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atorus-research · Jan 16, 2024 · 1242d08 · bms63 · Jan 16, 2024 · 1242d08
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,86 +1,62 @@
 Package: xportr
 Title: Utilities to Output CDISC SDTM/ADaM XPT Files
-Version: 0.3.1.9000
-Authors@R: 
-    c(
-    person(given = "Eli",
-           family = "Miller",
-           role = c("aut",  "cre"),
-           email = "[email protected]",
+Version: 0.3.1.9007
+Authors@R: c(
+    person("Eli", "Miller", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-2127-9456")),
-    person(given = "Vignesh ",
-           family = "Thanikachalam",
-           role = c("aut")),
-    person(given = "Ben", 
-           family = "Straub",
-           role = ("aut")),
-    person(given = "Ross",
-           family = "Didenko",
-           role = ("aut")),
-    person(given = "Zelos",
-           family = "Zhu",
-           role = ("aut")),
-    person(given = "Ethan",
-           family = "Brockmann",
-           role = ("aut")),
-    person(given = "Vedha",
-           family = "Viyash",
-           role = ("aut")),
-    person(given = "Andre",
-           family = "Verissimo",
-           role = ("aut")),
-    person(given = "Sophie",
-           family = "Shapcott",
-           role = ("aut")),
-    person(given = "Celine",
-           family = "Piraux",
-           role = ("aut")),
-    person(given = "Adrian",
-           family = "Chan",
-           role = ("aut")),
-   person(given = "Sadchla",
-           family = "Mascary",
-           role = ("aut")),
-    person(given = "Atorus/GSK JPT",
-           role = "cph"))
-Description: Tools to build CDISC compliant data sets and check for CDISC compliance.
+    person("Vignesh ", "Thanikachalam", role = "aut"),
+    person("Ben", "Straub", role = "aut"),
+    person("Ross", "Didenko", role = "aut"),
+    person("Zelos", "Zhu", role = "aut"),
+    person("Ethan", "Brockmann", role = "aut"),
+    person("Vedha", "Viyash", role = "aut"),
+    person("Andre", "Verissimo", role = "aut"),
+    person("Sophie", "Shapcott", role = "aut"),
+    person("Celine", "Piraux", role = "aut"),
+    person("Adrian", "Chan", role = "aut"),
+    person("Sadchla", "Mascary", role = "aut"),
+    person("Atorus/GSK JPT", role = "cph")
+  )
+Description: Tools to build CDISC compliant data sets and check for CDISC
+    compliance.
+License: MIT + file LICENSE
 URL: https://github.com/atorus-research/xportr
 BugReports: https://github.com/atorus-research/xportr/issues
+Depends: 
+    R (>= 3.5)
 Imports: 
     checkmate,
+    cli,
     dplyr (>= 1.0.2),
-    purrr (>= 0.3.4),
-    stringr (>= 1.4.0),
-    magrittr,
     glue (>= 1.4.2),
+    haven (>= 2.5.0),
+    janitor,
+    lifecycle,
+    magrittr,
+    purrr (>= 0.3.4),
+    readr,
     rlang (>= 0.4.10),
-    cli,
+    stringr (>= 1.4.0),
     tidyselect,
-    readr,
-    janitor,
-    tm,
-    haven (>= 2.5.0),
-    lifecycle
-License: MIT + file LICENSE
-Encoding: UTF-8
-LazyData: true
-Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+    tm
 Suggests: 
-    testthat (>= 3.0.0),
-    withr,
-    knitr,
-    rmarkdown,
-    readxl,
-    DT,
-    labelled,
     admiral,
     devtools,
+    DT,
+    knitr,
+    labelled,
+    lintr,
+    metacore,
+    readxl,
+    rmarkdown,
     spelling,
+    testthat (>= 3.0.0),
     usethis,
-    lintr,
-    metacore
+    withr
+VignetteBuilder: 
+    knitr
 Config/testthat/edition: 3
-VignetteBuilder: knitr
-Depends: 
-    R (>= 3.5)
+Encoding: UTF-8
+LazyData: true
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.3
diff --git a/NAMESPACE b/NAMESPACE
@@ -6,7 +6,6 @@ export(type_log)
 export(var_names_log)
 export(var_ord_msg)
 export(xportr_df_label)
-export(xportr_domain_name)
 export(xportr_format)
 export(xportr_label)
 export(xportr_length)
@@ -37,6 +36,7 @@ importFrom(cli,cli_alert_success)
 importFrom(cli,cli_div)
 importFrom(cli,cli_h2)
 importFrom(cli,cli_text)
+importFrom(dplyr,across)
 importFrom(dplyr,arrange)
 importFrom(dplyr,bind_cols)
 importFrom(dplyr,case_when)
@@ -75,6 +75,7 @@ importFrom(stringr,str_replace)
 importFrom(stringr,str_replace_all)
 importFrom(tidyselect,all_of)
 importFrom(tidyselect,any_of)
+importFrom(tidyselect,where)
 importFrom(tm,stemDocument)
 importFrom(utils,capture.output)
 importFrom(utils,packageVersion)

