fix: #91 resolve merge conflicts from #199

Merge remote-tracking branch 'origin/main' into 91-max-length # Conflicts: # R/length.R # man/metadata.Rd # man/xportr_length.Rd
atorus-research · Jan 29, 2024 · 4023016 · 4023016
2 parents 7bbfca8 + ea7c8e5
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: xportr
 Title: Utilities to Output CDISC SDTM/ADaM XPT Files
-Version: 0.3.1.9010
+Version: 0.3.1.9012
 Authors@R: c(
     person("Eli", "Miller", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-2127-9456")),

diff --git a/NEWS.md b/NEWS.md
@@ -2,6 +2,12 @@
 
 ## New Features and Bug Fixes
 
+* `xportr_metadata()` can set `verbose` for a whole pipeline, i.e. setting `verbose` in `xportr_metadata()` will populate to all `xportr` functions.  (#151)
+
+* All `xportr` functions now have `verbose = NULL` as the default (#151)
+
+## Documentation
+
 * `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).

diff --git a/R/label.R b/R/label.R
@@ -59,7 +59,7 @@
 xportr_label <- function(.df,
                          metadata = NULL,
                          domain = NULL,
-                         verbose = getOption("xportr.label_verbose", "none"),
+                         verbose = NULL,
                          metacore = deprecated()) {
   if (!missing(metacore)) {
     lifecycle::deprecate_stop(
@@ -76,6 +76,12 @@ xportr_label <- function(.df,
 
   metadata <- metadata %||% attr(.df, "_xportr.df_metadata_")
 
+  # Verbose should use an explicit verbose option first, then the value set in
+  # metadata, and finally fall back to the option value
+  verbose <- verbose %||%
+    attr(.df, "_xportr.df_verbose_") %||%
+    getOption("xportr.label_verbose", "none")
+
   ## End of common section
 
   assert_data_frame(.df)

diff --git a/R/length.R b/R/length.R
@@ -73,7 +73,7 @@ xportr_length <- function(.df,
                           metadata = NULL,
                           domain = NULL,
                           length = "metadata",
-                          verbose = getOption("xportr.length_verbose", "none"),
+                          verbose = NULL,
                           metacore = deprecated()) {
   length <- match.arg(length)
   if (!missing(metacore)) {
@@ -91,6 +91,12 @@ xportr_length <- function(.df,
 
   metadata <- metadata %||% attr(.df, "_xportr.df_metadata_")
 
+  # Verbose should use an explicit verbose option first, then the value set in
+  # metadata, and finally fall back to the option value
+  verbose <- verbose %||%
+    attr(.df, "_xportr.df_verbose_") %||%
+    getOption("xportr.length_verbose", "none")
+
   ## End of common section
 
   assert_data_frame(.df)

diff --git a/R/metadata.R b/R/metadata.R
@@ -40,7 +40,10 @@
 #'     xportr_type() %>%
 #'     xportr_order()
 #' }
-xportr_metadata <- function(.df, metadata = NULL, domain = NULL) {
+xportr_metadata <- function(.df,
+                            metadata = NULL,
+                            domain = NULL,
+                            verbose = NULL) {
   if (is.null(metadata) && is.null(domain)) {
     stop("Assertion failed on `metadata` and `domain`: Must provide either `metadata` or `domain` argument")
   }
@@ -55,6 +58,10 @@ xportr_metadata <- function(.df, metadata = NULL, domain = NULL) {
   assert_data_frame(.df)
   assert_metadata(metadata, include_fun_message = FALSE, null.ok = TRUE)
   assert_string(domain, null.ok = TRUE)
+  assert_choice(verbose, choices = .internal_verbose_choices, null.ok = TRUE)
 
-  structure(.df, `_xportr.df_metadata_` = metadata)
+  structure(.df,
+    `_xportr.df_metadata_` = metadata,
+    `_xportr.df_verbose_` = verbose
+  )
 }
diff --git a/R/order.R b/R/order.R
@@ -62,7 +62,7 @@
 xportr_order <- function(.df,
                          metadata = NULL,
                          domain = NULL,
-                         verbose = getOption("xportr.order_verbose", "none"),
+                         verbose = NULL,
                          metacore = deprecated()) {
   if (!missing(metacore)) {
     lifecycle::deprecate_stop(
@@ -79,6 +79,12 @@ xportr_order <- function(.df,
 
   metadata <- metadata %||% attr(.df, "_xportr.df_metadata_")
 
+  # Verbose should use an explicit verbose option first, then the value set in
+  # metadata, and finally fall back to the option value
+  verbose <- verbose %||%
+    attr(.df, "_xportr.df_verbose_") %||%
+    getOption("xportr.order_verbose", "none")
+
   ## End of common section
 
   assert_data_frame(.df)

diff --git a/R/type.R b/R/type.R
@@ -80,7 +80,7 @@
 xportr_type <- function(.df,
                         metadata = NULL,
                         domain = NULL,
-                        verbose = getOption("xportr.type_verbose", "none"),
+                        verbose = NULL,
                         metacore = deprecated()) {
   if (!missing(metacore)) {
     lifecycle::deprecate_stop(
@@ -97,6 +97,12 @@ xportr_type <- function(.df,
 
   metadata <- metadata %||% attr(.df, "_xportr.df_metadata_")
 
+  # Verbose should use an explicit verbose option first, then the value set in
+  # metadata, and finally fall back to the option value
+  verbose <- verbose %||%
+    attr(.df, "_xportr.df_verbose_") %||%
+    getOption("xportr.type_verbose", "none")
+
   ## End of common section
 
   assert_data_frame(.df)

diff --git a/R/write.R b/R/write.R
@@ -12,7 +12,8 @@
 #' @param strict_checks If TRUE, xpt validation will report errors and not write
 #'   out the dataset. If FALSE, xpt validation will report warnings and continue
 #'   with writing out the dataset. Defaults to FALSE
-#' @inheritParams xportr_length
+#' @inheritParams xportr_df_label
+#' @inheritSection xportr_df_label Metadata
 #'
 #' @details
 #'   * Variable and dataset labels are stored in the "label" attribute.
@@ -67,7 +68,8 @@ xportr_write <- function(.df,
   domain <- domain %||% attr(.df, "_xportr.df_arg_")
   if (!is.null(domain)) attr(.df, "_xportr.df_arg_") <- domain
 
-  metadata <- metadata %||% attr(.df, "_xportr.df_metadata_")
+  # metadata should not be inferred from the data frame if it is not provided
+  # by the user.
 
   ## End of common section
 

diff --git a/README.Rmd b/README.Rmd
@@ -145,7 +145,7 @@ The `xportr_metadata()` function can reduce duplication by setting the variable
 
 ```{r, message=FALSE, eval=FALSE}
 adsl %>%
-  xportr_metadata(var_spec, "ADSL") %>%
+  xportr_metadata(var_spec, "ADSL", verbose = "warn") %>%
   xportr_type() %>%
   xportr_length() %>%
   xportr_label() %>%

diff --git a/man/metadata.Rd b/man/metadata.Rd
diff --git a/man/xportr_label.Rd b/man/xportr_label.Rd
diff --git a/man/xportr_length.Rd b/man/xportr_length.Rd
diff --git a/man/xportr_order.Rd b/man/xportr_order.Rd
diff --git a/man/xportr_type.Rd b/man/xportr_type.Rd
diff --git a/man/xportr_write.Rd b/man/xportr_write.Rd