From 3297092b356158da65528aa971011c6a289027dc Mon Sep 17 00:00:00 2001
From: Thierry Onkelinx <thierry.onkelinx@inbo.be>
Date: Fri, 11 Oct 2024 12:12:14 +0200
Subject: [PATCH] update_metadata() gains a stage and force argument

---
 R/update_metadata.R                 | 21 ++++++++++++++++-----
 R/write_vc.R                        |  4 ++--
 man/update_metadata.Rd              | 12 +++++++++++-
 tests/testthat/test_d_description.R | 10 ++++++----
 4 files changed, 35 insertions(+), 12 deletions(-)

diff --git a/R/update_metadata.R b/R/update_metadata.R
index f09b6bb..96465b6 100644
--- a/R/update_metadata.R
+++ b/R/update_metadata.R
@@ -13,30 +13,41 @@
 #' @param name a character string with the new table name of the object.
 #' @param title a character string with the new title of the object.
 #' @param description a character string with the new description of the object.
+#' @param ... parameters used in some methods
 #' @family storage
 #' @export
 #' @importFrom assertthat assert_that has_name
 update_metadata <- function(
-  file, root = ".", field_description, name, title, description
+  file, root = ".", field_description, name, title, description, ...
 ) {
   UseMethod("update_metadata", root)
 }
 
 #' @export
 update_metadata.default <- function(
-  file, root = ".", field_description, name, title, description
+  file, root = ".", field_description, name, title, description, ...
 ) {
   stop("a 'root' of class ", class(root), " is not supported", call. = FALSE)
 }
 
 #' @export
+#' @importFrom assertthat assert_that is.string noNA
+#' @importFrom git2r add
+#' @inheritParams git2r::add
 update_metadata.git_repository <- function(
-    file, root = ".", field_description, name, title, description
+  file, root = ".", field_description, name, title, description, ...,
+  stage = FALSE, force = FALSE
 ) {
-  update_metadata(
+  assert_that(is.flag(stage), is.flag(force), noNA(stage), noNA(force))
+  file <- update_metadata(
     file = file, root = workdir(root), name = name, title = title,
     description = description, field_description = field_description
   )
+  if (!stage) {
+    return(invisible(file))
+  }
+  add(root, path = file, force = force)
+  return(invisible(file))
 }
 
 #' @export
@@ -83,7 +94,7 @@ update_metadata.character <- function(
     as.character() -> old[["..generic"]][["git2rdata"]]
   metadata_hash(old) -> old[["..generic"]][["hash"]]
   write_yaml(old, file["meta_file"])
-  return(invisible(NULL))
+  return(invisible(file["meta_file"]))
 }
 
 #' @importFrom assertthat assert_that is.string
diff --git a/R/write_vc.R b/R/write_vc.R
index a33de91..ee93e9b 100644
--- a/R/write_vc.R
+++ b/R/write_vc.R
@@ -188,12 +188,12 @@ setOldClass("git_repository")
 #' @inheritParams git2r::add
 #' @export
 #' @importFrom git2r workdir add
-#' @importFrom assertthat assert_that is.flag
+#' @importFrom assertthat assert_that is.flag noNA
 write_vc.git_repository <- function(
   x, file, root, sorting, strict = TRUE, optimize = TRUE, na = "NA", ...,
   stage = FALSE, force = FALSE
 ) {
-  assert_that(is.flag(stage), is.flag(force))
+  assert_that(is.flag(stage), is.flag(force), noNA(stage), noNA(force))
   hashes <- write_vc(
     x = x, file = file, root = workdir(root), sorting = sorting,
     strict = strict, optimize = optimize, na = na, ...
diff --git a/man/update_metadata.Rd b/man/update_metadata.Rd
index 968e138..864fc5f 100644
--- a/man/update_metadata.Rd
+++ b/man/update_metadata.Rd
@@ -4,7 +4,15 @@
 \alias{update_metadata}
 \title{Update the description of a \code{git2rdata} object}
 \usage{
-update_metadata(file, root = ".", field_description, name, title, description)
+update_metadata(
+  file,
+  root = ".",
+  field_description,
+  name,
+  title,
+  description,
+  ...
+)
 }
 \arguments{
 \item{file}{the name of the git2rdata object. Git2rdata objects cannot
@@ -24,6 +32,8 @@ The names of the vector must match the variable names.}
 \item{title}{a character string with the new title of the object.}
 
 \item{description}{a character string with the new description of the object.}
+
+\item{...}{parameters used in some methods}
 }
 \description{
 Allows to update the description of the fields, the table name, the title,
diff --git a/tests/testthat/test_d_description.R b/tests/testthat/test_d_description.R
index d6a3140..6b88b82 100644
--- a/tests/testthat/test_d_description.R
+++ b/tests/testthat/test_d_description.R
@@ -16,13 +16,14 @@ test_that("description", {
     "character"
   )
 
-  expect_null(
+  expect_type(
     update_metadata(
       file = "test", root = root, field_description = c(
         test_character = "Some information", test_factor = "Some information",
         test_integer = "Some information"
       )
-    )
+    ),
+    "character"
   )
 
   expect_is({
@@ -48,12 +49,13 @@ test_that("description", {
   git2r::add(root, ".gitignore")
   commit(root, "initial commit")
 
-  expect_null(
+  expect_type(
     update_metadata(
       file = "test", root = root, name = "my_table", title = "My Table",
       description = "This is description for the unit tests",
       field_description = c(test_character = NA, test_factor = "")
-    )
+    ),
+    "character"
   )
   expect_is({
       output <- read_vc("test", root = root)