R/get_example_files.R

In taxonomicallyinformedannotation/tima-r: Taxonomically Informed Metabolite Annotation

#' @title Get example files
#'
#' @description This function downloads example files
#'
#' @include get_default_paths.R
#' @include get_example_sirius.R
#' @include get_file.R
#' @include go_to_cache.R
#'
#' @param example The example(s) you want to download
#' @param in_cache Flag to indicate if storing the files in cache
#'
#' @return Example files.
#'
#' @export
#'
#' @examples
#' \dontrun{
#' get_example_files(example = c("features"), in_cache = FALSE)
#' }
get_example_files <- function(
  example = c("features", "metadata", "sirius", "spectra"),
  in_cache = TRUE
) {
  stopifnot(
    # "Example files available are `features`, `hmdb_is`, `metadata`, `sirius`, `spectra` and `spectral_lib_with_rt`." = example %in%
    "Example files available are `features`, `metadata`, `sirius`, `spectra` and `spectral_lib_with_rt`." = example %in%
      c(
        "features",
        # "hmdb_is",
        "metadata",
        "sirius",
        "spectra",
        "spectral_lib_with_rt"
      )
  )
  if (in_cache) {
    go_to_cache()
  }
  if ("features" %in% example) {
    logger::log_trace("Features")
    get_file(
      url = get_default_paths()$urls$examples$features,
      export = get_default_paths()$data$source$features
    )
  }
  # if ("hmdb_is" %in% example) {
  #   logger::log_trace("HMDB in silico")
  #   get_file(
  #     url = get_default_paths()$urls$hmdb$spectra$predicted,
  #     export = get_default_paths()$data$source$libraries$spectra$is$hmdb
  #   )
  # }
  if ("metadata" %in% example) {
    logger::log_trace("Metadata")
    get_file(
      url = get_default_paths()$urls$examples$metadata,
      export = get_default_paths()$data$source$metadata
    )
  }
  if ("sirius" %in% example) {
    logger::log_trace("Sirius")
    get_example_sirius()
  }
  if ("spectra" %in% example) {
    logger::log_trace("Spectra")
    get_file(
      url = get_default_paths()$urls$examples$spectra,
      # url = get_default_paths()$urls$examples$spectra_mini,
      export = get_default_paths()$data$source$spectra
    )
  }
  if ("spectral_lib_with_rt" %in% example) {
    logger::log_trace("Spectral library with retention times")
    get_file(
      url = get_default_paths()$urls$examples$spectral_lib_mini$with_rt,
      export = get_default_paths()$data$source$libraries$spectra$exp$with_rt
    )
  }
}