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# ==================================================================== #
# 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.gitab.io/AMR. #
# ==================================================================== #
#' Use predefined reference data set
#'
#' These functions can be used to predefine your own reference to be used in \code{\link{as.mo}} and consequently all \code{mo_*} functions like \code{\link{mo_genus}} and \code{\link{mo_gramstain}}.
#' @param path location of your reference file, see Details
#' @rdname mo_source
#' @name mo_source
#' @aliases set_mo_source get_mo_source
#' @details The reference file can be a text file seperated with commas (CSV) or pipes, an Excel file (old 'xls' format or new 'xlsx' format) or an R object file (extension '.rds'). To use an Excel file, you need to have the \code{readxl} package installed.
#'
#' \code{set_mo_source} will check the file for validity: it must be a \code{data.frame}, must have a column named \code{"mo"} which contains values from \code{microorganisms$mo} and must have a reference column with your own defined values. If all tests pass, \code{set_mo_source} will read the file into R and export it to \code{"~/.mo_source.rds"}. This compressed data file will then be used at default for MO determination (function \code{\link{as.mo}} and consequently all \code{mo_*} functions like \code{\link{mo_genus}} and \code{\link{mo_gramstain}}). The location of the original file will be saved as option with \code{\link{options}(mo_source = path)}. Its timestamp will be saved with \code{\link{options}(mo_source_datetime = ...)}.
#'
#' \code{get_mo_source} will return the data set by reading \code{"~/.mo_source.rds"} with \code{\link{readRDS}}. If the original file has changed (the file defined with \code{path}), it will call \code{set_mo_source} to update the data file automatically.
#'
#' Reading an Excel file (\code{.xlsx}) with only one row has a size of 8-9 kB. The compressed file will have a size of 0.1 kB and can be read by \code{get_mo_source} in only a couple of microseconds (a millionth of a second).
#' @importFrom dplyr select everything
#' @export
#' @inheritSection AMR Read more on our website!
#' @examples
#' \dontrun{
#'
#' # imagine this Excel file (mo codes looked up in `microorganisms` data set):
#' # A B
#' # 1 our code mo
#' # 2 lab_mo_ecoli B_ESCHR_COL
#' # 3 lab_mo_kpneumoniae B_KLBSL_PNE
#'
#' # 1. We save it as 'home/me/ourcodes.xlsx'
#'
#' # 2. We use it for input:
#' set_mo_source("C:\path\ourcodes.xlsx")
#' #> Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
#'
#' # 3. And use it in our functions:
#' as.mo("lab_mo_ecoli")
#' #> B_ESCHR_COL
#'
#' mo_genus("lab_mo_kpneumoniae")
#' #> "Klebsiella"
#'
#' # 4. It will look for changes itself:
#' # (add new row to the Excel file and save it)
#'
#' mo_genus("lab_mo_kpneumoniae")
#' #> Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
#' #> "Klebsiella"
#' }
set_mo_source <- function(path) {
if (!is.character(path) | length(path) > 1) {
stop("`path` must be a character of length 1.")
}
if (path == "") {
options(mo_source = NULL)
options(mo_source_timestamp = NULL)
if (file.exists("~/.mo_source.rds")) {
unlink("~/.mo_source.rds")
message("Removed mo_source file '~/.mo_source.rds'.")
}
return(invisible())
}
if (!file.exists(path)) {
stop("File not found: ", path)
}
is_valid <- function(df) {
valid <- TRUE
if (!is.data.frame(df)) {
valid <- FALSE
} else if (!"mo" %in% colnames(df)) {
valid <- FALSE
} else if (!all(df$mo %in% AMR::microorganisms$mo)) {
valid <- FALSE
} else if (NCOL(df) < 2) {
valid <- FALSE
}
valid
}
if (path %like% '[.]rds$') {
df <- readRDS(path)
} else if (path %like% '[.]xlsx?$') {
# is Excel file (old or new)
if (!"readxl" %in% utils::installed.packages()) {
stop("Install the 'readxl' package first.")
}
df <- readxl::read_excel(path)
} else {
# try comma first
try(
df <- utils::read.table(header = TRUE, sep = ",", stringsAsFactors = FALSE),
silent = TRUE)
if (!is_valid(df)) {
# try pipe
try(
df <- utils::read.table(header = TRUE, sep = "|", stringsAsFactors = FALSE),
silent = TRUE)
}
}
if (!is_valid(df)) {
stop("File must contain a column with self-defined values and a reference column `mo` with valid values from the `microorganisms` data set.")
}
if (colnames(df)[1] == "mo") {
# put mo to the end
df <- df %>% select(-"mo", everything(), "mo")
}
df <- as.data.frame(df, stringAsFactors = FALSE)
# success
if (file.exists("~/.mo_source.rds")) {
action <- "Updated"
} else {
action <- "Created"
}
saveRDS(df, "~/.mo_source.rds")
options(mo_source = path)
options(mo_source_timestamp = as.character(file.info(path)$mtime))
message(action, " mo_source file '~/.mo_source.rds' from '", path, "'.")
}
#' @rdname mo_source
#' @export
get_mo_source <- function() {
if (is.null(getOption("mo_source", NULL))) {
return(NULL)
} else {
old_time <- as.POSIXct(getOption("mo_source_timestamp"))
new_time <- as.POSIXct(as.character(file.info(getOption("mo_source", ""))$mtime))
if (is.na(new_time)) {
# source file was deleted, remove reference too
set_mo_source("")
return(NULL)
}
if (new_time != old_time) {
# set updated source
set_mo_source(getOption("mo_source"))
}
}
readRDS("~/.mo_source.rds")
}