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(v1.7.1.9049) unit tests

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dr. M.S. (Matthijs) Berends
2021-10-05 09:58:08 +02:00
parent d1b16ce641
commit 2bcf28281d
28 changed files with 64 additions and 44 deletions
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5
R/aa_helper_functions.R
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@ -296,12 +296,15 @@ stop_ifnot_installed <- function(package) {
return(invisible())
}
pkg_is_available <- function(pkg, also_load = TRUE) {
pkg_is_available <- function(pkg, also_load = TRUE, min_version = NULL) {
if (also_load == TRUE) {
out <- suppressWarnings(require(pkg, character.only = TRUE, warn.conflicts = FALSE))
} else {
out <- requireNamespace(pkg, quietly = TRUE)
}
if (!is.null(min_version)) {
out <- out && packageVersion(pkg) >= min_version
}
isTRUE(out)
}

12
R/mo.R
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@ -372,7 +372,7 @@ exec_as.mo <- function(x,
# Laboratory systems: remove (translated) entries like "no growth", etc.
x[trimws2(x) %like% translate_AMR("no .*growth", language = language)] <- NA_character_
x[trimws2(x) %like% paste0("^(", translate_AMR("no|not", language = language), ") [a-z]+")] <- "UNKNOWN"
if (initial_search == TRUE) {
# keep track of time - give some hints to improve speed if it takes a long time
start_time <- Sys.time()
@ -495,9 +495,13 @@ exec_as.mo <- function(x,
# Fill in fullnames and MO codes directly
known_names <- tolower(x_backup) %in% MO_lookup$fullname_lower
x[known_names] <- MO_lookup[match(tolower(x_backup)[known_names], MO_lookup$fullname_lower), property, drop = TRUE]
known_codes <- toupper(x_backup) %in% MO_lookup$mo
x[known_codes] <- MO_lookup[match(toupper(x_backup)[known_codes], MO_lookup$mo), property, drop = TRUE]
already_known <- known_names | known_codes
known_codes_mo <- toupper(x_backup) %in% MO_lookup$mo
x[known_codes_mo] <- MO_lookup[match(toupper(x_backup)[known_codes_mo], MO_lookup$mo), property, drop = TRUE]
known_codes_lis <- toupper(x_backup) %in% microorganisms.codes$code
x[known_codes_lis] <- MO_lookup[match(microorganisms.codes[match(toupper(x_backup)[known_codes_lis],
microorganisms.codes$code), "mo", drop = TRUE],
MO_lookup$mo), property, drop = TRUE]
already_known <- known_names | known_codes_mo | known_codes_lis
# now only continue where the right taxonomic output is not already known
if (any(!already_known)) {