R/id_converter.R

In rcrossref: Client for Various 'CrossRef' 'APIs'

#' Get a PMID from a DOI, and vice versa.
#'
#' @export
#' @param x (character) One or more of: doi, pmid, pmcid, or manuscript id, 
#' see examples. required.
#' @param type (character) one of doi, pmid, pmcid, or manuscript id
#' @param ... Curl args passed on to [crul::verb-GET]
#' @references https://www.ncbi.nlm.nih.gov/pmc/tools/id-converter-api/
#' @examples \dontrun{
#' # get a pmid/pmcid from a doi
#' id_converter("10.1038/ng.590")
#'
#' # pmid to doi/pmcid
#' id_converter("20495566", "pmid")
#' id_converter("20495566")
#' # id_converter("20495566", "doi") #error
#'
#' # pmcid to doi/pmid
#' id_converter("PMC2883744", "pmcid")
#' id_converter("PMC2883744")
#' 
#' # manuscript id
#' id_converter("NIHMS311352")
#' 
#' # more than 1 ID
#' id_converter(c("PMC3531190","PMC3245039"))
#'
#' # error, wrong type passed for id given
#' # id_converter("PMC2883744", "doi")
#' # error, 200 ids or less
#' # ids <- cr_r(100)
#' # id_converter(c(ids, ids, ids))
#' }
`id_converter` <- function(x, type = NULL, ...) {
  assert(x, c("numeric", "integer", "character"))
  if (length(x) > 1) {
    if (length(x) > 200) stop("200 ids or less please")
    x <- paste0(x, collapse = ",")
  }
  args <- cr_compact(list(tool = "rcrossref", email = "myrmecocystus@gmail.com",
    ids = x, idtype = type, format = "json"))
  cli <- crul::HttpClient$new(
    url = idcon_base(),
    headers = list(
      `User-Agent` = rcrossref_ua(), `X-USER-AGENT` = rcrossref_ua()
    )
  )
  res <- cli$get(query = args, ...)
  if (res$status_code > 201) {
    mssg <- jsonlite::fromJSON(res$parse("UTF-8"))$message
    stop(utils::URLdecode(mssg), call. = FALSE)
  }
  jsonlite::fromJSON(res$parse("UTF-8"))
}

idcon_base <- function() "https://www.ncbi.nlm.nih.gov/pmc/utils/idconv/v1.0/"