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fix message output for value error #47

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Merged
LucieContamin merged 2 commits into from
May 12, 2025
Merged

fix message output for value error #47

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4968b64
fix message err
LucieContamin May 12, 2025
35a821c
update NEWS
LucieContamin May 12, 2025
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2 changes: 2 additions & 0 deletions NEWS.md
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,8 @@
ignore stopping the validation if any `[valid_vals]` error (#40)
- add parameter `store_msg_val()` function to remove valid check (and non
compound id check) on output of the function (#44)
- fix message output style by removing unnecessary new line and output an
error if a value is incorrect instead of failure (#46)

# SMHvalidation 1.0.0

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31 changes: 16 additions & 15 deletions R/imports-hubValidations.R
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Expand Up @@ -131,9 +131,9 @@ compare_values_to_config <- function(tbl, output_type, output_type_config) {
details <-
c(details,
cli::format_inline("{cli::qty(length(invalid_vals))} Value{?s} ",
"{.val {invalid_vals}}\n cannot be coerced ",
"to expected data type {.val {values_type}}\n ",
" for output type {.val {output_type}}."))
"{.val {invalid_vals}} cannot be coerced ",
"to expected data type {.val {values_type}} ",
"for output type {.val {output_type}}."))
if (length(invalid_vals) > 0) values <- stats::na.omit(values)
if (length(values) == 0L) return(details)
}
Expand All @@ -144,8 +144,8 @@ compare_values_to_config <- function(tbl, output_type, output_type_config) {
details <-
c(details,
cli::format_inline("{cli::qty(length(invalid_int$vals))} Value{?s} ",
"{.val {invalid_int$vals}}\n cannot be ",
"coerced to expected data type\n ",
"{.val {invalid_int$vals}}cannot be ",
"coerced to expected data type ",
"{.val {values_type}} for output type ",
"{.val {output_type}}."))
}
Expand All @@ -156,11 +156,11 @@ compare_values_to_config <- function(tbl, output_type, output_type_config) {
details <-
c(details,
cli::format_inline("{cli::qty(sum(is_invalid))} Value{?s} ",
"{.val {unique(values[is_invalid])}}\n ",
" {cli::qty(sum(is_invalid))}{?is/are}\n ",
" greater than allowed maximum value ",
"{.val {value_max}} for output type\n ",
" {.val {output_type}}."))
"{.val {unique(values[is_invalid])}} ",
"{cli::qty(sum(is_invalid))}{?is/are} ",
"greater than allowed maximum value ",
"{.val {value_max}} for output type ",
"{.val {output_type}}."))
}
}
if (any(names(config) == "minimum")) {
Expand All @@ -170,10 +170,10 @@ compare_values_to_config <- function(tbl, output_type, output_type_config) {
details <-
c(details,
cli::format_inline("{cli::qty(sum(is_invalid))} Value{?s} ",
"{.val {unique(values[is_invalid])}}\n ",
" {cli::qty(sum(is_invalid))}{?is/are}\n ",
" smaller than allowed minimum value ",
"{.val {value_min}} for output type\n ",
"{.val {unique(values[is_invalid])}} ",
"{cli::qty(sum(is_invalid))}{?is/are} ",
"smaller than allowed minimum value ",
"{.val {value_min}} for output type ",
"{.val {output_type}}."))
}
}
Expand Down Expand Up @@ -222,7 +222,8 @@ check_tbl_value_col <- function(tbl, round_id, file_path, hub_path) {
msg_subject = "Values in column {.var value}",
msg_verbs = c("all", "are not all"),
msg_attribute = "valid with respect to modeling task config.",
details = details
details = details,
error = TRUE
)
}

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4 changes: 2 additions & 2 deletions tests/testthat/test_submission.R
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Expand Up @@ -288,7 +288,7 @@ test_that("Test validation process", {
check <- validate_submission(path_f, hub_path,
merge_sample_col = merge_sample_col)
expect_contains(attr(check$value_col_valid, "class"),
c("error", "check_failure"))
c("error", "check_error"))
expect_contains(attr(check$na_value, "class"), c("error", "check_error"))

### Negative value -----------
Expand All @@ -306,7 +306,7 @@ test_that("Test validation process", {
check <- validate_submission(path_f, hub_path,
merge_sample_col = merge_sample_col)
expect_contains(attr(check$value_col_valid, "class"),
c("error", "check_failure"))
c("error", "check_error"))

### Greater than population size -----------
df <-
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