From 29b6c1fc184a7a494c0f34fb2a4d4a60c3bc4943 Mon Sep 17 00:00:00 2001
From: Nicolas Casajus <rdev.nc@gmail.com>
Date: Tue, 29 Apr 2025 10:53:37 +0200
Subject: [PATCH 01/10] feat: yaml as argument of yaml_to_df()

---
 R/td_create_metadata_file.R | 2 +-
 R/utils_yaml.R              | 8 ++------
 2 files changed, 3 insertions(+), 7 deletions(-)

diff --git a/R/td_create_metadata_file.R b/R/td_create_metadata_file.R
index e75f6d0..27d90c8 100644
--- a/R/td_create_metadata_file.R
+++ b/R/td_create_metadata_file.R
@@ -68,7 +68,7 @@ td_create_metadata_file <- function(
 
       cat(metadata, file = filename, append = FALSE)
     } else {
-      metadata <- metadata_as_df()
+      metadata <- yaml_to_df(metadata)
       metadata[["dataset"]]$"value" <- gsub(
         "\\.dataset_key",
         name,
diff --git a/R/utils_yaml.R b/R/utils_yaml.R
index beed946..5109fa8 100644
--- a/R/utils_yaml.R
+++ b/R/utils_yaml.R
@@ -54,12 +54,10 @@ read_yaml_template <- function() {
 #'
 #' @noRd
 
-metadata_as_df <- function() {
-  metadata <- read_yaml_template()
-
+yaml_to_df <- function(metadata) {
   sheets <- list()
 
-  sheets[["status"]] <- data.frame("status" = "draft")
+  sheets[["status"]] <- data.frame("status" = metadata$"status")
 
   sheets[["dataset"]] <- data.frame(
     "key" = names(unlist(metadata$"dataset")), # to handle sublevel taxonomy
@@ -67,8 +65,6 @@ metadata_as_df <- function() {
   )
 
   rownames(sheets[["dataset"]]) <- NULL
-  # replace '.' by '_' for spelling harmonization
-  sheets[["dataset"]]$key <- gsub("\\.", "_", sheets[["dataset"]]$key)
 
   sheets[["traits"]] <- as.data.frame(metadata$"traits"[[1]])
   sheets[["traits"]] <- rbind(sheets[["traits"]], sheets[["traits"]])

From aeca92ada7152a6e6e3f36b7462703529146a798 Mon Sep 17 00:00:00 2001
From: Nicolas Casajus <rdev.nc@gmail.com>
Date: Tue, 29 Apr 2025 11:27:37 +0200
Subject: [PATCH 02/10] fix: deal w/ categorical traits

---
 DESCRIPTION    |  2 +-
 R/utils_yaml.R | 51 ++++++++++++++++++++++++++++----------------------
 2 files changed, 30 insertions(+), 23 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index ec11956..1933c81 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -19,7 +19,7 @@ RoxygenNote: 7.3.2
 Depends: 
     R (>= 4.1.0)
 Imports: 
-    glue,
+    plyr,
     readxl,
     utils,
     writexl,
diff --git a/R/utils_yaml.R b/R/utils_yaml.R
index 5109fa8..7b63364 100644
--- a/R/utils_yaml.R
+++ b/R/utils_yaml.R
@@ -66,28 +66,35 @@ yaml_to_df <- function(metadata) {
 
   rownames(sheets[["dataset"]]) <- NULL
 
-  sheets[["traits"]] <- as.data.frame(metadata$"traits"[[1]])
-  sheets[["traits"]] <- rbind(sheets[["traits"]], sheets[["traits"]])
-
-  trait_q <- as.data.frame(metadata$"traits"[[1]])
-  trait_q <- data.frame(
-    trait_q,
-    "levels_value" = NA,
-    "levels_description" = NA
-  )
-
-  trait_c <- as.data.frame(metadata$"traits"[[2]])
-  trait_c <- trait_c[, -grep("^levels", colnames(trait_c))]
-
-  trait_c <- data.frame(
-    trait_c,
-    "levels_value" = ".value",
-    "levels_description" = ".descr"
-  )
-
-  trait_c <- rbind(trait_c, trait_c)
-
-  sheets[["traits"]] <- rbind(trait_q, trait_c)
+  traits <- lapply(metadata$"traits", function(x) {
+    traits <- as.data.frame(t(unlist(x)))
+    if (traits$"type" == "categorical") {
+      check_key_in_yaml(x, "levels")
+      invisible(
+        lapply(x$"levels", function(y) check_key_in_yaml(y, "value"))
+      )
+      invisible(
+        lapply(x$"levels", function(y) check_key_in_yaml(y, "description"))
+      )
+
+      level_val_cols <- grep("^levels.value", colnames(traits))
+      level_descr_cols <- grep("^levels.description", colnames(traits))
+
+      categories <- data.frame(
+        "name" = traits[["name"]],
+        "levels_value" = unlist(traits[, level_val_cols]),
+        "levels_description" = unlist(traits[, level_descr_cols])
+      )
+
+      traits <- traits[, -c(level_val_cols, level_descr_cols)]
+
+      traits <- merge(traits, categories, by = "name")
+    }
+
+    traits
+  })
+
+  sheets[["traits"]] <- do.call(plyr::rbind.fill, traits)
 
   sheets
 }

From 164ccadd9e729f60de47c1c052701dceb4b4eb94 Mon Sep 17 00:00:00 2001
From: Nicolas Casajus <rdev.nc@gmail.com>
Date: Tue, 29 Apr 2025 11:42:23 +0200
Subject: [PATCH 03/10] fix: check if keys are presents

