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(v3.0.1.9039) cli fixes

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dr. M.S. (Matthijs) Berends
2026-03-23 10:38:28 +01:00
parent 975a690c10
commit 2a8a1eda97
24 changed files with 104 additions and 97 deletions
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18
R/interpretive_rules.R
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@@ -329,7 +329,7 @@ interpretive_rules <- function(x,
if (!"AMP" %in% names(cols_ab) && "AMX" %in% names(cols_ab)) {
# ampicillin column is missing, but amoxicillin is available
if (isTRUE(info)) {
message_("Using column '", cols_ab[names(cols_ab) == "AMX"], "' as input for ampicillin since many EUCAST rules depend on it.")
message_("Using column {.field ", font_bold(cols_ab[names(cols_ab) == "AMX"]), "} as input for ampicillin since many EUCAST rules depend on it.")
}
cols_ab <- c(cols_ab, c(AMP = unname(cols_ab[names(cols_ab) == "AMX"])))
}
@@ -510,8 +510,8 @@ interpretive_rules <- function(x,
## Set base to R where base + enzyme inhibitor is R ----
rule_current <- paste0(
ab_enzyme$base_name[i], " ({.field ", col_base, "}) = R if ",
tolower(ab_enzyme$enzyme_name[i]), " ({.field ", col_enzyme, "}) = R"
ab_enzyme$base_name[i], " ({.field ", font_bold(col_base), "}) = R if ",
tolower(ab_enzyme$enzyme_name[i]), " ({.field ", font_bold(col_enzyme), "}) = R"
)
if (isTRUE(info)) {
cat(word_wrap(rule_current,
@@ -551,8 +551,8 @@ interpretive_rules <- function(x,
## Set base + enzyme inhibitor to S where base is S ----
rule_current <- paste0(
ab_enzyme$enzyme_name[i], " ({.field ", col_enzyme, "}) = S if ",
tolower(ab_enzyme$base_name[i]), " ({.field ", col_base, "}) = S"
ab_enzyme$enzyme_name[i], " ({.field ", font_bold(col_enzyme), "}) = S if ",
tolower(ab_enzyme$base_name[i]), " ({.field ", font_bold(col_base), "}) = S"
)
if (isTRUE(info)) {
@@ -662,9 +662,9 @@ interpretive_rules <- function(x,
if (ab %in% names(cols_ab) && !ab_s %in% names(cols_ab)) {
if (isTRUE(info)) {
message_(
"Using column '", cols_ab[names(cols_ab) == ab],
"' as ", ab_name(ab_s, language = NULL, tolower = TRUE),
" since a column '", ab_s, "' is missing but required for the chosen rules"
"Using column {.field ", font_bold(cols_ab[names(cols_ab) == ab]),
"} as ", ab_name(ab_s, language = NULL, tolower = TRUE),
" since a column {.code ", ab_s, "} is missing but required for the chosen rules"
)
}
cols_ab <- c(cols_ab, stats::setNames(unname(cols_ab[names(cols_ab) == ab]), ab_s))
@@ -806,7 +806,7 @@ interpretive_rules <- function(x,
")$"
)
} else if (like_is_one_of != "like") {
stop("invalid value for column 'like.is.one_of'", call. = FALSE)
stop("invalid value for column {.field like.is.one_of}", call. = FALSE)
}
if (is.na(source_antibiotics)) {