R/add_reclassified_to_db.R

In LEEF-UZH/LEEF.analysis: Access Functions, Tests and Basic Analysis of the RRD Data from the LEEF Project

#' Title
#'
#' @param path path to the root directory of the reclassification
#' @param db fully qualified path to the sqlite database. Default, read from option \code{RRDdb}.
#'   If not set, defaults to option \code{RRDdb}; if this is not set, defaults to \code{LEEF.RRD.sqlite}
#' @param remove_timestamps vector of timestamps to be removed.
#' @param check_timestamps If `TRUE`, the data will ony be added when timestamp does not exist in db yet. If `FALSE`,
#'   it will always be added. Usually this should **NOT** be done.#'
#' @param backup_removed if \code{TRUE} data which will be replaced will be backed up.
#' @param method method to be added. If \code{NULL}, method will be determined by the sub-directories.
#' @param DBIDriver the DBI driver to use. Default is RSQLite::SQLite()
#'
#' @return
#' 
#' @importFrom DBI dbConnect dbDisconnect dbWriteTable dbGetQuery
#' @importFrom RSQLite SQLite
#' @importFrom utils read.csv
#' @
#' @export
#'
#' @examples
add_reclassified_to_db <- function(
    path,
    db = getOption("RRDdb", "LEEF.RRD.sqlite"),
    remove_timestamps = NULL,
    check_timestamps = TRUE,
    backup_removed = TRUE,
    methods = NULL,
    DBIDriver = RSQLite::SQLite()
) {
  if (!file.exists(db)) {
    LEEF.backend.sqlite::new_RRD(db)
  }

  if (is.null(methods)) {
    methods <- list.dirs(
      path,
      recursive = FALSE
    )
  }

  for (method in methods) {
    files <- list.files(file.path(path, method), full.names = TRUE)
    files <- grep("trajectories", files, invert = TRUE, value = TRUE)
    files <- sample(files)
    tables <- paste0(
      basename(method), "__",
      sapply(files, function(f) {
        strsplit(basename(f), "\\.")[[1]][[1]]
      })
    )
    names(tables) <- NULL

    message("Adding directory '", method, "' to the database")
    add_to_db(
      fns = files,
      tables = tables,
      db = db,
      remove_timestamps = remove_timestamps,
      check_timestamps = check_timestamps,
      backup_removed = backup_removed,
      DBIDriver = DBIDriver
    )
  }
}