---
 R/utils_yaml.R | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/R/utils_yaml.R b/R/utils_yaml.R
index 7b63364..9c32c11 100644
--- a/R/utils_yaml.R
+++ b/R/utils_yaml.R
@@ -67,12 +67,20 @@ yaml_to_df <- function(metadata) {
   rownames(sheets[["dataset"]]) <- NULL
 
   traits <- lapply(metadata$"traits", function(x) {
+    check_key_in_yaml(x, "name")
+    check_key_in_yaml(x, "variable")
+    check_key_in_yaml(x, "category")
+    check_key_in_yaml(x, "type")
+
     traits <- as.data.frame(t(unlist(x)))
+
     if (traits$"type" == "categorical") {
       check_key_in_yaml(x, "levels")
+
       invisible(
         lapply(x$"levels", function(y) check_key_in_yaml(y, "value"))
       )
+
       invisible(
         lapply(x$"levels", function(y) check_key_in_yaml(y, "description"))
       )
@@ -96,5 +104,29 @@ yaml_to_df <- function(metadata) {
 
   sheets[["traits"]] <- do.call(plyr::rbind.fill, traits)
 
+  if (!("units" %in% colnames(sheets[["traits"]]))) {
+    sheets[["traits"]]$"units" <- NA
+  }
+
+  if (!("levels_value" %in% colnames(sheets[["traits"]]))) {
+    sheets[["traits"]]$"levels_value" <- NA
+  }
+
+  if (!("levels_description" %in% colnames(sheets[["traits"]]))) {
+    sheets[["traits"]]$"levels_description" <- NA
+  }
+
+  col_order <- c(
+    "name",
+    "variable",
+    "category",
+    "type",
+    "units",
+    "levels_value",
+    "levels_description"
+  )
+
+  sheets[["traits"]] <- sheets[["traits"]][, col_order]
+
   sheets
 }

From 97f1f7e35420470934064bbf9daf2f2b2f273ff0 Mon Sep 17 00:00:00 2001
From: Nicolas Casajus <rdev.nc@gmail.com>
Date: Tue, 29 Apr 2025 11:44:10 +0200
Subject: [PATCH 04/10] fix: keep dot in column names

---
 R/utils_yaml.R | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/R/utils_yaml.R b/R/utils_yaml.R
index 9c32c11..2f1ed46 100644
--- a/R/utils_yaml.R
+++ b/R/utils_yaml.R
@@ -90,8 +90,8 @@ yaml_to_df <- function(metadata) {
 
       categories <- data.frame(
         "name" = traits[["name"]],
-        "levels_value" = unlist(traits[, level_val_cols]),
-        "levels_description" = unlist(traits[, level_descr_cols])
+        "levels.value" = unlist(traits[, level_val_cols]),
+        "levels.description" = unlist(traits[, level_descr_cols])
       )
 
       traits <- traits[, -c(level_val_cols, level_descr_cols)]
@@ -108,12 +108,12 @@ yaml_to_df <- function(metadata) {
     sheets[["traits"]]$"units" <- NA
   }
 
-  if (!("levels_value" %in% colnames(sheets[["traits"]]))) {
-    sheets[["traits"]]$"levels_value" <- NA
+  if (!("levels.value" %in% colnames(sheets[["traits"]]))) {
+    sheets[["traits"]]$"levels.value" <- NA
   }
 
-  if (!("levels_description" %in% colnames(sheets[["traits"]]))) {
-    sheets[["traits"]]$"levels_description" <- NA
+  if (!("levels.description" %in% colnames(sheets[["traits"]]))) {
+    sheets[["traits"]]$"levels.description" <- NA
   }
 
   col_order <- c(
@@ -122,8 +122,8 @@ yaml_to_df <- function(metadata) {
     "category",
     "type",
     "units",
-    "levels_value",
-    "levels_description"
+    "levels.value",
+    "levels.description"
   )
 
   sheets[["traits"]] <- sheets[["traits"]][, col_order]

From fe11d4ca71e9943eacbb7a8aa0b0ae13cb20d98f Mon Sep 17 00:00:00 2001
From: Nicolas Casajus <rdev.nc@gmail.com>
Date: Tue, 29 Apr 2025 11:45:55 +0200
Subject: [PATCH 05/10] fix: check first level keys in yaml

---
 R/utils_yaml.R | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/R/utils_yaml.R b/R/utils_yaml.R
index 2f1ed46..6177b3d 100644
--- a/R/utils_yaml.R
+++ b/R/utils_yaml.R
@@ -55,6 +55,10 @@ read_yaml_template <- function() {
 #' @noRd
 
 yaml_to_df <- function(metadata) {
+  check_key_in_yaml(metadata, "status")
+  check_key_in_yaml(metadata, "dataset")
+  check_key_in_yaml(metadata, "traits")
+
   sheets <- list()
 
   sheets[["status"]] <- data.frame("status" = metadata$"status")

From 3666d3a3591db67ab4a956d067f1ef21dbdc9228 Mon Sep 17 00:00:00 2001
From: Nicolas Casajus <rdev.nc@gmail.com>
Date: Tue, 29 Apr 2025 11:46:26 +0200
Subject: [PATCH 06/10] style: remove previous yaml_as_df() function

---
 R/format_yaml_xlsx.R | 97 --------------------------------------------
 1 file changed, 97 deletions(-)

