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(v1.3.0.9014) as.mo() speed improvement

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dr. M.S. (Matthijs) Berends
2020-09-03 12:31:48 +02:00
parent 18e52f2725
commit c4b87fe241
93 changed files with 739 additions and 609 deletions
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46
R/translate.R
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@ -23,15 +23,13 @@
#'
#' For language-dependent output of AMR functions, like [mo_name()], [mo_gramstain()], [mo_type()] and [ab_name()].
#' @inheritSection lifecycle Stable lifecycle
#' @details Strings will be translated to foreign languages if they are defined in a local translation file. Additions to this file can be suggested at our repository. The file can be found here: <https://github.com/msberends/AMR/blob/master/data-raw/translations.tsv>.
#' @details Strings will be translated to foreign languages if they are defined in a local translation file. Additions to this file can be suggested at our repository. The file can be found here: <https://github.com/msberends/AMR/blob/master/data-raw/translations.tsv>. This file will be read by all functions where a translated output can be desired, like all [mo_property()] functions ([mo_name()], [mo_gramstain()], [mo_type()], etc.).
#'
#' Currently supported languages are (besides English): `r paste(sort(gsub(";.*", "", ISOcodes::ISO_639_2[which(ISOcodes::ISO_639_2$Alpha_2 %in% unique(AMR:::translations_file$lang)), "Name"])), collapse = ", ")`. Please note that currently not all these languages have translations available for all antimicrobial agents and colloquial microorganism names.
#' Currently supported languages are: `r paste(sort(gsub(";.*", "", ISOcodes::ISO_639_2[which(ISOcodes::ISO_639_2$Alpha_2 %in% LANGUAGES_SUPPORTED), "Name"])), collapse = ", ")`. Please note that currently not all these languages have translations available for all antimicrobial agents and colloquial microorganism names.
#'
#' Please suggest your own translations [by creating a new issue on our repository](https://github.com/msberends/AMR/issues/new?title=Translations).
#'
#' This file will be read by all functions where a translated output can be desired, like all [mo_property()] functions ([mo_name()], [mo_gramstain()], [mo_type()], etc.).
#'
#' The system language will be used at default, if that language is supported. The system language can be overwritten with `Sys.setenv(AMR_locale = yourlanguage)`.
#' The system language will be used at default (as returned by [Sys.getlocale()]), if that language is supported. The language to be used can be overwritten by setting the option `AMR_locale`, e.g. `options(AMR_locale = "de")`.
#' @inheritSection AMR Read more on our website!
#' @rdname translate
#' @name translate
@ -66,10 +64,16 @@
#' #> "Staphylococcus coagulase negativo (CoNS)"
get_locale <- function() {
if (!is.null(getOption("AMR_locale", default = NULL))) {
return(getOption("AMR_locale"))
if (!language %in% LANGUAGES_SUPPORTED) {
stop_("unsupported language: '", language, "' - use one of: ",
paste0("'", LANGUAGES_SUPPORTED, "'", collapse = ", "),
call = FALSE)
} else {
return(getOption("AMR_locale"))
}
}
lang <- Sys.getlocale("LC_COLLATE")
lang <- Sys.getlocale()
# Check the locale settings for a start with one of these languages:
@ -107,10 +111,13 @@ translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE) {
}
df_trans <- translations_file # internal data file
from.bak <- from
from_unique <- unique(from)
from_unique_translated <- from_unique
stop_ifnot(language %in% df_trans$lang,
stop_ifnot(language %in% LANGUAGES_SUPPORTED,
"unsupported language: '", language, "' - use one of: ",
paste0("'", sort(unique(df_trans$lang)), "'", collapse = ", "),
paste0("'", LANGUAGES_SUPPORTED, "'", collapse = ", "),
call = FALSE)
df_trans <- subset(df_trans, lang == language)
@ -124,7 +131,7 @@ translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE) {
df_trans$fixed[is.na(df_trans$fixed)] <- TRUE
# check if text to look for is in one of the patterns
any_form_in_patterns <- tryCatch(any(from %like% paste0("(", paste(df_trans$pattern, collapse = "|"), ")")),
any_form_in_patterns <- tryCatch(any(from_unique %like% paste0("(", paste(df_trans$pattern, collapse = "|"), ")")),
error = function(e) {
warning("Translation not possible. Please open an issue on GitHub (https://github.com/msberends/AMR/issues).", call. = FALSE)
return(FALSE)
@ -133,15 +140,16 @@ translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE) {
return(from)
}
for (i in seq_len(nrow(df_trans))) {
from <- gsub(x = from,
pattern = df_trans$pattern[i],
replacement = df_trans$replacement[i],
fixed = df_trans$fixed[i],
ignore.case = df_trans$ignore.case[i])
}
lapply(seq_len(nrow(df_trans)),
function(i) from_unique_translated <<- gsub(pattern = df_trans$pattern[i],
replacement = df_trans$replacement[i],
x = from_unique_translated,
ignore.case = df_trans$ignore.case[i],
fixed = df_trans$fixed[i]))
# force UTF-8 for diacritics
base::enc2utf8(from)
from_unique_translated <- enc2utf8(from_unique_translated)
# a kind of left join to get all results back
from_unique_translated[match(from.bak, from_unique)]
}