R/get_file_list.R

In gtexr: Query the GTEx Portal API

#' Get File List
#'
#' @description Get all the files in GTEx dataset for Download page
#'
#'   [GTEx Portal API
#'   documentation](https://gtexportal.org/api/v2/redoc#tag/Datasets-Endpoints/operation/get_file_list_api_v2_dataset_fileList_get)
#'
#' @details The returned tibble includes a nested list column, "filesets". This
#'   details files, sub-categorised by fileset (see examples section).
#'
#' @return A tibble
#' @export
#' @family Datasets Endpoints
#'
#' @examples
#' \dontrun{
#' # Column "filesets" is a list column
#' get_file_list()
#'
#' # Get "GTEx Analysis V9" file list
#' gtex_v9_files <- get_file_list() |>
#'                    dplyr::filter(name == "GTEx Analysis V9") |>
#'                    dplyr::pull(filesets)
#'
#' # "GTEx Analysis V9" filesets
#' names(gtex_v9_files[[1]])
#'
#' # "GTEx Analysis V9", "snRNA-Seq Data" fileset files
#' names(gtex_v9_files[[1]][["snRNA-Seq Data"]]$files)
#' }
get_file_list <- function() {
  result <- gtex_query(endpoint = "dataset/fileList", return_raw = TRUE)
  result |>
    purrr::map(\(x) x |>
                 purrr::map_at("filesets", list) |>
                 tibble::as_tibble(),
               .progress = TRUE) |>
    dplyr::bind_rows() |>
    # add names to lists ('filesets' and 'files')
    dplyr::mutate("filesets" = purrr::map(.data[["filesets"]], \(x) {
      names(x) <- purrr::map_chr(x, \(y) y$name)
      x <- x |>
        purrr::map(\(x) x |>
                     purrr::map_at("files", \(y) {
                       names(y) <- purrr::map_chr(y, \(z) z$name)
                       y
                     }))
      x
    }))
}