}