AMR/R/mo_history.R

# ==================================================================== #
# TITLE                                                                #
# Antimicrobial Resistance (AMR) Analysis                              #
#                                                                      #
# SOURCE                                                               #
# https://gitlab.com/msberends/AMR                                     #
#                                                                      #
# LICENCE                                                              #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
#                                                                      #
# This R package is free software; you can freely use and distribute   #
# it for both personal and commercial purposes under the terms of the  #
# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
# the Free Software Foundation.                                        #
#                                                                      #
# This R package was created for academic research and was publicly    #
# released in the hope that it will be useful, but it comes WITHOUT    #
# ANY WARRANTY OR LIABILITY.                                           #
# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
# ==================================================================== #

# print successful as.mo coercions to AMR environment
#' @importFrom dplyr %>% distinct filter
set_mo_history <- function(x, mo, uncertainty_level, force = FALSE) {
  # disable function for now
  return(base::invisible())

  # if (base::interactive() | force == TRUE) {
  #   mo_hist <- read_mo_history(uncertainty_level = uncertainty_level, force = force)
  #   df <- data.frame(x, mo, stringsAsFactors = FALSE) %>%
  #     distinct(x, .keep_all = TRUE) %>%
  #     filter(!is.na(x) & !is.na(mo))
  #   if (nrow(df) == 0) {
  #     return(base::invisible())
  #   }
  #   x <- toupper(df$x)
  #   mo <- df$mo
  #   for (i in 1:length(x)) {
  #     # save package version too, as both the as.mo() algorithm and the reference data set may change
  #     if (NROW(mo_hist[base::which(mo_hist$x == x[i] &
  #                                  mo_hist$uncertainty_level >= uncertainty_level &
  #                                  mo_hist$package_v == utils::packageVersion("AMR")),]) == 0) {
  #       tryCatch(
  #         assign(x = "mo_history",
  #                value = rbind(mo_hist,
  #                              data.frame(
  #                                x = x[i],
  #                                mo = mo[i],
  #                                uncertainty_level = uncertainty_level,
  #                                package_v = base::as.character(utils::packageVersion("AMR")),
  #                                stringsAsFactors = FALSE)),
  #                envir = asNamespace("AMR")),
  #         error = function(e) invisible())
  #     }
  #   }
  # }
  # return(base::invisible())
}

get_mo_history <- function(x, uncertainty_level, force = FALSE) {
  # disable function for now
  return(NA)

  # history <- read_mo_history(uncertainty_level = uncertainty_level, force = force)
  # if (base::is.null(history)) {
  #   NA
  # } else {
  #   data.frame(x = toupper(x), stringsAsFactors = FALSE) %>%
  #     left_join(history, by = "x") %>%
  #     pull(mo)
  # }
}

#' @importFrom dplyr %>% filter distinct
read_mo_history <- function(uncertainty_level = 2, force = FALSE, unfiltered = FALSE) {
  # disable function for now
  return(NULL)

  # if ((!base::interactive() & force == FALSE)) {
  #   return(NULL)
  # }
  # uncertainty_level_param <- uncertainty_level
  #
  # history <- tryCatch(get("mo_history", envir = asNamespace("AMR")),
  #                       error = function(e) NULL)
  # if (is.null(history)) {
  #   return(NULL)
  # }
  # # Below: filter on current package version.
  # # Even current fullnames may be replaced by new taxonomic names, so new versions of
  # # the Catalogue of Life must not lead to data corruption.
  #
  # if (unfiltered == FALSE) {
  #   history <- history %>%
  #     filter(package_v == as.character(utils::packageVersion("AMR")),
  #            # only take unknowns if uncertainty_level_param is higher
  #            ((mo == "UNKNOWN" & uncertainty_level_param == uncertainty_level) |
  #               (mo != "UNKNOWN" & uncertainty_level_param >= uncertainty_level))) %>%
  #     arrange(desc(uncertainty_level)) %>%
  #     distinct(x, mo, .keep_all = TRUE)
  # }
  #
  # if (nrow(history) == 0) {
  #   NULL
  # } else {
  #   history
  # }
}

# @rdname as.mo
# @importFrom crayon red
# @importFrom utils menu
# @export
clean_mo_history <- function(...) {
  # if (!is.null(read_mo_history())) {
  #   if (interactive() & !isTRUE(list(...)$force)) {
  #     q <- menu(title = paste("This will remove all",
  #                             format(nrow(read_mo_history(999, unfiltered = TRUE)), big.mark = ","),
  #                             "microbial IDs determined previously in this session. Are you sure?"),
  #               choices = c("Yes", "No"),
  #               graphics = FALSE)
  #     if (q != 1) {
  #       return(invisible())
  #     }
  #   }
  #   tryCatch(
  #     assign(x = "mo_history",
  #            value = NULL,
  #            envir = asNamespace("AMR")),
  #     error = function(e) invisible())
  #   cat(red("History removed."))
  # }
}