diff --git a/NEWS.md b/NEWS.md
@@ -2,11 +2,24 @@
 
 ## New Features and Bug Fixes
 
+* `xportr_write()` now accepts `metadata` argument which can be used to set the dataset label to stay consistent with the other `xportr_*` functions. It is noteworthy that the dataset label set using the `xportr_df_label()` function will be retained during the `xportr_write()`.
+* Exporting a new dataset `dataset_spec` that contains the Dataset Specification for ADSL. (#179)
+* Added a check for character variable lengths up to 200 bytes in `xpt_validate()`(#91, #189).
+* File name check is moved to strict_checks condition to allow underscores in the file name. Underscores are allowed in xpt but not per FDA requirements. (#126)
 * Adds argument assertions to public functions using `{checkmate}` (#175)
 
+## Deprecation and Breaking Changes
+
+* The `domain` argument for xportr functions will no longer be dynamically 
+determined by the name of the data frame passed as the .df argument. This was
+done to make the use of xportr functions more explicit. (#182)
+* The `label` argument from the `xportr_write()` function is deprecated in favor of the `metadata` argument. (#179)
+* The `metacore` argument, which was renamed to `metadata` in the following six xportr functions: (`xportr_df_label()`, `xportr_format()`, `xportr_label()`, `xportr_length()`, `xportr_order()`, and `xportr_type()`) in version `0.3.0` with a soft deprecation warning, has now been hard deprecated. Please update your code to use the new `metadata` argument in place of `metacore`.
+
 ## Documentation
 
-## Deprecation and Breaking Changes
+* Created development version of the website (#187)
+* Additional guidance for options added in deep dive vignette (#81)
 
 # xportr 0.3.1
 

diff --git a/R/data.R b/R/data.R
@@ -56,7 +56,7 @@
 #' }
 "adsl"
 
-#' Example Dataset Specification
+#' Example Dataset Variable Specification
 #'
 #' @format ## `var_spec`
 #' A data frame with 216 rows and 19 columns:
@@ -82,3 +82,20 @@
 #'   \item{Developer Notes}{Developer Notes}
 #' }
 "var_spec"
+
+#' Example Dataset Specification
+#'
+#' @format ## `dataset_spec`
+#' A data frame with 1 row and 9 columns:
+#' \describe{
+#'   \item{Dataset}{<chr> Dataset}
+#'   \item{Description}{<chr> Dataset description}
+#'   \item{Class}{<chr> Dataset class}
+#'   \item{Structure}{<lgl> Logical, indicating if there's a specific structure}
+#'   \item{Purpose}{<chr> Purpose of the dataset}
+#'   \item{Key, Variables}{<chr> Join Key variables in the dataset}
+#'   \item{Repeating}{<chr> Indicates if the dataset is repeating}
+#'   \item{Reference Data}{<lgl> Regerence Data}
+#'   \item{Comment}{<chr> Additional comment}
+#' }
+"dataset_spec"
diff --git a/R/df_label.R b/R/df_label.R
@@ -44,12 +44,11 @@ xportr_df_label <- function(.df,
                             domain = attr(.df, "_xportr.df_arg_"),
                             metacore = deprecated()) {
   if (!missing(metacore)) {
-    lifecycle::deprecate_warn(
-      when = "0.3.0",
+    lifecycle::deprecate_stop(
+      when = "0.3.1.9005",
       what = "xportr_df_label(metacore = )",
       with = "xportr_df_label(metadata = )"
     )
-    metadata <- metacore
   }
   assert_data_frame(.df)
   assert_string(domain, null.ok = TRUE)
@@ -72,6 +71,10 @@ xportr_df_label <- function(.df,
     abort("Length of dataset label must be 40 characters or less.")
   }
 
+  if (stringr::str_detect(label, "[^[:ascii:]]")) {
+    abort("`label` cannot contain any non-ASCII, symbol or special characters.")
+  }
+
   attr(.df, "label") <- label
 
   .df

diff --git a/R/format.R b/R/format.R
@@ -46,12 +46,11 @@ xportr_format <- function(.df,
                           domain = attr(.df, "_xportr.df_arg_"),
                           metacore = deprecated()) {
   if (!missing(metacore)) {
-    lifecycle::deprecate_warn(
-      when = "0.3.0",
+    lifecycle::deprecate_stop(
+      when = "0.3.1.9005",
       what = "xportr_format(metacore = )",
       with = "xportr_format(metadata = )"
     )
-    metadata <- metacore
   }
   assert_data_frame(.df)
   assert_string(domain, null.ok = TRUE)
@@ -65,7 +64,7 @@ xportr_format <- function(.df,
 
   if (inherits(metadata, "Metacore")) metadata <- metadata$var_spec
 
-  if (domain_name %in% names(metadata)) {
+  if (domain_name %in% names(metadata) && !is.null(domain)) {
     metadata <- metadata %>%
       dplyr::filter(!!sym(domain_name) == domain & !is.na(!!sym(format_name)))
   } else {

