|
|
|
@ -146,7 +146,7 @@
|
|
|
|
|
#' mo_info("E. coli")
|
|
|
|
|
#' }
|
|
|
|
|
mo_name <- function(x, language = get_locale(), ...) {
|
|
|
|
|
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
|
|
|
|
|
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)
|
|
|
|
@ -159,7 +159,7 @@ mo_fullname <- mo_name
|
|
|
|
|
#' @rdname mo_property
|
|
|
|
|
#' @export
|
|
|
|
|
mo_shortname <- function(x, language = get_locale(), ...) {
|
|
|
|
|
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
|
|
|
|
|
meet_criteria(x, allow_NA = TRUE)
|
|
|
|
|
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
|
|
|
|
|
|
|
|
|
x.mo <- as.mo(x, language = language, ...)
|
|
|
|
@ -192,7 +192,7 @@ mo_shortname <- function(x, language = get_locale(), ...) {
|
|
|
|
|
#' @rdname mo_property
|
|
|
|
|
#' @export
|
|
|
|
|
mo_subspecies <- function(x, language = get_locale(), ...) {
|
|
|
|
|
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
|
|
|
|
|
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)
|
|
|
|
@ -201,7 +201,7 @@ mo_subspecies <- function(x, language = get_locale(), ...) {
|
|
|
|
|
#' @rdname mo_property
|
|
|
|
|
#' @export
|
|
|
|
|
mo_species <- function(x, language = get_locale(), ...) {
|
|
|
|
|
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
|
|
|
|
|
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)
|
|
|
|
@ -210,7 +210,7 @@ mo_species <- function(x, language = get_locale(), ...) {
|
|
|
|
|
#' @rdname mo_property
|
|
|
|
|
#' @export
|
|
|
|
|
mo_genus <- function(x, language = get_locale(), ...) {
|
|
|
|
|
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
|
|
|
|
|
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)
|
|
|
|
@ -219,7 +219,7 @@ mo_genus <- function(x, language = get_locale(), ...) {
|
|
|
|
|
#' @rdname mo_property
|
|
|
|
|
#' @export
|
|
|
|
|
mo_family <- function(x, language = get_locale(), ...) {
|
|
|
|
|
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
|
|
|
|
|
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)
|
|
|
|
@ -228,7 +228,7 @@ mo_family <- function(x, language = get_locale(), ...) {
|
|
|
|
|
#' @rdname mo_property
|
|
|
|
|
#' @export
|
|
|
|
|
mo_order <- function(x, language = get_locale(), ...) {
|
|
|
|
|
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
|
|
|
|
|
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)
|
|
|
|
@ -237,7 +237,7 @@ mo_order <- function(x, language = get_locale(), ...) {
|
|
|
|
|
#' @rdname mo_property
|
|
|
|
|
#' @export
|
|
|
|
|
mo_class <- function(x, language = get_locale(), ...) {
|
|
|
|
|
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
|
|
|
|
|
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)
|
|
|
|
@ -246,7 +246,7 @@ mo_class <- function(x, language = get_locale(), ...) {
|
|
|
|
|
#' @rdname mo_property
|
|
|
|
|
#' @export
|
|
|
|
|
mo_phylum <- function(x, language = get_locale(), ...) {
|
|
|
|
|
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
|
|
|
|
|
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)
|
|
|
|
@ -255,7 +255,7 @@ mo_phylum <- function(x, language = get_locale(), ...) {
|
|
|
|
|
#' @rdname mo_property
|
|
|
|
|
#' @export
|
|
|
|
|
mo_kingdom <- function(x, language = get_locale(), ...) {
|
|
|
|
|
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
|
|
|
|
|
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)
|
|
|
|
@ -268,7 +268,7 @@ mo_domain <- mo_kingdom
|
|
|
|
|
#' @rdname mo_property
|
|
|
|
|
#' @export
|
|
|
|
|
mo_type <- function(x, language = get_locale(), ...) {
|
|
|
|
|
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
|
|
|
|
|
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 = FALSE)
|
|
|
|
@ -277,7 +277,7 @@ mo_type <- function(x, language = get_locale(), ...) {
|
|
|
|
|
#' @rdname mo_property
|
|
|
|
|
#' @export
|
|
|
|
|
mo_gramstain <- function(x, language = get_locale(), ...) {
|
|
|
|
|
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
|
|
|
|
|
meet_criteria(x, allow_NA = TRUE)
|
|
|
|
|
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
|
|
|
|
|
|
|
|
|
x.mo <- as.mo(x, language = language, ...)
