P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 07:51:57 +02:00
Code Releases Activity

(v1.3.0.9018) language corrections

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-09-14 12:21:23 +02:00
parent 0f6760d427
commit 7b6dd676f7
30 changed files with 364 additions and 252 deletions
Download Patch File Download Diff File Expand all files Collapse all files

64
R/mo_property.R
View File

@ -141,7 +141,7 @@
#' mo_info("E. coli")
#' }
mo_name <- function(x, language = get_locale(), ...) {
translate_AMR(mo_validate(x = x, property = "fullname", ...), language = language, only_unknown = FALSE)
translate_AMR(mo_validate(x = x, property = "fullname", language = language, ...), language = language, only_unknown = FALSE)
}
#' @rdname mo_property
@ -151,7 +151,7 @@ mo_fullname <- mo_name
#' @rdname mo_property
#' @export
mo_shortname <- function(x, language = get_locale(), ...) {
x.mo <- as.mo(x, ...)
x.mo <- as.mo(x, language = language, ...)
metadata <- get_mo_failures_uncertainties_renamed()
@ -181,49 +181,49 @@ mo_shortname <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_subspecies <- function(x, language = get_locale(), ...) {
translate_AMR(mo_validate(x = x, property = "subspecies", ...), language = language, only_unknown = TRUE)
translate_AMR(mo_validate(x = x, property = "subspecies", language = language, ...), language = language, only_unknown = TRUE)
}
#' @rdname mo_property
#' @export
mo_species <- function(x, language = get_locale(), ...) {
translate_AMR(mo_validate(x = x, property = "species", ...), language = language, only_unknown = TRUE)
translate_AMR(mo_validate(x = x, property = "species", language = language, ...), language = language, only_unknown = TRUE)
}
#' @rdname mo_property
#' @export
mo_genus <- function(x, language = get_locale(), ...) {
translate_AMR(mo_validate(x = x, property = "genus", ...), language = language, only_unknown = TRUE)
translate_AMR(mo_validate(x = x, property = "genus", language = language, ...), language = language, only_unknown = TRUE)
}
#' @rdname mo_property
#' @export
mo_family <- function(x, language = get_locale(), ...) {
translate_AMR(mo_validate(x = x, property = "family", ...), language = language, only_unknown = TRUE)
translate_AMR(mo_validate(x = x, property = "family", language = language, ...), language = language, only_unknown = TRUE)
}
#' @rdname mo_property
#' @export
mo_order <- function(x, language = get_locale(), ...) {
translate_AMR(mo_validate(x = x, property = "order", ...), language = language, only_unknown = TRUE)
translate_AMR(mo_validate(x = x, property = "order", language = language, ...), language = language, only_unknown = TRUE)
}
#' @rdname mo_property
#' @export
mo_class <- function(x, language = get_locale(), ...) {
translate_AMR(mo_validate(x = x, property = "class", ...), language = language, only_unknown = TRUE)
translate_AMR(mo_validate(x = x, property = "class", language = language, ...), language = language, only_unknown = TRUE)
}
#' @rdname mo_property
#' @export
mo_phylum <- function(x, language = get_locale(), ...) {
translate_AMR(mo_validate(x = x, property = "phylum", ...), language = language, only_unknown = TRUE)
translate_AMR(mo_validate(x = x, property = "phylum", language = language, ...), language = language, only_unknown = TRUE)
}
#' @rdname mo_property
#' @export
mo_kingdom <- function(x, language = get_locale(), ...) {
translate_AMR(mo_validate(x = x, property = "kingdom", ...), language = language, only_unknown = TRUE)
translate_AMR(mo_validate(x = x, property = "kingdom", language = language, ...), language = language, only_unknown = TRUE)
}
#' @rdname mo_property
@ -233,13 +233,13 @@ mo_domain <- mo_kingdom
#' @rdname mo_property
#' @export
mo_type <- function(x, language = get_locale(), ...) {
translate_AMR(mo_validate(x = x, property = "kingdom", ...), language = language, only_unknown = FALSE)
translate_AMR(mo_validate(x = x, property = "kingdom", language = language, ...), language = language, only_unknown = FALSE)
}
#' @rdname mo_property
#' @export
