P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 22:41:52 +02:00
Code Releases Activity

(v1.2.0.9011) mo_domain(), improved error handling

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-06-22 11:18:40 +02:00
parent e88d7853f5
commit 93a158aebd
49 changed files with 523 additions and 590 deletions
Download Patch File Download Diff File Expand all files Collapse all files

17
R/mo_source.R
View File

@ -112,9 +112,7 @@ set_mo_source <- function(path) {
file_location <- path.expand("~/mo_source.rds")
if (length(path) > 1) {
stop("`path` must be of length 1.")
}
stop_ifnot(length(path) == 1, "`path` must be of length 1")
if (is.null(path) || path %in% c(FALSE, "")) {
options(mo_source = NULL)
@ -126,9 +124,8 @@ set_mo_source <- function(path) {
return(invisible())
}
if (!file.exists(path)) {
stop("File not found: ", path)
}
stop_ifnot(file.exists(path),
"file not found: ", path)
if (path %like% "[.]rds$") {
df <- readRDS(path)
@ -231,21 +228,21 @@ mo_source_isvalid <- function(x, refer_to_name = "`reference_df`", stop_on_error
}
if (is.null(x)) {
if (stop_on_error == TRUE) {
stop(refer_to_name, " cannot be NULL.", call. = FALSE)
stop(refer_to_name, " cannot be NULL", call. = FALSE)
} else {
return(FALSE)
}
}
if (!is.data.frame(x)) {
if (stop_on_error == TRUE) {
stop(refer_to_name, " must be a data.frame.", call. = FALSE)
stop(refer_to_name, " must be a data.frame", call. = FALSE)
} else {
return(FALSE)
}
}
if (!"mo" %in% colnames(x)) {
if (stop_on_error == TRUE) {
stop(refer_to_name, " must contain a column 'mo'.", call. = FALSE)
stop(refer_to_name, " must contain a column 'mo'", call. = FALSE)
} else {
return(FALSE)
}
@ -260,7 +257,7 @@ mo_source_isvalid <- function(x, refer_to_name = "`reference_df`", stop_on_error
}
stop("Value", plural, " ", paste0("'", invalid[, 1, drop = TRUE], "'", collapse = ", "),
" found in ", tolower(refer_to_name),
", but with invalid microorganism code", plural, " ", paste0("'", invalid$mo, "'", collapse = ", "), ".",
", but with invalid microorganism code", plural, " ", paste0("'", invalid$mo, "'", collapse = ", "),
call. = FALSE)
} else {
return(FALSE)