diff --git a/R/format_yaml_xlsx.R b/R/format_yaml_xlsx.R
index 0c43961..497c1de 100644
--- a/R/format_yaml_xlsx.R
+++ b/R/format_yaml_xlsx.R
@@ -1,100 +1,3 @@
-#' Transform a yaml metadata to data.frame
-#'
-#' @description
-#' This function transform a metadata written in yaml to
-#' a metadata in data.frame format with three items:
-#' `status`, `dataset`, and `traits`.
-#' The structure of the metadata must follow the structure in `metadata_as_yaml()`
-#'
-#' @param x a `character` of length 1. It could be a filename with extension '.yaml' or a full yaml string.
-#'
-#' @return A list with three data.frames: `status`, `dataset`, and `traits`.
-#'
-#' @export
-#'
-#' @examples
-#' \dontrun{
-#' metadata_as_yaml() |> yaml_as_df()
-#' }
-yaml_as_df <- function(x) {
-  # here 'x' could be a text or a filename
-  check_character_arg(x)
-  # might need some more testing
-  if (substr(x, nchar(x) - 3, nchar(x)) == ".yml") {
-    metadata <- yaml::read_yaml(file = x, readLines.warn = FALSE)
-  } else {
-    metadata <- yaml::read_yaml(text = x)
-  }
-
-  # load the expected structure of metadata
-  skeleton <- metadata_as_yaml() |>
-    yaml::read_yaml(text = _)
-
-  # check the main structure of the metadata
-  # make sure that status, dataset and traits are in metadata
-  if (any(!names(skeleton) %in% names(metadata))) {
-    miss <- paste(
-      names(skeleton)[!names(skeleton) %in% names(metadata)],
-      sep = " "
-    )
-    stop(paste(
-      "Missing level",
-      miss,
-      "\n Check the expected structure of the yaml file with 'metadata_as_yaml()'"
-    ))
-  }
-
-  sheets <- list()
-
-  # status
-  if (length(metadata$"status") != 1) {
-    stop(paste("status should contain a single value"))
-  } else {
-    sheets[["status"]] <- data.frame("status" = metadata$"status")
-  }
-
-  # dataset
-  expected_dataset <- names(unlist(skeleton$"dataset"))
-  if (any(!expected_dataset %in% names(unlist(metadata$"dataset")))) {
-    miss <- expected_dataset[
-      !expected_dataset %in% names(unlist(metadata$"dataset"))
-    ]
-    warning(paste(
-      "Missing field in 'dataset':",
-      paste(miss, collapse = ","),
-      "\n Check the expected structure of the yaml file with 'metadata_as_yaml()'"
-    ))
-  }
-
-  sheets[["dataset"]] <- data.frame(
-    "key" = names(unlist(metadata$"dataset")), # to handle sublevel taxonomy
-    "value" = unlist(metadata$"dataset")
-  )
-  rownames(sheets[["dataset"]]) <- NULL
-  # replace '.' by '_' for spelling harmonization
-  sheets[["dataset"]]$key <- gsub("\\.", "_", sheets[["dataset"]]$key)
-
-  # traits
-  expected_traits <- unique(names(unlist(skeleton$"traits")))
-  if (any(!expected_traits %in% names(unlist(metadata$"traits")))) {
-    miss <- expected_traits[
-      !expected_traits %in% names(unlist(metadata$"traits"))
-    ]
-    warning(paste(
-      "Missing field in 'traits':",
-      paste(miss, collapse = ","),
-      "\n Check the expected structure of the yaml file with 'metadata_as_yaml()'"
-    ))
-  }
-  simple_trait <- lapply(metadata$"traits", FUN = handle_traits_yml)
-
-  sheets[["traits"]] <- data.frame(
-    do.call(rbind, simple_trait)
-  )
-
-  sheets
-}
-
 #' Create a xlsx file from a yaml metadata
 #'
 #' @description

From f1c1edf505d54121f940806eb21abcf9e4dc2267 Mon Sep 17 00:00:00 2001
From: Nicolas Casajus <rdev.nc@gmail.com>
Date: Tue, 29 Apr 2025 12:19:36 +0200
Subject: [PATCH 07/10] chore: disable old functions

---
 NAMESPACE            |   3 -
 R/format_yaml_xlsx.R | 483 +++++++++++++++++++++----------------------
 man/xlsx_to_yaml.Rd  |  29 ---
 man/yaml_as_df.Rd    |  25 ---
 man/yaml_to_xlsx.Rd  |  30 ---
 5 files changed, 241 insertions(+), 329 deletions(-)
 delete mode 100644 man/xlsx_to_yaml.Rd
 delete mode 100644 man/yaml_as_df.Rd
 delete mode 100644 man/yaml_to_xlsx.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 8ff846c..a4b5919 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,6 +1,3 @@
 # Generated by roxygen2: do not edit by hand
 
