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(v1.1.0.9004) lose dependencies

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dr. M.S. (Matthijs) Berends
2020-05-16 13:05:47 +02:00
parent 9fce546901
commit 7f3da74b17
111 changed files with 3211 additions and 2345 deletions
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31
R/mo_property.R
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@ -358,30 +358,32 @@ mo_info <- function(x, language = get_locale(), ...) {
}
#' @rdname mo_property
#' @importFrom utils browseURL
#' @importFrom dplyr %>% left_join select mutate case_when
#' @export
mo_url <- function(x, open = FALSE, ...) {
mo <- as.mo(x = x, ... = ...)
mo_names <- mo_name(mo)
metadata <- get_mo_failures_uncertainties_renamed()
df <- data.frame(mo, stringsAsFactors = FALSE) %>%
left_join(select(microorganisms, mo, source, species_id), by = "mo") %>%
mutate(url = case_when(source == "CoL" ~
paste0(gsub("{year}", catalogue_of_life$year, catalogue_of_life$url_CoL, fixed = TRUE), "details/species/id/", species_id),
source == "DSMZ" ~
paste0(catalogue_of_life$url_DSMZ, "/", unlist(lapply(strsplit(mo_names, ""), function(x) x[1]))),
TRUE ~
NA_character_))
left_join(select(microorganisms, mo, source, species_id), by = "mo")
df$url <- ifelse(df$source == "CoL",
paste0(gsub("{year}",
catalogue_of_life$year,
catalogue_of_life$url_CoL,
fixed = TRUE),
"details/species/id/",
df$species_id),
ifelse(df$source == "DSMZ",
paste0(catalogue_of_life$url_DSMZ, "/", unlist(lapply(strsplit(mo_names, ""), function(x) x[1]))),
NA_character_))
u <- df$url
names(u) <- mo_names
if (open == TRUE) {
if (length(u) > 1) {
warning("only the first URL will be opened, as `browseURL()` only suports one string.")
}
browseURL(u[1L])
utils::browseURL(u[1L])
}
load_mo_failures_uncertainties_renamed(metadata)
@ -390,7 +392,6 @@ mo_url <- function(x, open = FALSE, ...) {
#' @rdname mo_property
#' @importFrom data.table data.table as.data.table setkey
#' @export
mo_property <- function(x, property = "fullname", language = get_locale(), ...) {
if (length(property) != 1L) {
@ -419,7 +420,7 @@ mo_validate <- function(x, property, ...) {
# try to catch an error when inputting an invalid parameter
# so the 'call.' can be set to FALSE
tryCatch(x[1L] %in% microorganisms[1, property],
tryCatch(x[1L] %in% MO_lookup[1, property, drop = TRUE],
error = function(e) stop(e$message, call. = FALSE))
if (is.mo(x)
@ -428,7 +429,7 @@ mo_validate <- function(x, property, ...) {
# 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(microorganisms, property))
} 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, ...)