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support veterinary MIC/disk translation

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dr. M.S. (Matthijs) Berends
2024-02-24 15:16:52 +01:00
parent 74ea6c8c60
commit 7be4dabbc0
69 changed files with 34521 additions and 30207 deletions
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11
R/mo_source.R
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@ -125,14 +125,13 @@
#' If the original file (in the previous case an Excel file) is moved or deleted, the `mo_source.rds` file will be removed upon the next use of [as.mo()] or any [`mo_*`][mo_property()] function.
#' @export
set_mo_source <- function(path, destination = getOption("AMR_mo_source", "~/mo_source.rds")) {
stop_ifnot(interactive(), "this function can only be used in interactive mode, since it must ask for the user's permission to write a file to their file system.")
meet_criteria(path, allow_class = "character", has_length = 1, allow_NULL = TRUE)
meet_criteria(destination, allow_class = "character", has_length = 1)
stop_ifnot(destination %like% "[.]rds$", "the `destination` must be a file location with file extension .rds.")
mo_source_destination <- path.expand(destination)
stop_ifnot(interactive(), "this function can only be used in interactive mode, since it must ask for the user's permission to write a file to their file system.")
if (is.null(path) || path %in% c(FALSE, "")) {
AMR_env$mo_source <- NULL
if (file.exists(mo_source_destination)) {
@ -247,6 +246,12 @@ get_mo_source <- function(destination = getOption("AMR_mo_source", "~/mo_source.
}
return(NULL)
}
if (destination %unlike% "[.]rds$") {
current_ext <- regexpr("\\.([[:alnum:]]+)$", destination)
current_ext <- ifelse(current_ext > -1L, substring(destination, current_ext + 1L), "")
vowel <- ifelse(current_ext %like% "^[AEFHILMNORSX]", "n", "")
stop_("The AMR mo source must be an RDS file, not a", vowel, " ", toupper(current_ext), " file. If `\"", basename(destination), "\"` was meant as your input file, use `set_mo_source()` on this file. In any case, the option `AMR_mo_source` must be set to another path.")
}
if (is.null(AMR_env$mo_source)) {
AMR_env$mo_source <- readRDS_AMR(path.expand(destination))
}