R/gni_parse.R

In ropensci/taxize: Taxonomic Information from Around the Web

#' Parse scientific names using EOL's name parser.
#'
#' @export
#' @param names A vector of length 1 or more of taxonomic names
#' @param ... Curl options passed on to [crul::verb-GET]
#' @return A data.frame with results, the submitted names, and the
#' parsed names with additional information.
#' @seealso [gbif_parse()], [gn_parse()]
#' @references http://gni.globalnames.org/
#' @examples \dontrun{
#' gni_parse("Cyanistes caeruleus")
#' gni_parse("Plantago minor")
#' gni_parse("Plantago minor minor")
#' gni_parse(c("Plantago minor minor","Helianthus annuus texanus"))
#'
#' # pass on curl options
#' gni_parse("Cyanistes caeruleus", verbose = TRUE)
#' }
gni_parse <- function(names, ...) {
  names <- paste0(names, collapse = "|")
  cli <- crul::HttpClient$new(paste0(gni_base(), "parsers.json"),
    headers = tx_ual, opts = list(...))
  tt <- cli$get(query = list(names = names))
  tt$raise_for_status()
  out <- jsonlite::fromJSON(tt$parse("UTF-8"), FALSE)
  dt2df(lapply(out, gni_parser), idcol = FALSE)
}

gni_parser <- function(x) {
  positions_names <- vapply(x$scientificName$positions, function(y)
    paste("position_", y[[1]], sep = ""), "", USE.NAMES = FALSE)
  nums <- vapply(x$scientificName$positions, function(y) y[[2]], 1,
    USE.NAMES = FALSE)
  pv <- data.frame(as.list(setNames(nums, positions_names)),
    stringsAsFactors = FALSE)

  nmz <- c("verbatim","canonical", "normalized","hybrid","parsed")
  singles <- data.frame(x$scientificName[names(x$scientificName) %in% nmz],
    stringsAsFactors = FALSE)
  
  details2 <- data.frame()
  if (x$scientificName$parsed) {
    details_ <- x$scientificName$details[[1]]
    details_ <- details_[!names(details_) %in% 'status']
    details <- dt2df(Map(function(x, y) data.frame(y, x,
      stringsAsFactors = FALSE), details_, names(details_)),
      idcol = FALSE)[,-3]
    details2 <- as.data.frame(t(data.frame(details[,2])))
    names(details2) <- details[,1]
    row.names(details2) <- NULL
  }
  
  data.frame(Filter(NROW, list(details2, singles, pv)),
    stringsAsFactors = FALSE)
}