diff --git a/R/label.R b/R/label.R
@@ -62,12 +62,11 @@ xportr_label <- function(.df,
                          verbose = getOption("xportr.label_verbose", "none"),
                          metacore = deprecated()) {
   if (!missing(metacore)) {
-    lifecycle::deprecate_warn(
-      when = "0.3.0",
+    lifecycle::deprecate_stop(
+      when = "0.3.1.9005",
       what = "xportr_label(metacore = )",
       with = "xportr_label(metadata = )"
     )
-    metadata <- metacore
   }
   assert_data_frame(.df)
   assert_string(domain, null.ok = TRUE)
@@ -82,7 +81,7 @@ xportr_label <- function(.df,
 
   if (inherits(metadata, "Metacore")) metadata <- metadata$var_spec
 
-  if (domain_name %in% names(metadata)) {
+  if (domain_name %in% names(metadata) && !is.null(domain)) {
     metadata <- metadata %>%
       dplyr::filter(!!sym(domain_name) == domain)
   } else {

diff --git a/R/length.R b/R/length.R
@@ -9,8 +9,8 @@
 #' @param metadata A data frame containing variable level metadata. See
 #'   'Metadata' section for details.
 #' @param domain Appropriate CDSIC dataset name, e.g. ADAE, DM. Used to subset
-#'   the metadata object. If none is passed, then name of the dataset passed as
-#'   .df will be used.
+#'   the metadata object. If none is passed, then  [xportr_metadata()] must be
+#'   called before hand to set the domain as an attribute of `.df`.
 #' @param verbose The action this function takes when an action is taken on the
 #'   dataset or function validation finds an issue. See 'Messaging' section for
 #'   details. Options are 'stop', 'warn', 'message', and 'none'
@@ -69,12 +69,11 @@ xportr_length <- function(.df,
                           verbose = getOption("xportr.length_verbose", "none"),
                           metacore = deprecated()) {
   if (!missing(metacore)) {
-    lifecycle::deprecate_warn(
-      when = "0.3.0",
+    lifecycle::deprecate_stop(
+      when = "0.3.1.9005",
       what = "xportr_length(metacore = )",
       with = "xportr_length(metadata = )"
     )
-    metadata <- metacore
   }
   assert_data_frame(.df)
   assert_string(domain, null.ok = TRUE)
@@ -89,7 +88,7 @@ xportr_length <- function(.df,
 
   if (inherits(metadata, "Metacore")) metadata <- metadata$var_spec
 
-  if (domain_name %in% names(metadata)) {
+  if (domain_name %in% names(metadata) && !is.null(domain)) {
     metadata <- metadata %>%
       filter(!!sym(domain_name) == domain)
   } else {

diff --git a/R/metadata.R b/R/metadata.R
@@ -1,9 +1,10 @@
 #' Set variable specifications and domain
 #'
-#' Sets metadata for a dataset in a way that can be accessed by other xportr
-#' functions. If used at the start of an xportr pipeline, it removes the need to
-#' set metadata and domain at each step individually. For details on the format
-#' of the metadata, see the 'Metadata' section for each function in question.
+#' Sets metadata and/or domain for a dataset in a way that can be accessed by
+#' other xportr functions. If used at the start of an xportr pipeline, it
+#' removes the need to set metadata and domain at each step individually. For
+#' details on the format of the metadata, see the 'Metadata' section for each
+#' function in question.
 #'
 #' @inheritParams xportr_length
 #'
@@ -35,36 +36,21 @@
 #'   library(magrittr)
 #'
 #'   adlb %>%
-#'     xportr_domain_name("adlb") %>%
 #'     xportr_metadata(metadata, "test") %>%
 #'     xportr_type() %>%
 #'     xportr_order()
 #' }
-xportr_metadata <- function(.df, metadata, domain = attr(.df, "_xportr.df_arg_")) {
+xportr_metadata <- function(.df, metadata = NULL, domain = NULL) {
   assert_data_frame(.df)
-  assert_metadata(metadata, include_fun_message = FALSE)
+  if (is.null(metadata) && is.null(domain)) {
+    stop("Assertion failed on `metadata` and `domain`: Must provide either `metadata` or `domain` argument")
+  }
+  assert_metadata(metadata, include_fun_message = FALSE, null.ok = TRUE)
   assert_string(domain, null.ok = TRUE)
+
+  ## Common section to detect domain from argument or attribute
 
   if (!is.null(domain)) .df <- xportr_domain_name(.df, domain)
 
   structure(.df, "_xportr.df_metadata_" = metadata)
 }
-
-
-#' Update Metadata Domain Name
-#'
-#' Similar to `xportr_metadata`, but just added the domain and not the metadata.
-#'
-#' @inheritParams xportr_length
-#'
-#' @return `.df` dataset with domain argument set
-#' @export
-#'
-#' @rdname metadata
-xportr_domain_name <- function(.df, domain) {
-  assert_data_frame(.df)
-  assert_string(domain)
-  attr(.df, "_xportr.df_arg_") <- domain
-
-  .df
-}