mo_gramstain <- function(x, language = get_locale(), ...) {
x.mo <- as.mo(x, ...)
x.mo <- as.mo(x, language = language, ...)
metadata <- get_mo_failures_uncertainties_renamed()
x.phylum <- mo_phylum(x.mo)
@ -269,20 +269,20 @@ mo_gramstain <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_snomed <- function(x, ...) {
mo_validate(x = x, property = "snomed", ...)
mo_snomed <- function(x, language = get_locale(), ...) {
mo_validate(x = x, property = "snomed", language = language, ...)
}
#' @rdname mo_property
#' @export
mo_ref <- function(x, ...) {
mo_validate(x = x, property = "ref", ...)
mo_ref <- function(x, language = get_locale(), ...) {
mo_validate(x = x, property = "ref", language = language, ...)
}
#' @rdname mo_property
#' @export
mo_authors <- function(x, ...) {
x <- mo_validate(x = x, property = "ref", ...)
mo_authors <- function(x, language = get_locale(), ...) {
x <- mo_validate(x = x, property = "ref", language = language, ...)
# remove last 4 digits and presumably the comma and space that preceed them
x[!is.na(x)] <- gsub(",? ?[0-9]{4}", "", x[!is.na(x)])
suppressWarnings(x)
@ -290,8 +290,8 @@ mo_authors <- function(x, ...) {
#' @rdname mo_property
#' @export
mo_year <- function(x, ...) {
x <- mo_validate(x = x, property = "ref", ...)
mo_year <- function(x, language = get_locale(), ...) {
x <- mo_validate(x = x, property = "ref", language = language, ...)
# get last 4 digits
x[!is.na(x)] <- gsub(".*([0-9]{4})$", "\\1", x[!is.na(x)])
suppressWarnings(as.integer(x))
@ -299,14 +299,14 @@ mo_year <- function(x, ...) {
#' @rdname mo_property
#' @export
mo_rank <- function(x, ...) {
mo_validate(x = x, property = "rank", ...)
mo_rank <- function(x, language = get_locale(), ...) {
mo_validate(x = x, property = "rank", language = language, ...)
}
#' @rdname mo_property
#' @export
mo_taxonomy <- function(x, language = get_locale(), ...) {
x <- as.mo(x, ...)
x <- as.mo(x, language = language, ...)
metadata <- get_mo_failures_uncertainties_renamed()
result <- list(kingdom = mo_kingdom(x, language = language),
@ -324,8 +324,8 @@ mo_taxonomy <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_synonyms <- function(x, ...) {
x <- as.mo(x, ...)
mo_synonyms <- function(x, language = get_locale(), ...) {
x <- as.mo(x, language = language, ...)
metadata <- get_mo_failures_uncertainties_renamed()
IDs <- mo_name(x = x, language = NULL)
@ -351,7 +351,7 @@ mo_synonyms <- function(x, ...) {
#' @rdname mo_property
#' @export
mo_info <- function(x, language = get_locale(), ...) {
x <- as.mo(x, ...)
x <- as.mo(x, language = language, ...)
metadata <- get_mo_failures_uncertainties_renamed()
info <- lapply(x, function(y)
@ -373,8 +373,8 @@ mo_info <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_url <- function(x, open = FALSE, ...) {
mo <- as.mo(x = x, ... = ...)
mo_url <- function(x, open = FALSE, language = get_locale(), ...) {
mo <- as.mo(x = x, language = language, ... = ...)
mo_names <- mo_name(mo)
metadata <- get_mo_failures_uncertainties_renamed()
@ -407,10 +407,10 @@ mo_property <- function(x, property = "fullname", language = get_locale(), ...)
stop_ifnot(property %in% colnames(microorganisms),
"invalid property: '", property, "' - use a column name of the `microorganisms` data set")
translate_AMR(mo_validate(x = x, property = property, ...), language = language, only_unknown = TRUE)
translate_AMR(mo_validate(x = x, property = property, language = language, ...), language = language, only_unknown = TRUE)
}
mo_validate <- function(x, property, ...) {
mo_validate <- function(x, property, language, ...) {
check_dataset_integrity()
@ -439,11 +439,11 @@ mo_validate <- function(x, property, ...) {
& !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, ...)
x <- exec_as.mo(x, property = property, initial_search = FALSE, language = language, ...)
} else if (!all(x %in% MO_lookup[, property, drop = TRUE])
| Becker %in% c(TRUE, "all")
| Lancefield %in% c(TRUE, "all")) {
x <- exec_as.mo(x, property = property, ...)
x <- exec_as.mo(x, property = property, language = language, ...)
}
if (property == "mo") {