AMR/R/mo_history.R

218 lines
8.5 KiB
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 a options entry
#' @importFrom dplyr %>% distinct filter
#' @importFrom utils write.csv
set_mo_history <- function(x, mo, uncertainty_level, force = FALSE, disable = FALSE) {
if (isTRUE(disable)) {
return(base::invisible())
}
# don't save codes that are in a code data set already
mo <- mo[!x %in% microorganisms.codes$code & !x %in% microorganisms.translation$mo_old]
x <- x[!x %in% microorganisms.codes$code & !x %in% microorganisms.translation$mo_old]
warning_new_write <- FALSE
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 seq_len(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_version == utils::packageVersion("AMR")), ]) == 0) {
# # Not using the file system:
# tryCatch(options(mo_remembered_results = rbind(mo_hist,
# data.frame(
# x = x[i],
# mo = mo[i],
# uncertainty_level = uncertainty_level,
# package_version = base::as.character(utils::packageVersion("AMR")),
# stringsAsFactors = FALSE))),
# error = function(e) base::invisible())
# # don't remember more than 1,000 different input values
# if (tryCatch(nrow(getOption("mo_remembered_results")), error = function(e) 1001) > 1000) {
# return(base::invisible())
# }
if (is.null(mo_hist) & interactive()) {
warning_new_write <- TRUE
}
tryCatch(write.csv(rbind(mo_hist,
data.frame(
x = x[i],
mo = mo[i],
uncertainty_level = uncertainty_level,
package_version = base::as.character(utils::packageVersion("AMR")),
stringsAsFactors = FALSE)),
row.names = FALSE,
file = mo_history_file()),
error = function(e) {
warning_new_write <- FALSE; base::invisible()
})
}
}
}
if (warning_new_write == TRUE) {
message(blue(paste0("NOTE: results are saved to ", mo_history_file(), ".")))
}
return(base::invisible())
}
get_mo_history <- function(x, uncertainty_level, force = FALSE, disable = FALSE) {
if (isTRUE(disable)) {
return(to_class_mo(NA))
}
history <- read_mo_history(uncertainty_level = uncertainty_level, force = force)
if (base::is.null(history)) {
result <- NA
} else {
result <- data.frame(x = as.character(toupper(x)), stringsAsFactors = FALSE) %>%
left_join(history, by = "x") %>%
pull(mo)
}
to_class_mo(result)
}
#' @importFrom dplyr %>% filter distinct
#' @importFrom utils read.csv
read_mo_history <- function(uncertainty_level = 2, force = FALSE, unfiltered = FALSE, disable = FALSE) {
if (isTRUE(disable)) {
return(NULL)
}
if ((!base::interactive() & force == FALSE)) {
return(NULL)
}
uncertainty_level_param <- uncertainty_level
# # Not using the file system:
# history <- tryCatch(getOption("mo_remembered_results"),
# error = function(e) NULL)
history <- tryCatch(read.csv(mo_history_file(), stringsAsFactors = FALSE),
warning = function(w) invisible(),
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_version == 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
clear_mo_history <- function(...) {
if (!is.null(read_mo_history())) {
if (interactive() & !isTRUE(list(...)$force)) {
q <- menu(title = paste("This will clear all",
format(nrow(read_mo_history(999, unfiltered = TRUE)), big.mark = ","),
"previously determined microbial IDs. Are you sure?"),
choices = c("Yes", "No"),
graphics = FALSE)
if (q != 1) {
return(invisible())
}
}
# # Not using the file system:
# success <- tryCatch(options(mo_remembered_results = NULL),
# error = function(e) FALSE)
success <- create_blank_mo_history()
if (!isFALSE(success)) {
cat(red(paste("File", mo_history_file(), "cleared.")))
}
}
}
#' @importFrom utils write.csv
create_blank_mo_history <- function() {
tryCatch(
write.csv(x = data.frame(x = character(0),
mo = character(0),
uncertainty_level = integer(0),
package_version = character(0),
stringsAsFactors = FALSE),
row.names = FALSE,
file = mo_history_file()),
warning = function(w) invisible(),
error = function(e) TRUE)
}
# Borrowed all below code from the extrafont package,
# https://github.com/wch/extrafont/blob/254c3f99b02f11adb59affbda699a92aec8624f5/R/utils.r
inst_path <- function() {
envname <- environmentName(parent.env(environment()))
# If installed in package, envname == "AMR"
# If loaded with load_all, envname == "package:AMR"
# (This is kind of strange)
if (envname == "AMR") {
system.file(package = "AMR")
} else {
srcfile <- attr(attr(inst_path, "srcref"), "srcfile")
file.path(dirname(dirname(srcfile$filename)), "inst")
}
}
# Get the path where extrafontdb is installed
db_path <- function() {
system.file(package = "AMR")
}
# fonttable file
mo_history_file <- function() {
file.path(mo_history_path(), "mo_history.csv")
}
# Path of fontmap directory
mo_history_path <- function() {
file.path(db_path(), "mo_history")
}