R/shaman_conf.R

In tanaylab/shaman: shaman - Sampling HiC contAct Matrices for Aparametric Normalization

#' Dump config file templates.
#'
#' Dump templates of config files required by the package.
#'
#' @param config_dir Directory to dump to files to.
#'
#'

.shaman_dump_config <- function(config_dir) {
    config_files <- dir(system.file("config", package = "shaman"), full.names = T)
    dir.create(config_dir, recursive = T, showWarnings = FALSE)
    ret <- file.copy(config_files, config_dir, recursive = T, overwrite = FALSE)
    if (!all(ret)) {
        warning("couldn't dump config files to ", config_dir, "\n  Perhaps they're already there? ")
    } else {
        message("Dumped config files to: ", config_dir)
    }
}

#' Load all the configuration files required for the package.
#'
#' Loads the configuration files which were filled by the user. Accepts either directory path
#' from \code{config_dir}, or individual files supplied by the other parameters.
#'
#' @param config_dir A directory with all the defined config files. Should have the same
#' files as those that were exported with \code{shaman_dump_config}.
#' @param shaman_config Parameter file
#'
#'
.shaman_load_config <- function(config_dir, shaman_config = file.path(config_dir, "shaman.conf"), reset = FALSE) {
    op <- options()
    all_paths <- list("shaman.shaman_conf_path" = shaman_config)

    op.shaman <- init_params(shaman_config)
    op.shaman <- c(op.shaman, all_paths)

    # Check if some params were saved already
    already_set <- names(op) %in% names(op.shaman)
    if (any(already_set) & reset == TRUE) {
        message(sprintf(
            "%i parameters were already defined in this sessions and they will be overwritten!",
            sum(already_set)
        ))
    }

    if (!reset) {
        op.shaman <- op.shaman[!already_set]
    }
    options(op.shaman)

    #    gset_input_mode(autocompletion = FALSE, interactive = FALSE)
    invisible()
}


#######################################################################
# .shaman_check_config
#
# internal function for checking that the configuration has been loaded
########################################################################
.shaman_check_config <- function(params) {
    if (!all(params %in% names(options()))) {
        .shaman_load_config(system.file("config", package = "shaman"))
    }
}