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mirror of https://github.com/msberends/AMR.git synced 2025-07-10 14:21:48 +02:00

(v2.1.1.9227) unit test fixes

This commit is contained in:
2025-03-27 15:36:27 +01:00
parent 969a42cc8c
commit d77ad6bd6e
11 changed files with 21 additions and 17 deletions

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@ -1299,7 +1299,13 @@ font_purple_bg <- function(..., collapse = " ") {
try_colour(font_black(..., collapse = collapse, adapt = FALSE), before = "\033[48;5;89m", after = "\033[49m", collapse = collapse)
}
font_rose_bg <- function(..., collapse = " ") {
try_colour(font_black(..., collapse = collapse, adapt = FALSE), before = "\033[48;5;217m", after = "\033[49m", collapse = collapse)
if (is_dark()) {
# this is #ed553b (picked to be colourblind-safe with other SIR colours)
try_colour(font_black(..., collapse = collapse, adapt = FALSE), before = "\033[48;5;203m", after = "\033[49m", collapse = collapse)
} else {
# also colourblind-safe but softer
try_colour(font_black(..., collapse = collapse, adapt = FALSE), before = "\033[48;5;217m", after = "\033[49m", collapse = collapse)
}
}
font_na <- function(..., collapse = " ") {
font_red(..., collapse = collapse)

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@ -253,7 +253,7 @@ print.custom_eucast_rules <- function(x, ...) {
if (is.na(rule$result_value)) {
val <- font_red("<NA>")
} else if (rule$result_value == "R") {
val <- font_red_bg(" R ")
val <- font_rose_bg(" R ")
} else if (rule$result_value == "S") {
val <- font_green_bg(" S ")
} else {
@ -297,7 +297,7 @@ format_custom_query_rule <- function(query, colours = has_colour()) {
query <- gsub(" %in% ", sub("{text}", " is one of ", txt, fixed = TRUE), query, fixed = TRUE)
query <- gsub(" %like% ", sub("{text}", " resembles ", txt, fixed = TRUE), query, fixed = TRUE)
if (colours == TRUE) {
query <- gsub('"R"', font_red_bg(" R "), query, fixed = TRUE)
query <- gsub('"R"', font_rose_bg(" R "), query, fixed = TRUE)
query <- gsub('"S"', font_green_bg(" S "), query, fixed = TRUE)
query <- gsub('"I"', font_orange_bg(" I "), query, fixed = TRUE)
}

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@ -656,7 +656,9 @@ eucast_rules <- function(x,
if (isTRUE(ampc_cephalosporin_resistance)) {
ampc_cephalosporin_resistance <- "R"
}
eucast_rules_df[which(eucast_rules_df$reference.rule %like% "ampc"), "to_value"] <- as.character(ampc_cephalosporin_resistance)
if (!is.null(eucast_rules_df$reference.rule)) {
eucast_rules_df[which(eucast_rules_df$reference.rule %like% "ampc"), "to_value"] <- as.character(ampc_cephalosporin_resistance)
}
}
# sometimes, the screenings are missing but the names are actually available

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@ -1715,11 +1715,7 @@ pillar_shaft.sir <- function(x, ...) {
out[x == "S"] <- font_green_bg(" S ")
out[x == "I"] <- font_orange_bg(" I ")
out[x == "SDD"] <- font_orange_bg(" SDD ")
if (is_dark()) {
out[x == "R"] <- font_red_bg(" R ")
} else {
out[x == "R"] <- font_rose_bg(" R ")
}
out[x == "R"] <- font_rose_bg(" R ")
}
create_pillar_column(out, align = "left", width = 5)
}

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