|
|
|
|
@ -311,7 +311,7 @@ mo_gramstain <- function(x, language = get_locale(), ...) {
|
|
|
|
|
#' @rdname mo_property
|
|
|
|
|
#' @export
|
|
|
|
|
is_gram_negative <- function(x, ...) {
|
|
|
|
|
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
|
|
|
|
|
meet_criteria(x, allow_NA = TRUE)
|
|
|
|
|
grams <- mo_gramstain(x, language = NULL, ...)
|
|
|
|
|
"Gram-negative" == grams & !is.na(grams)
|
|
|
|
|
}
|
|
|
|
@ -319,7 +319,7 @@ is_gram_negative <- function(x, ...) {
|
|
|
|
|
#' @rdname mo_property
|
|
|
|
|
#' @export
|
|
|
|
|
is_gram_positive <- function(x, ...) {
|
|
|
|
|
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
|
|
|
|
|
meet_criteria(x, allow_NA = TRUE)
|
|
|
|
|
grams <- mo_gramstain(x, language = NULL, ...)
|
|
|
|
|
"Gram-positive" == grams & !is.na(grams)
|
|
|
|
|
}
|
|
|
|
@ -327,7 +327,7 @@ is_gram_positive <- function(x, ...) {
|
|
|
|
|
#' @rdname mo_property
|
|
|
|
|
#' @export
|
|
|
|
|
mo_snomed <- function(x, language = get_locale(), ...) {
|
|
|
|
|
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
|
|
|
|
|
meet_criteria(x, allow_NA = TRUE)
|
|
|
|
|
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
|
|
|
|
|
|
|
|
|
mo_validate(x = x, property = "snomed", language = language, ...)
|
|
|
|
@ -336,7 +336,7 @@ mo_snomed <- function(x, language = get_locale(), ...) {
|
|
|
|
|
#' @rdname mo_property
|
|
|
|
|
#' @export
|
|
|
|
|
mo_ref <- function(x, language = get_locale(), ...) {
|
|
|
|
|
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
|
|
|
|
|
meet_criteria(x, allow_NA = TRUE)
|
|
|
|
|
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
|
|
|
|
|
|
|
|
|
mo_validate(x = x, property = "ref", language = language, ...)
|
|
|
|
@ -345,7 +345,7 @@ mo_ref <- function(x, language = get_locale(), ...) {
|
|
|
|
|
#' @rdname mo_property
|
|
|
|
|
#' @export
|
|
|
|
|
mo_authors <- function(x, language = get_locale(), ...) {
|
|
|
|
|
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
|
|
|
|
|
meet_criteria(x, allow_NA = TRUE)
|
|
|
|
|
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
|
|
|
|
|
|
|
|
|
x <- mo_validate(x = x, property = "ref", language = language, ...)
|
|
|
|
@ -357,7 +357,7 @@ mo_authors <- function(x, language = get_locale(), ...) {
|
|
|
|
|
#' @rdname mo_property
|
|
|
|
|
#' @export
|
|
|
|
|
mo_year <- function(x, language = get_locale(), ...) {
|
|
|
|
|
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
|
|
|
|
|
meet_criteria(x, allow_NA = TRUE)
|
|
|
|
|
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
|
|
|
|
|
|
|
|
|
x <- mo_validate(x = x, property = "ref", language = language, ...)
|
|
|
|
@ -369,7 +369,7 @@ mo_year <- function(x, language = get_locale(), ...) {
|
|
|
|
|
#' @rdname mo_property
|
|
|
|
|
#' @export
|
|
|
|
|
mo_rank <- function(x, language = get_locale(), ...) {
|
|
|
|
|
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
|
|
|
|
|
meet_criteria(x, allow_NA = TRUE)
|
|
|
|
|
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
|
|
|
|
|
|
|
|
|
mo_validate(x = x, property = "rank", language = language, ...)
|
|
|
|
@ -378,20 +378,20 @@ mo_rank <- function(x, language = get_locale(), ...) {
|
|
|
|
|
#' @rdname mo_property
|
|
|
|
|
#' @export
|
|
|
|
|
mo_taxonomy <- function(x, language = get_locale(), ...) {
|
|
|
|
|
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
|
|
|
|
|
meet_criteria(x, allow_NA = TRUE)
|
|
|
|
|
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
|
|
|
|
|
|
|
|
|
x <- as.mo(x, language = language, ...)
