R/process_raw_comp_none.R

In femoerman/LEEF-BEMOVI: Data Package Containing Only Data and Data Information

#' Process all queues in the correct order
#'
#' This function is an example and can be used as a template for processing the
#' queues in a script. It uses the archiver "none" for the raw and pre-processed
#' data, useful for already compressed and large data, e.g. bemovi.
#' @return invisibly \code{TRUE}
#'
#' @param submitter name of the submitter of the data to the pipeline. Will be added to the metadata.
#' @param timestamp timestamp of the submission of the data to the pipeline.
#' This should be in the format \code{YYYYMMDD} and will be used to identify the sampling day.
#' @param ... additional arguments for the different queues
#'
#' @importFrom yaml yaml.load_file write_yaml
#'
#' @export
#'
#' @examples
#' \dontrun{
#'  process()
#' }

process_raw_comp_none <- function(
  submitter,
  timestamp,
  ...
) {

  # Set sample metadata -----------------------------------------------------

  smdf <- file.path(opt_directories()$raw, "sample_metadata.yml")

  smd <- yaml::yaml.load_file(smdf)

  if (!missing(submitter)) {
    smd$submitter <- submitter
  } else if (smd$submitter == "<<TO BE ENTERED>>") {
    stop(
      "A submitter needs to be specified!\n",
      "This can be done\n",
      "  - in the 'sample_metadata.yml' file in the raw data directory or \n",
      "  - as an argument for the function 'process()'!"
    )
  }

  if (!missing(timestamp)) {
    smd$timestamp <- timestamp
  } else if (smd$timestamp == "<<TO BE ENTERED>>") {
    smd$timestamp <- format( Sys.time() , "%Y-%m-%d--%H-%M-%S" )
  }

  yaml::write_yaml(
    smd,
    smdf
  )

  # Process queues ----------------------------------------------------------

  message("\n########################################################\n")
  message("\narchiving raw data ...\n")
  LEEF.archive.default::run_archive_none(
    input = getOption("LEEF")$directories$raw,
    output = file.path(getOption("LEEF")$directories$archive, "raw")
  )
  message("done\n")
  message("\n########################################################\n")

  message("\n########################################################\n")
  message("\npre_processing ...\n")
  run_pre_processors()
  message("done\n")
  message("\n########################################################\n")

  message("\n########################################################\n")
  message("\narchiving pre-processed data...\n")
  LEEF.archive.default::run_archive_none(
    input = getOption("LEEF")$directories$pre_processed,
    output = file.path(getOption("LEEF")$directories$archive, "pre_processed")
  )
  message("done\n")
  message("\n########################################################\n")

  message("\n########################################################\n")
  message("\nextracting ...\n")
  run_extractors()
  message("done\n")
  message("\n########################################################\n")

  message("\n########################################################\n")
  message("\narchiving extracted data ...\n")
  run_archivers(
    input = getOption("LEEF")$directories$extracted,
    output = file.path(getOption("LEEF")$directories$archive, "extracted")
  )
  message("done\n")
  message("\n########################################################\n")

  message("\n########################################################\n")
  message("\nadding...\n")
  run_additors()
  message("done\n")
  message("\n########################################################\n")


  # Finalize ----------------------------------------------------------------


  invisible(TRUE)
}