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(v2.1.1.9136) console colours, updated Suggests, added as.ab() improvement

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dr. M.S. (Matthijs) Berends
2025-01-31 16:01:52 +01:00
parent 700522b466
commit 22afd918e6
13 changed files with 114 additions and 101 deletions
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49
R/aa_helper_functions.R
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@ -1169,57 +1169,12 @@ message_not_thrown_before <- function(fn, ..., entire_session = FALSE) {
}
has_colour <- function() {
# this is a base R version of crayon::has_color, but disables colours on emacs
if (Sys.getenv("EMACS") != "" || Sys.getenv("INSIDE_EMACS") != "") {
# disable on emacs, which only supports 8 colours
return(FALSE)
}
enabled <- getOption("crayon.enabled")
if (!is.null(enabled)) {
return(isTRUE(enabled))
}
rstudio_with_ansi_support <- function(x) {
if (Sys.getenv("RSTUDIO", "") == "") {
return(FALSE)
}
if ((cols <- Sys.getenv("RSTUDIO_CONSOLE_COLOR", "")) != "" && !is.na(as.double(cols))) {
return(TRUE)
}
tryCatch(getExportedValue("isAvailable", ns = asNamespace("rstudioapi"))(), error = function(e) {
return(FALSE)
}) &&
tryCatch(getExportedValue("hasFun", ns = asNamespace("rstudioapi"))("getConsoleHasColor"), error = function(e) {
return(FALSE)
})
}
if (rstudio_with_ansi_support() && sink.number() == 0) {
return(TRUE)
}
if (!isatty(stdout())) {
return(FALSE)
}
if (tolower(Sys.info()["sysname"]) == "windows") {
if (Sys.getenv("ConEmuANSI") == "ON") {
return(TRUE)
}
if (Sys.getenv("CMDER_ROOT") != "") {
return(TRUE)
}
return(FALSE)
}
if ("COLORTERM" %in% names(Sys.getenv())) {
return(TRUE)
}
if (Sys.getenv("TERM") == "dumb") {
return(FALSE)
}
grepl(
pattern = "^screen|^xterm|^vt100|color|ansi|cygwin|linux",
x = Sys.getenv("TERM"),
ignore.case = TRUE,
perl = TRUE
)
has_color <- import_fn("has_color", "crayon")
!is.null(has_color) && isTRUE(has_color())
}
# set colours if console has_colour()

38
R/ab.R
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@ -324,7 +324,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
# INITIAL SEARCH - More uncertain results ----
if (loop_time <= 2 && fast_mode == FALSE) {
# only run on first and second try
# try by removing all spaces
if (x[i] %like% " ") {
found <- suppressWarnings(as.ab(gsub(" +", "", x[i], perl = TRUE), loop_time = loop_time + 2))
@ -333,7 +333,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
next
}
}
# try by removing all spaces and numbers
if (x[i] %like% " " || x[i] %like% "[0-9]") {
found <- suppressWarnings(as.ab(gsub("[ 0-9]", "", x[i], perl = TRUE), loop_time = loop_time + 2))
@ -342,6 +342,40 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
next
}
}
# reverse a combination, e.g. clavulanic acid/amoxicillin
if (x[i] %like% " ") {
split <- strsplit(x[i], " ")[[1]]
permute <- function(x) {
if (length(x) == 1) return(list(x))
result <- vector("list", factorial(length(x)))
index <- 1
for (i in seq_along(x)) {
sub_perms <- permute(x[-i]) # Recursively get permutations of remaining elements
for (sub in sub_perms) {
result[[index]] <- c(x[i], sub)
index <- index + 1
}
}
return(result)
}
permutations <- permute(split)
found_perms <- character(length(permutations))
for (s in seq_len(length(permutations))) {
concat <- paste0(permutations[[s]], collapse = " ")
if (concat %in% AMR_env$AB_lookup$generalised_name) {
found_perms[s] <- AMR_env$AB_lookup[which(AMR_env$AB_lookup$generalised_name == concat), "ab", drop = TRUE]
} else {
found_perms[s] <- suppressWarnings(as.ab(concat, loop_time = loop_time + 2))
}
}
found_perms <- found_perms[!is.na(found_perms)]
if (length(found_perms) > 0) {
found <- found_perms[order(nchar(found_perms), decreasing = TRUE)][1]
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
}
# transform back from other languages and try again
x_translated <- paste(