|
|
|
|
|
metadata <- get_mo_failures_uncertainties_renamed()
|
|
|
|
|
|
|
|
|
|
result <- list(kingdom = mo_kingdom(x, language = language),
|
|
|
|
|
phylum = mo_phylum(x, language = language),
|
|
|
|
|
class = mo_class(x, language = language),
|
|
|
|
|
order = mo_order(x, language = language),
|
|
|
|
|
family = mo_family(x, language = language),
|
|
|
|
|
genus = mo_genus(x, language = language),
|
|
|
|
|
species = mo_species(x, language = language),
|
|
|
|
|
subspecies = mo_subspecies(x, language = language))
|
|
|
|
|
phylum = mo_phylum(x, language = language),
|
|
|
|
|
class = mo_class(x, language = language),
|
|
|
|
|
order = mo_order(x, language = language),
|
|
|
|
|
family = mo_family(x, language = language),
|
|
|
|
|
genus = mo_genus(x, language = language),
|
|
|
|
|
species = mo_species(x, language = language),
|
|
|
|
|
subspecies = mo_subspecies(x, language = language))
|
|
|
|
|
|
|
|
|
|
load_mo_failures_uncertainties_renamed(metadata)
|
|
|
|
|
result
|
|
|
|
@ -400,7 +400,7 @@ mo_taxonomy <- function(x, language = get_locale(), ...) {
|
|
|
|
|
#' @rdname mo_property
|
|
|
|
|
#' @export
|
|
|
|
|
mo_synonyms <- function(x, language = get_locale(), ...) {
|
|
|
|
|
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
|
|
|
|
|
meet_criteria(x, allow_NA = TRUE)
|
|
|
|
|
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
|
|
|
|
|
|
|
|
|
x <- as.mo(x, language = language, ...)
|
|
|
|
@ -429,7 +429,7 @@ mo_synonyms <- function(x, language = get_locale(), ...) {
|
|
|
|
|
#' @rdname mo_property
|
|
|
|
|
#' @export
|
|
|
|
|
mo_info <- function(x, language = get_locale(), ...) {
|
|
|
|
|
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
|
|
|
|
|
meet_criteria(x, allow_NA = TRUE)
|
|
|
|
|
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
|
|
|
|
|
|
|
|
|
x <- as.mo(x, language = language, ...)
|
|
|
|
@ -455,7 +455,7 @@ mo_info <- function(x, language = get_locale(), ...) {
|
|
|
|
|
#' @rdname mo_property
|
|
|
|
|
#' @export
|
|
|
|
|
mo_url <- function(x, open = FALSE, language = get_locale(), ...) {
|
|
|
|
|
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
|
|
|
|
|
meet_criteria(x, allow_NA = TRUE)
|
|
|
|
|
meet_criteria(open, allow_class = "logical", has_length = 1)
|
|
|
|
|
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
|
|
|
|
|
|
|
|
@ -464,7 +464,7 @@ mo_url <- function(x, open = FALSE, language = get_locale(), ...) {
|
|
|
|
|
metadata <- get_mo_failures_uncertainties_renamed()
|
|
|
|
|
|
|
|
|
|
df <- data.frame(mo, stringsAsFactors = FALSE) %pm>%
|
|
|
|
|
pm_left_join(pm_select(microorganisms, mo, source, species_id), by = "mo")
|
|
|
|
|
pm_left_join(pm_select(microorganisms, mo, source, species_id), by = "mo")
|
|
|
|
|
df$url <- ifelse(df$source == "CoL",
|
|
|
|
|
paste0(catalogue_of_life$url_CoL, "details/species/id/", df$species_id, "/"),
|
|
|
|
|
ifelse(df$source == "DSMZ",
|
|
|
|
@ -488,7 +488,7 @@ mo_url <- function(x, open = FALSE, language = get_locale(), ...) {
|
|
|
|
|
#' @rdname mo_property
|
|
|
|
|
#' @export
|
|
|
|
|
mo_property <- function(x, property = "fullname", language = get_locale(), ...) {
|
|
|
|
|
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
|
|
|
|
|
meet_criteria(x, allow_NA = TRUE)
|
|
|
|
|
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)
|
|
|
|
|
|
|
|
|
|