 export(td_create_metadata_file)
-export(xlsx_to_yaml)
-export(yaml_as_df)
-export(yaml_to_xlsx)
diff --git a/R/format_yaml_xlsx.R b/R/format_yaml_xlsx.R
index 497c1de..4da5ca4 100644
--- a/R/format_yaml_xlsx.R
+++ b/R/format_yaml_xlsx.R
@@ -1,242 +1,241 @@
-#' Create a xlsx file from a yaml metadata
-#'
-#' @description
-#' This function transform a metadata saved in yaml format
-#' into a metadata saved in a xlsx file.
-#'
-#' @param name a `character` of length 1. The trait dataset identifier used to
-#'   create files and folders. Should be short, explicit and without special
-#'   characters (including accents).
-#'
-#' @param path a `character` of length 1. The folder name to stored the
-#'   metadata template file in. Must exist.
-#'   Default is the current directory.
-#'
-#' @param out_suffix a `character` of length 1. The suffix to be added to the output file.
-#'
-#' @param overwrite a `logical` of length 1. If `TRUE` overwrites the metadata
-#'   template file.
-#'   Default is `FALSE`.
-#'
-#' @return No return value.
-#'
-#' @export
-#'
-yaml_to_xlsx <- function(
-  name,
-  path = ".",
-  out_suffix = '',
-  overwrite = FALSE
-) {
-  check_character_arg(name)
-  check_nonascii_char(name)
-  check_character_arg(path)
-  check_path_exists(path)
-  check_logical_arg(overwrite)
-
-  dir_path <- file.path(path, name)
-  infile <- file.path(dir_path, paste0(name, "_metadata.yml"))
-  outfile <- file.path(dir_path, paste0(name, "_metadata", out_suffix, ".xlsx"))
-
-  if (file.exists(outfile) & !overwrite) {
-    stop(
-      "The file '",
-      outfile,
-      "' already exists.",
-      "\nUse 'overwrite = TRUE' to replace its content."
-    )
-  }
-
-  if (!file.exists(infile)) {
-    stop(
-      "The file '",
-      infile,
-      "' can not be found.",
-      "\nMake sure 'path' and 'name' are spelled correctly."
-    )
-  }
-
-  metadata <- yaml_as_df(infile)
-
-  writexl::write_xlsx(x = metadata, path = outfile)
-}
-
-#' Create a yaml file from a xlsx metadata
-#'
-#' @description
-#' This function transform a metadata saved in yaml format
-#' into a metadata saved in a xlsx file.
-#'
-#' @param name a `character` of length 1. The trait dataset identifier used to
-#'   create files and folders. Should be short, explicit and without special
-#'   characters (including accents).
-#'
-#' @param path a `character` of length 1. The folder name to stored the
-#'   metadata template file in. Must exist.
-#'   Default is the current directory.
-#'
-#' @param out_suffix a `character` of length 1. The suffix to be added to the output file.
-#'
-#' @param overwrite a `logical` of length 1. If `TRUE` overwrites the metadata
-#'   template file. Default is `FALSE`.
-#'
-#' @return No return value.
-#'
-#' @export
-#'
-xlsx_to_yaml <- function(
-  name,
-  path = ".",
-  out_suffix = '',
-  overwrite = FALSE
-) {
-  check_character_arg(name)
-  check_nonascii_char(name)
-  check_character_arg(path)
-  check_path_exists(path)
-  check_logical_arg(overwrite)
-
-  dir_path <- file.path(path, name)
-  infile <- file.path(dir_path, paste0(name, "_metadata.xlsx"))
-  outfile <- file.path(dir_path, paste0(name, "_metadata", out_suffix, ".yml"))
-
-  if (file.exists(outfile) & !overwrite) {
-    stop(
-      "The file '",
-      outfile,
-      "' already exists.",
-      "\nUse 'overwrite = TRUE' to replace its content."
-    )
-  }
-
-  if (!file.exists(infile)) {
-    stop(
-      "The file '",
-      infile,
-      "' can not be found.",
-      "\nMake sure 'path' and 'name' are spelled correctly."
-    )
-  }
-
-  status <- readxl::read_xlsx(path = infile, sheet = "status")
-  dataset <- readxl::read_xlsx(path = infile, sheet = "dataset")
-  traits <- readxl::read_xlsx(path = infile, sheet = "traits")
-
-  # load the expected structure of metadata
-  skeleton_df <- metadata_as_yaml() |>
-    yaml_as_df()
-
-  # status
-  if (length(status) != 1) {
-    stop(paste("'status' should contain a single value"))
-  } else {
-    yml_status <- paste(names(status), as.character(status), sep = ": ")
-  }
-  cat(yml_status, sep = "\n", file = outfile)
-
-  # dataset
-  cat("dataset:", sep = "\n", file = outfile, append = TRUE)
-
-  if (any(names(dataset) != names(skeleton_df$dataset))) {
-    stop(paste(
-      "'dataset' should have two columns: ",
-      paste(names(skeleton_df$dataset), collapse = ", ")
-    ))
-  }
-  if (any(!skeleton_df$dataset$key %in% dataset$key)) {
-    miss <- skeleton_df$dataset$key[!skeleton_df$dataset$key %in% dataset$key]
-    warning(paste("Missing field in 'dataset':", paste(miss, collapse = ",")))
-  }
-  # make sure col separator is surrounded by ' '
-  yml_dataset <- paste0("  ", dataset$key, ": ", dataset$value)
-  cat(check_yaml(yml_dataset), sep = "\n", file = outfile, append = TRUE)
-
-  # traits
-  cat("traits:", sep = "\n", file = outfile, append = TRUE)
-  if (any(!names(traits) %in% names(skeleton_df$traits))) {
-    stop(paste(
-      "'dataset' should have seven columns: ",
-      paste(names(skeleton_df$traits), collapse = ", ")
-    ))
-  }
-  col_levels <- grep("^levels_", names(traits))
-  for (trait_i in unique(traits$variable)) {
-    row_i <- which(traits$variable %in% trait_i)
-    if (length(row_i) == 1) {
-      yaml_i <- paste0(
-        "  ",
-        names(traits)[-col_levels],
-        ": ",
-        traits[row_i, -col_levels]
-      )
-    } else {
-      key_row <- row_i[which.min(apply(
-        is.na(traits[row_i, -col_levels]),
-        1,
-        sum
-      ))]
-      yaml_i <- paste0(
-        "  ",
-        names(traits)[-col_levels],
-        ": ",
-        traits[key_row, -col_levels]
-      )
-      var_level <- gsub("^levels_", "    ", names(traits)[col_levels])
-      # add '-' at the stat of a new trait
-      var_level[1] <- gsub("^    ", "  - ", var_level[1])
-      yaml_level <- apply(
-        traits[row_i, col_levels],
-        1,
-        function(x) paste(var_level, x, sep = ": ")
-      )
-    }
