Correct failing tests

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

@@ -20,10 +20,10 @@
 #'
 #' @examples
 #'
-#' has_pkgs <- require(admiral, quietly = TRUE) &&
-#'   require(dplyr, quietly = TRUE) &&
-#'   require(readxl, quietly = TRUE) &&
-#'   require(rlang, quietly = TRUE)
+#' 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
@@ -64,7 +64,7 @@ xportr <- function(.df,
                    path,
                    strict_checks = FALSE) {
   .df %>%
-    xportr_metadata(var_metadata, domain, verbose) %>%
+    xportr_metadata(var_metadata, domain = domain, verbose = verbose) %>%
     xportr_type() %>%
     xportr_length() %>%
     xportr_label() %>%

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", verbose = "warn") %>%
+  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() %>%

tests/testthat/test-metadata.R

@@ -594,13 +594,13 @@ test_that("xportr_metadata: Variable ordering messaging is correct", {
   )
 
   # Metadata versions
-  xportr_metadata(df, df_meta, verbose = "message") %>%
+  xportr_metadata(df, df_meta, domain = "df", verbose = "message") %>%
     xportr_order() %>%
     expect_message("All variables in specification file are in dataset") %>%
     expect_condition("4 reordered in dataset") %>%
     expect_message("Variable reordered in `.df`: `a`, `b`, `c`, and `d`")
 
-  xportr_metadata(df2, df_meta, verbose = "message") %>%
+  xportr_metadata(df2, df_meta, domain = "df2", verbose = "message") %>%
     xportr_order() %>%
     expect_message("2 variables not in spec and moved to end") %>%
     expect_message("Variable moved to end in `.df`: `a` and `z`") %>%
@@ -623,13 +623,13 @@ test_that("xportr_type: Variable types are coerced as expected and can raise mes
 
   # Metadata version of the last statement
   df %>%
-    xportr_metadata(meta_example, verbose = "warn") %>%
+    xportr_metadata(meta_example, domain = "df", verbose = "warn") %>%
     xportr_type() %>%
     expect_warning()
 
   # Metadata version
   df %>%
-    xportr_metadata(meta_example, verbose = "message") %>%
+    xportr_metadata(meta_example, domain = "df", verbose = "message") %>%
     xportr_type() %>%
     expect_message("Variable type\\(s\\) in dataframe don't match metadata")
 })
@@ -654,7 +654,8 @@ test_that("xportr_metadata: Check metadata interaction with other functions", {
               `_xportr.df_metadata_` = var_spec,
               `_xportr.df_verbose_` = "none"),
     suppressMessages(
-      xportr_metadata(adsl, var_spec, domain = "adsl") %>% xportr_type()
+      xportr_metadata(adsl, var_spec, domain = "adsl", verbose = "none") %>%
+        xportr_type()
     )
   )
 
@@ -663,7 +664,8 @@ test_that("xportr_metadata: Check metadata interaction with other functions", {
               `_xportr.df_metadata_` = var_spec,
               `_xportr.df_verbose_` = "none"),
     suppressMessages(
-      xportr_metadata(adsl, var_spec, domain = "adsl") %>% xportr_length()
+      xportr_metadata(adsl, var_spec, domain = "adsl", verbose = "none") %>%
+        xportr_length()
     )
   )
 
@@ -672,7 +674,8 @@ test_that("xportr_metadata: Check metadata interaction with other functions", {
               `_xportr.df_metadata_` = var_spec,
               `_xportr.df_verbose_` = "none"),
     suppressMessages(
-      xportr_metadata(adsl, var_spec, domain = "adsl") %>% xportr_label()
+      xportr_metadata(adsl, var_spec, domain = "adsl", verbose = "none") %>%
+        xportr_label()
     )
   )
 
@@ -681,7 +684,8 @@ test_that("xportr_metadata: Check metadata interaction with other functions", {
               `_xportr.df_metadata_` = var_spec,
               `_xportr.df_verbose_` = "none"),
     suppressMessages(
-      xportr_metadata(adsl, var_spec, domain = "adsl") %>% xportr_order()
+      xportr_metadata(adsl, var_spec, domain = "adsl", verbose = "none") %>%
+        xportr_order()
     )
   )
 
@@ -690,7 +694,8 @@ test_that("xportr_metadata: Check metadata interaction with other functions", {
               `_xportr.df_metadata_` = var_spec,
               `_xportr.df_verbose_` = "none"),
     suppressMessages(
-      xportr_metadata(adsl, var_spec, domain = "adsl") %>% xportr_format()
+      xportr_metadata(adsl, var_spec, domain = "adsl", verbose = "none") %>%
+        xportr_format()
     )
   )
 })

tests/testthat/test-xportr.R

@@ -0,0 +1,52 @@
+test_that("pipeline results match `xportr()` results", {
+
+  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)
+
+    test_dir <- tempdir()
+
+    pipeline_path <- file.path(test_dir, "adslpipe.xpt")
+    xportr_path <- file.path(test_dir, "adslxptr.xpt")
+
+    pipeline_df <- adsl %>%
+      xportr_metadata(var_spec, "ADSL", verbose = "none") %>%
+      xportr_type() %>%
+      xportr_length() %>%
+      xportr_label() %>%
+      xportr_order() %>%
+      xportr_format() %>%
+      xportr_df_label(dataset_spec) %>%
+      xportr_write(pipeline_path)
+
+    # `xportr()` can be used to apply a whole pipeline at once
+    xportr_df <- xportr(adsl,
+      var_metadata = var_spec,
+      df_metadata = dataset_spec,
+      domain = "ADSL",
+      verbose = "none",
+      path = xportr_path
+    )
+
+    expect_identical(pipeline_df, xportr_df)
+
+    expect_identical(
+      haven::read_xpt(pipeline_path),
+      haven::read_xpt(xportr_path)
+    )
+  }
+})