R/transformBasicStudyDesign.R

In RGLab/R2i: Tools for preparing an ImmPort Data Submission

#########################################
###          Main Function            ###
#########################################

#' @title Transform R dataframes into ImmPort basicStudyDesign.csv format
#'
#' @description Based on ImmPort's specifications, the function validates
#' a group of dataframes holding metaData and then outputs a csv
#' for submission to the database.
#'
#' @param blocks a named list of the 9 data frames that comprise basic study design template
#' @param outputDir filepath to directory for output csv
#' @param validate boolean determining whether to use ImmPort validation scripts on output csv
#' @param ... other arguments to pass down
#' @export
transform_basicStudyDesign <- function(blocks,
                                       outputDir = NULL,
                                       validate = TRUE,
                                       ...) {

  # Any errors in checkObj will stop transformation
  # if quiet = FALSE.
  res <- mapply(checkTemplate,
    df = blocks,
    ...
  )

  # ----- Convert to Vector / Lists -------
  # Convert to vector if empty DF so that no
  # extra rows are written in output file.
  # Must be done after checks because checks
  # assume data.frame input.
  blocks <- lapply(blocks, function(x) {
    chk <- unique(unname(unlist(x[1, ])))
    if (all(chk == "" | is.na(chk))) {
      return(colnames(x))
    } else {
      return(x)
    }
  })

  # Convert 'study' and 'protocol' to lists
  # to preserve data types and prepare for
  # write out.
  if (is.data.frame(blocks$study)) {
    blocks$study <- as.list(blocks$study)
  }

  if (is.data.frame(blocks$protocol)) {
    blocks$protocol <- as.list(blocks$protocol)
  }

  # --------- Generate tsv output -------------
  name <- "basic_study_design"
  if (is.null(outputDir)) {
    outputDir <- getwd()
  }
  file <- file.path(outputDir, paste0(name, ".txt"))

  write_txt(
    name = name,
    blocks = blocks,
    file = file
  )

  # ---------- Validate output -----------------
  # TODO: waiting on patrick for scripts

  return(res)
}