-    # add '-' at the stat of a new trait
-    yaml_i[1] <- gsub("^  ", "- ", yaml_i[1])
-    cat(check_yaml(yaml_i), sep = "\n", file = outfile, append = TRUE)
-    if (length(row_i) > 1) {
-      cat("  levels:", sep = "\n", file = outfile, append = TRUE)
-      cat(check_yaml(yaml_level), sep = "\n", file = outfile, append = TRUE)
-    }
-  }
-}
-
-
-#' Handy function to convert traits in yaml to df
-#'
-#' @noRd
-handle_traits_yml <- function(x) {
-  if ("levels" %in% names(x)) {
-    # base trait information
-    base_i <- x[-grep("^levels", names(x))]
-    # add levels information
-    levels_i <- do.call(rbind, x$"levels")
-    colnames(levels_i) <- paste("levels", colnames(levels_i), sep = "_")
-    levels_i <- apply(levels_i, 2, unlist)
-    # merge the two together
-    out_i <- data.frame(
-      base_i,
-      levels_i
-    )
-  } else {
-    out_i <- data.frame(
-      x,
-      "levels_value" = NA,
-      "levels_description" = NA
-    )
-  }
-  return(out_i)
-}
-
-#' Function to transform NA and logical values for readibility in yaml format
-#'
-#' @noRd
-check_yaml <- function(x) {
-  # replace NA
-  x <- gsub(": NA", ": .na", x)
-  # replace TRUE and FALSE
-  x <- gsub(": FALSE", ": no", x)
-  x <- gsub(": TRUE", ": yes", x)
-  # yaml doesn't like ending ','
-  x <- gsub(",$", "','", x)
-  return(x)
-}
+# #' Create a xlsx file from a yaml metadata
+# #'
+# #' @description
+# #' This function transform a metadata saved in yaml format
+# #' into a metadata saved in a xlsx file.
+# #'
+# #' @param name a `character` of length 1. The trait dataset identifier used to
+# #'   create files and folders. Should be short, explicit and without special
+# #'   characters (including accents).
+# #'
+# #' @param path a `character` of length 1. The folder name to stored the
+# #'   metadata template file in. Must exist.
+# #'   Default is the current directory.
+# #'
+# #' @param out_suffix a `character` of length 1. The suffix to be added to the output file.
+# #'
+# #' @param overwrite a `logical` of length 1. If `TRUE` overwrites the metadata
+# #'   template file.
+# #'   Default is `FALSE`.
+# #'
+# #' @return No return value.
+# #'
+# #' @export
+# #'
+# yaml_to_xlsx <- function(
+#   name,
+#   path = ".",
+#   out_suffix = '',
+#   overwrite = FALSE
+# ) {
+#   check_character_arg(name)
+#   check_nonascii_char(name)
+#   check_character_arg(path)
+#   check_path_exists(path)
+#   check_logical_arg(overwrite)
+
+#   dir_path <- file.path(path, name)
+#   infile <- file.path(dir_path, paste0(name, "_metadata.yml"))
+#   outfile <- file.path(dir_path, paste0(name, "_metadata", out_suffix, ".xlsx"))
+
+#   if (file.exists(outfile) & !overwrite) {
+#     stop(
+#       "The file '",
+#       outfile,
+#       "' already exists.",
+#       "\nUse 'overwrite = TRUE' to replace its content."
+#     )
+#   }
+
+#   if (!file.exists(infile)) {
+#     stop(
+#       "The file '",
+#       infile,
+#       "' can not be found.",
+#       "\nMake sure 'path' and 'name' are spelled correctly."
+#     )
+#   }
+
+#   metadata <- yaml_as_df(infile)
+
+#   writexl::write_xlsx(x = metadata, path = outfile)
+# }
+
+# #' Create a yaml file from a xlsx metadata
+# #'
+# #' @description
+# #' This function transform a metadata saved in yaml format
+# #' into a metadata saved in a xlsx file.
+# #'
+# #' @param name a `character` of length 1. The trait dataset identifier used to
+# #'   create files and folders. Should be short, explicit and without special
+# #'   characters (including accents).
+# #'
+# #' @param path a `character` of length 1. The folder name to stored the
+# #'   metadata template file in. Must exist.
+# #'   Default is the current directory.
+# #'
+# #' @param out_suffix a `character` of length 1. The suffix to be added to the output file.
+# #'
+# #' @param overwrite a `logical` of length 1. If `TRUE` overwrites the metadata
+# #'   template file. Default is `FALSE`.
+# #'
+# #' @return No return value.
+# #'
+# #' @export
+# #'
+# xlsx_to_yaml <- function(
+#   name,
+#   path = ".",
+#   out_suffix = '',
+#   overwrite = FALSE
+# ) {
+#   check_character_arg(name)
+#   check_nonascii_char(name)
+#   check_character_arg(path)
+#   check_path_exists(path)
+#   check_logical_arg(overwrite)
+
+#   dir_path <- file.path(path, name)
+#   infile <- file.path(dir_path, paste0(name, "_metadata.xlsx"))
+#   outfile <- file.path(dir_path, paste0(name, "_metadata", out_suffix, ".yml"))
+
+#   if (file.exists(outfile) & !overwrite) {
+#     stop(
+#       "The file '",
+#       outfile,
+#       "' already exists.",
+#       "\nUse 'overwrite = TRUE' to replace its content."
+#     )
+#   }
+
+#   if (!file.exists(infile)) {
+#     stop(
+#       "The file '",
+#       infile,
+#       "' can not be found.",
+#       "\nMake sure 'path' and 'name' are spelled correctly."
+#     )
+#   }
+
+#   status <- readxl::read_xlsx(path = infile, sheet = "status")
+#   dataset <- readxl::read_xlsx(path = infile, sheet = "dataset")
+#   traits <- readxl::read_xlsx(path = infile, sheet = "traits")
+
+#   # load the expected structure of metadata
+#   skeleton_df <- metadata_as_yaml() |>
+#     yaml_as_df()
+
+#   # status
+#   if (length(status) != 1) {
+#     stop(paste("'status' should contain a single value"))
+#   } else {
+#     yml_status <- paste(names(status), as.character(status), sep = ": ")
+#   }
+#   cat(yml_status, sep = "\n", file = outfile)
+
+#   # dataset
+#   cat("dataset:", sep = "\n", file = outfile, append = TRUE)
+
+#   if (any(names(dataset) != names(skeleton_df$dataset))) {
+#     stop(paste(
+#       "'dataset' should have two columns: ",
+#       paste(names(skeleton_df$dataset), collapse = ", ")
+#     ))
+#   }
+#   if (any(!skeleton_df$dataset$key %in% dataset$key)) {
+#     miss <- skeleton_df$dataset$key[!skeleton_df$dataset$key %in% dataset$key]
+#     warning(paste("Missing field in 'dataset':", paste(miss, collapse = ",")))
+#   }
+#   # make sure col separator is surrounded by ' '
