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(v0.7.1.9061) mo_property improvement

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dr. M.S. (Matthijs) Berends
2019-08-26 10:03:37 +02:00
parent 05dcb43660
commit 13d4fef801
12 changed files with 26 additions and 21 deletions
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17
R/mo_property.R
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@ -144,7 +144,6 @@ mo_name <- function(x, language = get_locale(), ...) {
mo_fullname <- mo_name
#' @rdname mo_property
#' @importFrom dplyr %>% mutate pull
#' @export
mo_shortname <- function(x, language = get_locale(), ...) {
x.mo <- AMR::as.mo(x, ...)
@ -416,13 +415,19 @@ mo_validate <- function(x, property, ...) {
# so the 'call.' can be set to FALSE
tryCatch(x[1L] %in% AMR::microorganisms[1, property],
error = function(e) stop(e$message, call. = FALSE))
if (!all(x %in% pull(AMR::microorganisms, property))
| Becker %in% c(TRUE, "all")
| Lancefield %in% c(TRUE, "all")) {
if (is.mo(x)
& !Becker %in% c(TRUE, "all")
& !Lancefield %in% c(TRUE, "all")) {
# this will not reset mo_uncertainties and mo_failures
# because it's already a valid MO
x <- exec_as.mo(x, property = property, initial_search = FALSE, ...)
} else if (!all(x %in% pull(AMR::microorganisms, property))
| Becker %in% c(TRUE, "all")
| Lancefield %in% c(TRUE, "all")) {
x <- exec_as.mo(x, property = property, ...)
}
if (property == "mo") {
return(to_class_mo(x))
} else if (property == "col_id") {