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Closes #207 xportr_length for missing length in metadata #238

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2 changes: 2 additions & 0 deletions NEWS.md
Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,8 @@

* New argument in `xportr_length()` allows selection between the length from metadata, as previously done, or from the calculated maximum length per variable when `length_source` is set to “data” (#91)

* `xportr_length()` assigns the maximum length value instead of 200 for a character variable when the length is missing in the metadata (#207)

## Deprecation and Breaking Changes

* The `domain` argument for xportr functions will no longer be dynamically
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36 changes: 17 additions & 19 deletions R/length.R
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
#'
#' Assigns the SAS length to a specified data frame, either from a metadata object
#' or based on the calculated maximum data length. If a length isn't present for
#' a variable the length value is set to 200 for character columns, and 8
#' a variable the length value is set to maximum data length for character columns, and 8
#' for non-character columns. This value is stored in the 'width' attribute of the column.
#'
#' @inheritParams xportr
Expand Down Expand Up @@ -118,31 +118,39 @@ xportr_length <- function(.df,
check_multiple_var_specs(metadata, variable_name)
}

# Get max length for missing length and when length_source == "data"
var_length_max <- variable_max_length(.df)

length_data <- var_length_max[[variable_length]]
names(length_data) <- var_length_max[[variable_name]]

# Check any variables missed in metadata but present in input data ---
miss_vars <- setdiff(names(.df), metadata[[variable_name]])

length_log(miss_vars, verbose)

miss_length <- as.character()
if (length_source == "metadata") {
length_metadata <- metadata[[variable_length]]
names(length_metadata) <- metadata[[variable_name]]

# Check any variables with missing length in metadata
miss_length <- names(length_metadata[is.na(length_metadata)])

for (i in names(.df)) {
if (i %in% miss_vars) {
attr(.df[[i]], "width") <- impute_length(.df[[i]])
attr(.df[[i]], "width") <- length_data[[i]]
} else if (is.na(length_metadata[[i]])) {
attr(.df[[i]], "width") <- length_data[[i]]
} else {
attr(.df[[i]], "width") <- length_metadata[[i]]
}
}
}

# Message for missing var and missing length
length_log(miss_vars, miss_length, verbose)

# Assign length from data
if (length_source == "data") {
var_length_max <- variable_max_length(.df)

length_data <- var_length_max[[variable_length]]
names(length_data) <- var_length_max[[variable_name]]

for (i in names(.df)) {
attr(.df[[i]], "width") <- length_data[[i]]
}
Expand All @@ -156,13 +164,3 @@ xportr_length <- function(.df,

.df
}

impute_length <- function(col) {
characterTypes <- getOption("xportr.character_types")
# first_class will collapse to character if it is the option
if (first_class(col) %in% "character") {
200
} else {
8
}
}
8 changes: 5 additions & 3 deletions R/messages.R
Original file line number Diff line number Diff line change
Expand Up @@ -102,17 +102,19 @@ type_log <- function(meta_ordered, type_mismatch_ind, verbose) {
#' Utility for Lengths
#'
#' @param miss_vars Variables missing from metadata
#' @param miss_length Variables with missing length in metadata
#' @param verbose Provides additional messaging for user
#'
#' @return Output to Console
#' @noRd
length_log <- function(miss_vars, verbose) {
length_log <- function(miss_vars, miss_length, verbose) {
assert_character(miss_vars)
assert_character(miss_length)
assert_choice(verbose, choices = .internal_verbose_choices)

if (length(miss_vars) > 0) {
if (length(c(miss_vars, miss_length)) > 0) {
cli_h2("Variable lengths missing from metadata.")
cli_alert_success("{ length(miss_vars) } lengths resolved")
cli_alert_success("{ length(c(miss_vars, miss_length)) } lengths resolved {encode_vars(c(miss_vars, miss_length))}")

xportr_logger(
glue(
Expand Down
3 changes: 2 additions & 1 deletion man/xportr-package.Rd

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2 changes: 1 addition & 1 deletion man/xportr_length.Rd

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11 changes: 0 additions & 11 deletions tests/testthat/test-length.R
Original file line number Diff line number Diff line change
Expand Up @@ -163,17 +163,6 @@ test_that("xportr_length: Domain not in character format", {
)
})

test_that("xportr_length: Column length of known/unkown character types is 200/8 ", {
expect_equal(impute_length(123), 8)
expect_equal(impute_length(123L), 8)
expect_equal(impute_length("string"), 200)
expect_equal(impute_length(Sys.Date()), 8)
expect_equal(impute_length(Sys.time()), 8)

withr::local_options(list(xportr.character_types = c("character", "date")))
expect_equal(impute_length(Sys.time()), 8)
})

test_that("xportr_length: error when metadata is not set", {
adsl <- minimal_table(30)

Expand Down
4 changes: 2 additions & 2 deletions tests/testthat/test-messages.R
Original file line number Diff line number Diff line change
Expand Up @@ -22,9 +22,9 @@ test_that("length_log: Missing lengths messages are shown", {
# Remove empty lines in cli theme
local_cli_theme()

length_log(c("var1", "var2", "var3"), "message") %>%
length_log(c("var1", "var2", "var3"), c("var4"), "message") %>%
expect_message("Variable lengths missing from metadata.") %>%
expect_message("lengths resolved") %>%
expect_message("lengths resolved `var1`.*`var2`.*`var3`.*`var4`") %>%
expect_message("Problem with `var1`.*`var2`.*`var3`")
})

Expand Down
6 changes: 3 additions & 3 deletions tests/testthat/test-metadata.R
Original file line number Diff line number Diff line change
Expand Up @@ -513,12 +513,12 @@ test_that("xportr_length: Check if length gets imputed when a new variable is pa
xportr_length(df, df_meta, domain = "df")
)

# 200 is the imputed length for character and 8 for other data types as in impute_length()
expect_equal(c(x = 1, y = 200, z = 8), map_dbl(df_with_width, attr, "width"))
# Max length is the imputed length for character and 8 for other data types as in impute_length()
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expect_equal(c(x = 1, y = 1, z = 8), map_dbl(df_with_width, attr, "width"))
expect_equal(df_with_width, structure(
list(
x = structure("a", width = 1),
y = structure("b", width = 200),
y = structure("b", width = 1),
z = structure(3, width = 8)
),
row.names = c(NA, -1L), `_xportr.df_arg_` = "df", class = "data.frame"
Expand Down
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