+#   yml_dataset <- paste0("  ", dataset$key, ": ", dataset$value)
+#   cat(check_yaml(yml_dataset), sep = "\n", file = outfile, append = TRUE)
+
+#   # traits
+#   cat("traits:", sep = "\n", file = outfile, append = TRUE)
+#   if (any(!names(traits) %in% names(skeleton_df$traits))) {
+#     stop(paste(
+#       "'dataset' should have seven columns: ",
+#       paste(names(skeleton_df$traits), collapse = ", ")
+#     ))
+#   }
+#   col_levels <- grep("^levels_", names(traits))
+#   for (trait_i in unique(traits$variable)) {
+#     row_i <- which(traits$variable %in% trait_i)
+#     if (length(row_i) == 1) {
+#       yaml_i <- paste0(
+#         "  ",
+#         names(traits)[-col_levels],
+#         ": ",
+#         traits[row_i, -col_levels]
+#       )
+#     } else {
+#       key_row <- row_i[which.min(apply(
+#         is.na(traits[row_i, -col_levels]),
+#         1,
+#         sum
+#       ))]
+#       yaml_i <- paste0(
+#         "  ",
+#         names(traits)[-col_levels],
+#         ": ",
+#         traits[key_row, -col_levels]
+#       )
+#       var_level <- gsub("^levels_", "    ", names(traits)[col_levels])
+#       # add '-' at the stat of a new trait
+#       var_level[1] <- gsub("^    ", "  - ", var_level[1])
+#       yaml_level <- apply(
+#         traits[row_i, col_levels],
+#         1,
+#         function(x) paste(var_level, x, sep = ": ")
+#       )
+#     }
+#     # add '-' at the stat of a new trait
+#     yaml_i[1] <- gsub("^  ", "- ", yaml_i[1])
+#     cat(check_yaml(yaml_i), sep = "\n", file = outfile, append = TRUE)
+#     if (length(row_i) > 1) {
+#       cat("  levels:", sep = "\n", file = outfile, append = TRUE)
+#       cat(check_yaml(yaml_level), sep = "\n", file = outfile, append = TRUE)
+#     }
+#   }
+# }
+
+# #' Handy function to convert traits in yaml to df
+# #'
+# #' @noRd
+# handle_traits_yml <- function(x) {
+#   if ("levels" %in% names(x)) {
+#     # base trait information
+#     base_i <- x[-grep("^levels", names(x))]
+#     # add levels information
+#     levels_i <- do.call(rbind, x$"levels")
+#     colnames(levels_i) <- paste("levels", colnames(levels_i), sep = "_")
+#     levels_i <- apply(levels_i, 2, unlist)
+#     # merge the two together
+#     out_i <- data.frame(
+#       base_i,
+#       levels_i
+#     )
+#   } else {
+#     out_i <- data.frame(
+#       x,
+#       "levels_value" = NA,
+#       "levels_description" = NA
+#     )
+#   }
+#   return(out_i)
+# }
+
+# #' Function to transform NA and logical values for readibility in yaml format
+# #'
+# #' @noRd
+# check_yaml <- function(x) {
+#   # replace NA
+#   x <- gsub(": NA", ": .na", x)
+#   # replace TRUE and FALSE
+#   x <- gsub(": FALSE", ": no", x)
+#   x <- gsub(": TRUE", ": yes", x)
+#   # yaml doesn't like ending ','
+#   x <- gsub(",$", "','", x)
+#   return(x)
+# }
diff --git a/man/xlsx_to_yaml.Rd b/man/xlsx_to_yaml.Rd
deleted file mode 100644
index 726f883..0000000
--- a/man/xlsx_to_yaml.Rd
+++ /dev/null
@@ -1,29 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/format_yaml_xlsx.R
-\name{xlsx_to_yaml}
-\alias{xlsx_to_yaml}
-\title{Create a yaml file from a xlsx metadata}
-\usage{
-xlsx_to_yaml(name, path = ".", out_suffix = "", overwrite = FALSE)
-}
-\arguments{
-\item{name}{a \code{character} of length 1. The trait dataset identifier used to
-create files and folders. Should be short, explicit and without special
-characters (including accents).}
-
-\item{path}{a \code{character} of length 1. The folder name to stored the
-metadata template file in. Must exist.
-Default is the current directory.}
-
-\item{out_suffix}{a \code{character} of length 1. The suffix to be added to the output file.}
-
-\item{overwrite}{a \code{logical} of length 1. If \code{TRUE} overwrites the metadata
-template file. Default is \code{FALSE}.}
-}
-\value{
-No return value.
-}
-\description{
-This function transform a metadata saved in yaml format
-into a metadata saved in a xlsx file.
-}
diff --git a/man/yaml_as_df.Rd b/man/yaml_as_df.Rd
deleted file mode 100644
index 8fc2317..0000000
--- a/man/yaml_as_df.Rd
+++ /dev/null
@@ -1,25 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/format_yaml_xlsx.R
-\name{yaml_as_df}
-\alias{yaml_as_df}
-\title{Transform a yaml metadata to data.frame}
-\usage{
-yaml_as_df(x)
-}
-\arguments{
-\item{x}{a \code{character} of length 1. It could be a filename with extension '.yaml' or a full yaml string.}
-}
-\value{
-A list with three data.frames: \code{status}, \code{dataset}, and \code{traits}.
-}
-\description{
-This function transform a metadata written in yaml to
-a metadata in data.frame format with three items:
-\code{status}, \code{dataset}, and \code{traits}.
-The structure of the metadata must follow the structure in \code{metadata_as_yaml()}
-}
-\examples{
-\dontrun{
-metadata_as_yaml() |> yaml_as_df()
-}
-}
diff --git a/man/yaml_to_xlsx.Rd b/man/yaml_to_xlsx.Rd
deleted file mode 100644
index d08dedf..0000000
--- a/man/yaml_to_xlsx.Rd
+++ /dev/null
@@ -1,30 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/format_yaml_xlsx.R
-\name{yaml_to_xlsx}
-\alias{yaml_to_xlsx}
-\title{Create a xlsx file from a yaml metadata}
-\usage{
-yaml_to_xlsx(name, path = ".", out_suffix = "", overwrite = FALSE)
-}
-\arguments{
-\item{name}{a \code{character} of length 1. The trait dataset identifier used to
-create files and folders. Should be short, explicit and without special
-characters (including accents).}
-
-\item{path}{a \code{character} of length 1. The folder name to stored the
-metadata template file in. Must exist.
-Default is the current directory.}
-
-\item{out_suffix}{a \code{character} of length 1. The suffix to be added to the output file.}
-
-\item{overwrite}{a \code{logical} of length 1. If \code{TRUE} overwrites the metadata
-template file.
-Default is \code{FALSE}.}
-}
-\value{
-No return value.
-}
-\description{
-This function transform a metadata saved in yaml format
-into a metadata saved in a xlsx file.
-}

