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language updates

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dr. M.S. (Matthijs) Berends
2022-08-19 12:33:14 +02:00
parent 4b19c3dc5e
commit 3f2f60ab77
23 changed files with 543 additions and 506 deletions
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36
R/mo_property.R
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@ -178,10 +178,10 @@ mo_name <- function(x, language = get_AMR_locale(), ...) {
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
translate_AMR(mo_validate(x = x, property = "fullname", language = language, ...),
language = language,
only_unknown = FALSE,
only_affect_mo_names = TRUE)
translate_into_language(mo_validate(x = x, property = "fullname", language = language, ...),
language = language,
only_unknown = FALSE,
only_affect_mo_names = TRUE)
}
#' @rdname mo_property
@ -223,7 +223,7 @@ mo_shortname <- function(x, language = get_AMR_locale(), ...) {
shortnames[is.na(x.mo)] <- NA_character_
load_mo_failures_uncertainties_renamed(metadata)
translate_AMR(shortnames, language = language, only_unknown = FALSE, only_affect_mo_names = TRUE)
translate_into_language(shortnames, language = language, only_unknown = FALSE, only_affect_mo_names = TRUE)
}
@ -238,7 +238,7 @@ mo_subspecies <- function(x, language = get_AMR_locale(), ...) {
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
translate_AMR(mo_validate(x = x, property = "subspecies", language = language, ...), language = language, only_unknown = TRUE)
translate_into_language(mo_validate(x = x, property = "subspecies", language = language, ...), language = language, only_unknown = TRUE)
}
#' @rdname mo_property
@ -251,7 +251,7 @@ mo_species <- function(x, language = get_AMR_locale(), ...) {
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
translate_AMR(mo_validate(x = x, property = "species", language = language, ...), language = language, only_unknown = TRUE)
translate_into_language(mo_validate(x = x, property = "species", language = language, ...), language = language, only_unknown = TRUE)
}
#' @rdname mo_property
@ -264,7 +264,7 @@ mo_genus <- function(x, language = get_AMR_locale(), ...) {
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
translate_AMR(mo_validate(x = x, property = "genus", language = language, ...), language = language, only_unknown = TRUE)
translate_into_language(mo_validate(x = x, property = "genus", language = language, ...), language = language, only_unknown = TRUE)
}
#' @rdname mo_property
@ -277,7 +277,7 @@ mo_family <- function(x, language = get_AMR_locale(), ...) {
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
translate_AMR(mo_validate(x = x, property = "family", language = language, ...), language = language, only_unknown = TRUE)
translate_into_language(mo_validate(x = x, property = "family", language = language, ...), language = language, only_unknown = TRUE)
}
#' @rdname mo_property
@ -290,7 +290,7 @@ mo_order <- function(x, language = get_AMR_locale(), ...) {
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
translate_AMR(mo_validate(x = x, property = "order", language = language, ...), language = language, only_unknown = TRUE)
translate_into_language(mo_validate(x = x, property = "order", language = language, ...), language = language, only_unknown = TRUE)
}
#' @rdname mo_property
@ -303,7 +303,7 @@ mo_class <- function(x, language = get_AMR_locale(), ...) {
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
translate_AMR(mo_validate(x = x, property = "class", language = language, ...), language = language, only_unknown = TRUE)
translate_into_language(mo_validate(x = x, property = "class", language = language, ...), language = language, only_unknown = TRUE)
}
#' @rdname mo_property
@ -316,7 +316,7 @@ mo_phylum <- function(x, language = get_AMR_locale(), ...) {
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
translate_AMR(mo_validate(x = x, property = "phylum", language = language, ...), language = language, only_unknown = TRUE)
translate_into_language(mo_validate(x = x, property = "phylum", language = language, ...), language = language, only_unknown = TRUE)
}
#' @rdname mo_property
@ -329,7 +329,7 @@ mo_kingdom <- function(x, language = get_AMR_locale(), ...) {
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
translate_AMR(mo_validate(x = x, property = "kingdom", language = language, ...), language = language, only_unknown = TRUE)
translate_into_language(mo_validate(x = x, property = "kingdom", language = language, ...), language = language, only_unknown = TRUE)
}
#' @rdname mo_property
@ -349,7 +349,7 @@ mo_type <- function(x, language = get_AMR_locale(), ...) {
x.mo <- as.mo(x, language = language, ...)
out <- mo_kingdom(x.mo, language = NULL)
out[which(mo_is_yeast(x.mo))] <- "Yeasts"
translate_AMR(out, language = language, only_unknown = FALSE)
translate_into_language(out, language = language, only_unknown = FALSE)
}
#' @rdname mo_property
@ -380,7 +380,7 @@ mo_gramstain <- function(x, language = get_AMR_locale(), ...) {
| x.mo == "B_GRAMP"] <- "Gram-positive"
load_mo_failures_uncertainties_renamed(metadata)
translate_AMR(x, language = language, only_unknown = FALSE)
translate_into_language(x, language = language, only_unknown = FALSE)
}
#' @rdname mo_property
@ -435,9 +435,7 @@ mo_is_yeast <- function(x, language = get_AMR_locale(), ...) {
metadata <- get_mo_failures_uncertainties_renamed()
x.kingdom <- mo_kingdom(x.mo, language = NULL)
x.phylum <- mo_phylum(x.mo, language = NULL)
x.class <- mo_class(x.mo, language = NULL)
x.order <- mo_order(x.mo, language = NULL)
load_mo_failures_uncertainties_renamed(metadata)
@ -705,7 +703,7 @@ mo_property <- function(x, property = "fullname", language = get_AMR_locale(), .
meet_criteria(property, allow_class = "character", has_length = 1, is_in = colnames(microorganisms))
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
translate_AMR(mo_validate(x = x, property = property, language = language, ...), language = language, only_unknown = TRUE)
translate_into_language(mo_validate(x = x, property = property, language = language, ...), language = language, only_unknown = TRUE)
}
mo_validate <- function(x, property, language, ...) {
@ -724,7 +722,7 @@ mo_validate <- function(x, property, language, ...) {
if (tryCatch(all(x[!is.na(x)] %in% MO_lookup$mo) & !has_Becker_or_Lancefield, error = function(e) FALSE)) {
# special case for mo_* functions where class is already <mo>
x <- MO_lookup[match(x, MO_lookup$mo), property, drop = TRUE]
} else {
# try to catch an error when inputting an invalid argument
# so the 'call.' can be set to FALSE