6
R/mo.R
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@ -340,17 +340,17 @@ as.mo <- function(x,
filtr <- which(MO_lookup_current$full_first %like_case% first_chars)
} else if (nchar(x_out) == 3) {
# no space and 3 characters - probably a code such as SAU or ECO
msg <<- c(msg, paste0("Input \"", x_search, "\" was assumed to be a microorganism code - tried to match on \"", totitle(substr(x_out, 1, 1)), AMR_env$dots, " ", substr(x_out, 2, 3), AMR_env$dots, "\""))
msg <<- c(msg, paste0("Input \"", x_search, "\" was assumed to be a microorganism code - tried to match on \"", totitle(substr(x_out, 1, 1)), AMR_env$ellipsis_icon, " ", substr(x_out, 2, 3), AMR_env$ellipsis_icon, "\""))
filtr <- which(MO_lookup_current$fullname_lower %like_case% paste0("(^| )", substr(x_out, 1, 1), ".* ", substr(x_out, 2, 3)))
} else if (nchar(x_out) == 4) {
# no space and 4 characters - probably a code such as STAU or ESCO
msg <<- c(msg, paste0("Input \"", x_search, "\" was assumed to be a microorganism code - tried to match on \"", totitle(substr(x_out, 1, 2)), AMR_env$dots, " ", substr(x_out, 3, 4), AMR_env$dots, "\""))
msg <<- c(msg, paste0("Input \"", x_search, "\" was assumed to be a microorganism code - tried to match on \"", totitle(substr(x_out, 1, 2)), AMR_env$ellipsis_icon, " ", substr(x_out, 3, 4), AMR_env$ellipsis_icon, "\""))
filtr <- which(MO_lookup_current$fullname_lower %like_case% paste0("(^| )", substr(x_out, 1, 2), ".* ", substr(x_out, 3, 4)))
} else if (nchar(x_out) <= 6) {
# no space and 5-6 characters - probably a code such as STAAUR or ESCCOL
first_part <- paste0(substr(x_out, 1, 2), "[a-z]*", substr(x_out, 3, 3))
second_part <- substr(x_out, 4, nchar(x_out))
msg <<- c(msg, paste0("Input \"", x_search, "\" was assumed to be a microorganism code - tried to match on \"", gsub("[a-z]*", AMR_env$dots, totitle(first_part), fixed = TRUE), " ", second_part, AMR_env$dots, "\""))
msg <<- c(msg, paste0("Input \"", x_search, "\" was assumed to be a microorganism code - tried to match on \"", gsub("[a-z]*", AMR_env$ellipsis_icon, totitle(first_part), fixed = TRUE), " ", second_part, AMR_env$ellipsis_icon, "\""))
filtr <- which(MO_lookup_current$fullname_lower %like_case% paste0("(^| )", first_part, ".* ", second_part))
} else {
# for genus or species or subspecies

12
R/zzz.R
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@ -82,15 +82,15 @@ AMR_env$chmatch <- import_fn("chmatch", "data.table", error_on_fail = FALSE)
AMR_env$chin <- import_fn("%chin%", "data.table", error_on_fail = FALSE)
# take cli symbols and error function if available
AMR_env$info_icon <- import_fn("symbol", "cli", error_on_fail = FALSE)$info %or% "i"
AMR_env$bullet_icon <- import_fn("symbol", "cli", error_on_fail = FALSE)$bullet %or% "*"
AMR_env$bullet_icon <- import_fn("symbol", "cli", error_on_fail = FALSE)$bullet %or% "*"
AMR_env$ellipsis_icon <- import_fn("symbol", "cli", error_on_fail = FALSE)$ellipsis %or% "..."
AMR_env$info_icon <- import_fn("symbol", "cli", error_on_fail = FALSE)$info %or% "i"
AMR_env$sup_1_icon <- import_fn("symbol", "cli", error_on_fail = FALSE)$sup_1 %or% "*"
AMR_env$cli_abort <- import_fn("cli_abort", "cli", error_on_fail = FALSE)
AMR_env$cross_icon <- if (isTRUE(base::l10n_info()$`UTF-8`)) "\u00d7" else "x"
AMR_env$dots <- import_fn("symbol", "cli", error_on_fail = FALSE)$ellipsis %or% "..."
AMR_env$sup_1_icon <- import_fn("symbol", "cli", error_on_fail = FALSE)$sup_1 %or% "*"
AMR_env$cli_abort <- import_fn("cli_abort", "cli", error_on_fail = FALSE)
.onLoad <- function(lib, pkg) {
# Support for tibble headers (type_sum) and tibble columns content (pillar_shaft)
# without the need to depend on other packages. This was suggested by the