From b2a4e6f85fe3f813814f66b0e2a9fe8f285166b8 Mon Sep 17 00:00:00 2001
From: Nicolas Casajus <rdev.nc@gmail.com>
Date: Tue, 29 Apr 2025 13:06:04 +0200
Subject: [PATCH 08/10] factor: clean_database_name()

---
 R/td_create_metadata_file.R |  7 +------
 R/utils_yaml.R              | 14 ++++++++++++++
 2 files changed, 15 insertions(+), 6 deletions(-)

diff --git a/R/td_create_metadata_file.R b/R/td_create_metadata_file.R
index 27d90c8..1b7898b 100644
--- a/R/td_create_metadata_file.R
+++ b/R/td_create_metadata_file.R
@@ -43,12 +43,7 @@ td_create_metadata_file <- function(
   check_format_value(format)
   check_logical_arg(overwrite)
 
-  name <- name |>
-    tolower() |>
-    trimws() |>
-    gsub("\\s+", "_", x = _) |>
-    gsub("[[:punct:]]", "_", x = _) |>
-    gsub("_+", "_", x = _)
+  name <- clean_database_name(name)
 
   dir_path <- file.path(path, name)
   file_ext <- ifelse(format == "yaml", ".yml", ".xlsx")
diff --git a/R/utils_yaml.R b/R/utils_yaml.R
index 6177b3d..62836ae 100644
--- a/R/utils_yaml.R
+++ b/R/utils_yaml.R
@@ -134,3 +134,17 @@ yaml_to_df <- function(metadata) {
 
   sheets
 }
+
+
+#' Clean database name
+#'
+#' @noRd
+
+clean_database_name <- function(name) {
+  name |>
+    tolower() |>
+    trimws() |>
+    gsub("\\s+", "_", x = _) |>
+    gsub("[[:punct:]]", "_", x = _) |>
+    gsub("_+", "_", x = _)
+}

From 35ccc66c40e06d000c0d242925d66c5ca6a73ed8 Mon Sep 17 00:00:00 2001
From: Nicolas Casajus <rdev.nc@gmail.com>
Date: Tue, 29 Apr 2025 16:57:20 +0200
Subject: [PATCH 09/10] fix: improve name cleaning

---
 R/utils_yaml.R | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/R/utils_yaml.R b/R/utils_yaml.R
index 62836ae..3a96d76 100644
--- a/R/utils_yaml.R
+++ b/R/utils_yaml.R
@@ -146,5 +146,7 @@ clean_database_name <- function(name) {
     trimws() |>
     gsub("\\s+", "_", x = _) |>
     gsub("[[:punct:]]", "_", x = _) |>
-    gsub("_+", "_", x = _)
+    gsub("_+", "_", x = _) |>
+    gsub("^_", "", x = _) |>
+    gsub("_$", "", x = _)
 }

From dd7c3abc6b7d03e9252f71fcaf237662c35e39b6 Mon Sep 17 00:00:00 2001
From: Nicolas Casajus <rdev.nc@gmail.com>
Date: Tue, 29 Apr 2025 16:57:33 +0200
Subject: [PATCH 10/10] test: add unit tests

---
 tests/testthat/test-clean_database_name.R |  12 ++
 tests/testthat/test-yaml_to_df.R          | 193 ++++++++++++++++++++++
 2 files changed, 205 insertions(+)
 create mode 100644 tests/testthat/test-clean_database_name.R
 create mode 100644 tests/testthat/test-yaml_to_df.R

