Closes #137 - Add xportr_process() to apply all and write

NAMESPACE

@@ -5,6 +5,7 @@ export(length_log)
 export(type_log)
 export(var_names_log)
 export(var_ord_msg)
+export(xportr)
 export(xportr_df_label)
 export(xportr_format)
 export(xportr_label)

NEWS.md

@@ -7,6 +7,12 @@
 
 * Added a check for character variable lengths up to 200 bytes in `xpt_validate()`(#91, #189).
 
+* `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. If left `NULL`, the previous default of `getOption("xportr.[fn_name]_verbose")` is used (#151)
+
+## Documentation
+
 ## Deprecation and Breaking Changes
 
 * The `domain` argument for xportr functions will no longer be dynamically 

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(
@@ -99,6 +99,12 @@ xportr_label <- function(.df,
   # Check any variables missed in metadata but present in input data ---
   miss_vars <- setdiff(names(.df), metadata[[variable_name]])
 
+  # 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")
+
   label_log(miss_vars, verbose)
 
   label <- metadata[[variable_label]]

R/length.R

@@ -66,7 +66,7 @@
 xportr_length <- function(.df,
                           metadata = NULL,
                           domain = NULL,
-                          verbose = getOption("xportr.length_verbose", "none"),
+                          verbose = NULL,
                           metacore = deprecated()) {
   if (!missing(metacore)) {
     lifecycle::deprecate_stop(
@@ -106,6 +106,12 @@ xportr_length <- function(.df,
   # Check any variables missed in metadata but present in input data ---
   miss_vars <- setdiff(names(.df), metadata[[variable_name]])
 
+  # 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")
+
   length_log(miss_vars, verbose)
 
   length <- metadata[[variable_length]]

R/metadata.R

@@ -40,16 +40,19 @@
 #'     xportr_type() %>%
 #'     xportr_order()
 #' }
-xportr_metadata <- function(.df, metadata = NULL, domain = NULL) {
-  if (is.null(metadata) && is.null(domain)) {
-    stop("Must provide either metadata or domain argument")
-  }
-  ## Common section to detect domain from argument or attribute
+xportr_metadata <- function(.df,
+                            metadata = NULL,
+                            domain = NULL,
+                            verbose = NULL) {
+  ## Common section to detect domain from argument or pipes
 
   domain <- get_domain(.df, domain)
   if (!is.null(domain)) attr(.df, "_xportr.df_arg_") <- domain
 
   ## End of common section
 
-  structure(.df, `_xportr.df_metadata_` = metadata)
+  structure(.df,
+    `_xportr.df_metadata_` = metadata,
+    `_xportr.df_verbose_` = verbose
+  )
 }

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(
@@ -120,6 +120,12 @@ xportr_order <- function(.df,
   # Used in warning message for how many vars have been moved
   reorder_vars <- names(df_re_ord)[names(df_re_ord) != names(.df)]
 
+  # 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")
+
   # Function is located in messages.R
   var_ord_msg(reorder_vars, names(drop_vars), verbose)
 

R/type.R

@@ -79,7 +79,7 @@
 xportr_type <- function(.df,
                         metadata = NULL,
                         domain = NULL,
-                        verbose = getOption("xportr.type_verbose", "none"),
+                        verbose = NULL,
                         metacore = deprecated()) {
   if (!missing(metacore)) {
     lifecycle::deprecate_stop(
@@ -146,6 +146,12 @@ xportr_type <- function(.df,
       type.y = if_else(type.y %in% numericTypes, "_numeric", type.y)
     )
 
+  # 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")
+
   # It is possible that a variable exists in the table that isn't in the metadata
   # it will be silently ignored here. This may happen depending on what a user
   # passes and the options they choose. The check_core function is the place

R/xportr-package.R

@@ -91,6 +91,7 @@
 #'
 #'
 #' @keywords internal
+#' @aliases xportr-package
 #'
 #' @import rlang haven
 #' @importFrom dplyr left_join bind_cols filter select rename rename_with n

R/xportr.R

@@ -0,0 +1,75 @@
+#' Wrapper to apply all core xportr functions and write xpt
+#'
+#' @param .df A data frame of CDISC standard.
+#' @param var_metadata A data frame containing variable level metadata
+#' @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.
+#' @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'
+#' @param df_metadata A data frame containing dataset level metadata.
+#' @param path Path where transport file will be written. File name sans will be
+#'   used as `xpt` name.
+#' @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
+#'
+#' @return Returns the input dataframe invisibly
+#' @export
+#'
+#' @examples
+#'
+#' has_pkgs <- requireNamespace("admiral", quietly = TRUE) &&
+#'   requireNamespace("dplyr", quietly = TRUE) &&
+#'   requireNamespace("readxl", quietly = TRUE) &&
+#'   requireNamespace("rlang", quietly = TRUE)
+#'
+#' if (has_pkgs) {
+#'   adsl <- admiral::admiral_adsl
+#'
+#'   spec_path <- system.file(paste0("specs/", "ADaM_admiral_spec.xlsx"), package = "xportr")
+#'
+#'   var_spec <- readxl::read_xlsx(spec_path, sheet = "Variables") %>%
+#'     dplyr::rename(type = "Data Type") %>%
+#'     rlang::set_names(tolower)
+#'   dataset_spec <- readxl::read_xlsx(spec_path, sheet = "Datasets") %>%
+#'     dplyr::rename(label = "Description") %>%
+#'     rlang::set_names(tolower)
+#'
+#'   adsl %>%
+#'     xportr_metadata(var_spec, "ADSL", verbose = "warn") %>%
+#'     xportr_type() %>%
+#'     xportr_length() %>%
+#'     xportr_label() %>%
+#'     xportr_order() %>%
+#'     xportr_format() %>%
+#'     xportr_df_label(dataset_spec) %>%
+#'     xportr_write("adsl.xpt")
+#'
+#'   # `xportr()` can be used to apply a whole pipeline at once
+#'   xportr(adsl,
+#'     var_metadata = var_spec,
+#'     df_metadata = dataset_spec,
+#'     domain = "ADSL",
+#'     verbose = "warn",
+#'     path = "adsl.xpt"
+#'   )
+#' }
+xportr <- function(.df,
+                   var_metadata = NULL,
+                   df_metadata = NULL,
+                   domain = NULL,
+                   verbose = NULL,
+                   path,
+                   strict_checks = FALSE) {
+  .df %>%
+    xportr_metadata(var_metadata, domain = domain, verbose = verbose) %>%
+    xportr_type() %>%
+    xportr_length() %>%
+    xportr_label() %>%
+    xportr_order() %>%
+    xportr_format() %>%
+    xportr_df_label(df_metadata) %>%
+    xportr_write(path)
+}

README.Rmd

@@ -143,9 +143,9 @@ adsl %>%
 
 The `xportr_metadata()` function can reduce duplication by setting the variable specification and domain explicitly at the top of a pipeline. If you would like to use the `verbose` argument, you will need to set in each function call.
 
-```{r, message=FALSE, eval=FALSE}
+```{r, warning=FALSE, message=FALSE, eval=FALSE}
 adsl %>%
-  xportr_metadata(var_spec, "ADSL") %>%
+  xportr_metadata(var_spec, domain = "ADSL") %>%
   xportr_type() %>%
   xportr_length() %>%
   xportr_label() %>%

README.md

@@ -155,7 +155,7 @@ each function call.
 
 ``` r
 adsl %>%
-  xportr_metadata(var_spec, "ADSL") %>%
+  xportr_metadata(var_spec, domain = "ADSL") %>%
   xportr_type() %>%
   xportr_length() %>%
   xportr_label() %>%