##' Query ProbeMap URL of Datasets

##'

##' If dataset has no ProbeMap, it will be ignored.

##'

##' @author Shixiang Wang <w_shixiang@163.com>

##' @param x a [XenaHub] object

##' @return a `data.frame` contains hosts, datasets and url

##' @importFrom dplyr filter select pull rename mutate

##' @export

##' @examples

##' xe = XenaGenerate(subset = XenaHostNames == "tcgaHub")

##' hosts(xe)

##' \dontrun{

##' xe_query = XenaQueryProbeMap(xe)

##' }

XenaQueryProbeMap <- function(x) {

  message("Check ProbeMap urls of datasets.")

  datasetsName <- datasets(x)

  query <- UCSCXenaTools::XenaData %>%

    dplyr::filter((XenaDatasets %in% datasetsName) & (!is.na(ProbeMap)))

  if (nrow(query) == 0) {

    invisible(data.frame(stringsAsFactors = FALSE))

  } else {

    query <- query %>%

      dplyr::rename(hosts = XenaHosts, datasets = ProbeMap) %>%

      dplyr::mutate(url = ifelse(.data$XenaHostNames %in% c("gdcHub", "gdcHubV18"),

        file.path(hosts, "download", url_encode(basename(datasets))),

        file.path(hosts, "download", url_encode(datasets))

      )) %>%

      dplyr::mutate(url = ifelse(!sapply(url, http_error2),

        url, paste0(url, ".gz")

      )) %>%

      dplyr::select(hosts, datasets, url) %>%

      as.data.frame()

    invisible(unique(query))

  }

}