diff --git a/tests/testthat/test-clean_database_name.R b/tests/testthat/test-clean_database_name.R
new file mode 100644
index 0000000..e6b459d
--- /dev/null
+++ b/tests/testthat/test-clean_database_name.R
@@ -0,0 +1,12 @@
+## clean_database_name() ----
+
+test_that("clean_database_name() succeeds", {
+  x <- clean_database_name("Middolo 2023")
+
+  expect_true(class(x) == "character")
+  expect_equal(length(x), 1L)
+  expect_true(x == "middolo_2023")
+
+  x <- clean_database_name("  Middolo - 2023..")
+  expect_true(x == "middolo_2023")
+})
diff --git a/tests/testthat/test-yaml_to_df.R b/tests/testthat/test-yaml_to_df.R
new file mode 100644
index 0000000..9920c28
--- /dev/null
+++ b/tests/testthat/test-yaml_to_df.R
@@ -0,0 +1,193 @@
+## yaml_to_df() ----
+
+test_that("yaml_to_df() fails", {
+  metadata <- read_yaml_template()
+  metadata <- metadata[-1]
+
+  expect_error(
+    yaml_to_df(metadata),
+    "No key 'status' found in the YAML file",
+    fixed = TRUE
+  )
+
+  metadata <- read_yaml_template()
+  metadata <- metadata[-2]
+
+  expect_error(
+    yaml_to_df(metadata),
+    "No key 'dataset' found in the YAML file",
+    fixed = TRUE
+  )
+
+  metadata <- read_yaml_template()
+  metadata <- metadata[-3]
+
+  expect_error(
+    yaml_to_df(metadata),
+    "No key 'traits' found in the YAML file",
+    fixed = TRUE
+  )
+
+  metadata <- read_yaml_template()
+  metadata[[3]][[1]] <- metadata[[3]][[1]][-1]
+
+  expect_error(
+    yaml_to_df(metadata),
+    "No key 'variable' found in the YAML file",
+    fixed = TRUE
+  )
+
+  metadata <- read_yaml_template()
+  metadata[[3]][[1]] <- metadata[[3]][[1]][-2]
+
+  expect_error(
+    yaml_to_df(metadata),
+    "No key 'name' found in the YAML file",
+    fixed = TRUE
+  )
+
+  metadata <- read_yaml_template()
+  metadata[[3]][[1]] <- metadata[[3]][[1]][-3]
+
+  expect_error(
+    yaml_to_df(metadata),
+    "No key 'category' found in the YAML file",
+    fixed = TRUE
+  )
+
+  metadata <- read_yaml_template()
+  metadata[[3]][[1]] <- metadata[[3]][[1]][-4]
+
+  expect_error(
+    yaml_to_df(metadata),
+    "No key 'type' found in the YAML file",
+    fixed = TRUE
+  )
+
+  metadata <- read_yaml_template()
+  metadata[[3]][[2]] <- metadata[[3]][[2]][-1]
+
+  expect_error(
+    yaml_to_df(metadata),
+    "No key 'variable' found in the YAML file",
+    fixed = TRUE
+  )
+
+  metadata <- read_yaml_template()
+  metadata[[3]][[2]] <- metadata[[3]][[2]][-2]
+
+  expect_error(
+    yaml_to_df(metadata),
+    "No key 'name' found in the YAML file",
+    fixed = TRUE
+  )
+
+  metadata <- read_yaml_template()
+  metadata[[3]][[2]] <- metadata[[3]][[2]][-3]
+
+  expect_error(
+    yaml_to_df(metadata),
+    "No key 'category' found in the YAML file",
+    fixed = TRUE
+  )
+
+  metadata <- read_yaml_template()
+  metadata[[3]][[2]] <- metadata[[3]][[2]][-4]
+
+  expect_error(
+    yaml_to_df(metadata),
+    "No key 'type' found in the YAML file",
+    fixed = TRUE
+  )
+
+  metadata <- read_yaml_template()
+  metadata[[3]][[2]]$"levels"[[1]] <- metadata[[3]][[2]]$"levels"[[1]][-1]
+
+  expect_error(
+    yaml_to_df(metadata),
+    "No key 'value' found in the YAML file",
+    fixed = TRUE
+  )
+
+  metadata <- read_yaml_template()
+  metadata[[3]][[2]]$"levels"[[1]] <- metadata[[3]][[2]]$"levels"[[1]][-2]
+
+  expect_error(
+    yaml_to_df(metadata),
+    "No key 'description' found in the YAML file",
+    fixed = TRUE
+  )
+
+  metadata <- read_yaml_template()
+  metadata[[3]][[2]]$"levels"[[2]] <- metadata[[3]][[2]]$"levels"[[2]][-1]
+
+  expect_error(
+    yaml_to_df(metadata),
+    "No key 'value' found in the YAML file",
+    fixed = TRUE
+  )
+
+  metadata <- read_yaml_template()
+  metadata[[3]][[2]]$"levels"[[2]] <- metadata[[3]][[2]]$"levels"[[2]][-2]
+
+  expect_error(
+    yaml_to_df(metadata),
+    "No key 'description' found in the YAML file",
+    fixed = TRUE
+  )
+})
+
+
+test_that("yaml_to_df() succeeds - Mixed traits", {
+  metadata <- read_yaml_template()
+  x <- yaml_to_df(metadata)
+
+  expect_true(is.list(x))
+  expect_true(!is.null(names(x)))
+  expect_true("status" %in% names(x))
+  expect_true("dataset" %in% names(x))
+  expect_true("traits" %in% names(x))
+
+  expect_true(is.data.frame(x[["status"]]))
+  expect_true(ncol(x[["status"]]) == 1L)
+  expect_true(nrow(x[["status"]]) == 1L)
+  expect_true(x[["status"]][1, "status"] == "draft")
+
+  expect_true(is.data.frame(x[["dataset"]]))
+  expect_true(ncol(x[["dataset"]]) == 2L)
+  expect_true(nrow(x[["dataset"]]) == 23L)
+  expect_true(x[["dataset"]][20, "key"] == "taxonomy.genus")
+
+  expect_true(is.data.frame(x[["traits"]]))
+  expect_true(ncol(x[["traits"]]) == 7L)
+  expect_true(nrow(x[["traits"]]) == 3L)
+  expect_true(x[["traits"]][2, "variable"] == x[["traits"]][3, "variable"])
+})
+
+
+test_that("yaml_to_df() succeeds - One quantitative trait", {
+  metadata <- read_yaml_template()
+  metadata[["traits"]] <- metadata[["traits"]][-2]
+  x <- yaml_to_df(metadata)
+
+  expect_true(ncol(x[["traits"]]) == 7L)
+  expect_true(nrow(x[["traits"]]) == 1L)
+  expect_true("levels.value" %in% colnames(x[["traits"]]))
+  expect_true("levels.description" %in% colnames(x[["traits"]]))
+  expect_true(is.na(x[["traits"]][1, "levels.value"]))
+  expect_true(is.na(x[["traits"]][1, "levels.description"]))
+})
+
+
+test_that("yaml_to_df() succeeds - One categorical trait", {
+  metadata <- read_yaml_template()
+  metadata[["traits"]] <- metadata[["traits"]][-1]
+  metadata[["traits"]][[1]] <- metadata[["traits"]][[1]][-5]
+  x <- yaml_to_df(metadata)
+
+  expect_true(ncol(x[["traits"]]) == 7L)
+  expect_true(nrow(x[["traits"]]) == 2L)
+  expect_true("units" %in% colnames(x[["traits"]]))
+  expect_true(is.na(x[["traits"]][1, "units"]))
+  expect_true(is.na(x[["traits"]][2, "units"]))
+})