Add support for loading missing values in resources as additional cols

DESCRIPTION

@@ -35,7 +35,9 @@ Imports:
     purrr,
     readr (>= 2.1.0),
     utils,
-    yaml
+    yaml,
+    tidyselect,
+    rlang
 Suggests:
     hms,
     knitr,

R/read_resource.R

@@ -16,6 +16,10 @@
 #' @param col_select Character vector of the columns to include in the result,
 #'   in the order provided.
 #'   Selecting columns can improve read speed.
+#' @param channels A character vector representing the data channels to load.
+#'   Available channels are `"values"` and `"missing"`. Use named vectors to
+#'   control column suffixes, e.g.
+#'   `c(values = "__values", missing = "__missing")`.
 #' @return A [tibble()] data frame with the Data Resource's tabular data.
 #'   If there are parsing problems, a warning will alert you.
 #'   You can retrieve the full details by calling [problems()] on your data
@@ -199,7 +203,8 @@
 #'
 #' # Read data from the resource "deployments" with column selection
 #' read_resource(package, "deployments", col_select = c("latitude", "longitude"))
-read_resource <- function(package, resource_name, col_select = NULL) {
+read_resource <- function(package, resource_name, col_select = NULL,
+                          channels = c("values")) {
   # Get resource, includes check_package()
   resource <- get_resource(package, resource_name)
 
@@ -361,10 +366,11 @@ read_resource <- function(package, resource_name, col_select = NULL) {
   } else if (resource$read_from == "path" || resource$read_from == "url") {
     dataframes <- list()
     for (i in seq_along(paths)) {
-      data <- readr::read_delim(
+      data <- read_delim_ext(
         file = paths[i],
         delim = replace_null(dialect$delimiter, ","),
         quote = replace_null(dialect$quoteChar, "\""),
+        channels = channels,
         escape_backslash = ifelse(
           replace_null(dialect$escapeChar, "not set") == "\\", TRUE, FALSE
         ),
@@ -385,7 +391,7 @@ read_resource <- function(package, resource_name, col_select = NULL) {
         trim_ws = replace_null(dialect$skipInitialSpace, FALSE),
         # Skip header row when present
         skip = ifelse(replace_null(dialect$header, TRUE), 1, 0),
-        skip_empty_rows = TRUE
+        skip_empty_rows = TRUE,
       )
       dataframes[[i]] <- data
     }

R/utils_ext.R

@@ -0,0 +1,111 @@
+#' Standardize channel names / suffixes from channel options
+#'
+#' @param channels A character vector representing the data channels to load.
+#'   Available channels are `"values"` and `"missing"`. Use named vectors to
+#'   control column suffixes, e.g.
+#'   `c(values = "_values", missing = "_missing")`.
+#' @return A named list. Names are channel names, values are suffixes.
+#' @family helper functions
+#' @noRd
+channel_opt_standardize <- function(channels) {
+  default_suffixes <- c(
+    values = "_values",
+    missing = "_missing"
+  )
+
+  if (is.null(names(channels))) {
+    names(channels) <- rlang::rep_along(channels, "")
+  }
+
+  if (length(channels) == 1 && names(channels) == "") {
+    channel_suffixes <- ""
+  } else {
+    channel_suffixes <- purrr::map2_vec(
+      channels,
+      names(channels),
+      \(x, n) if (n == "") { default_suffixes[[x]] } else { x }
+    )
+  }
+
+  channel_names <- purrr::map2_vec(
+    channels,
+    names(channels),
+    \(x, n) dplyr::if_else(n == "", x, n)
+  )
+
+  purrr::set_names(channel_suffixes, channel_names)
+}
+
+#' Proposed extension of readr::read_delim
+#'
+#' Adds a `channels` argument that facilitates the loading of missing values
+#'
+#'
+#' @inheritParams readr::read_delim
+#' @param channels A character vector representing the data channels to load.
+#'   Available channels are `"values"` and `"missing"`. Use named vectors to
+#'   control column suffixes, e.g.
+#'   `c(values = "_values", missing = "_missing")`.
+#' @return A `tibble()` of loaded values.
+#' @family helper functions
+#' @noRd
+read_delim_ext <- function(file, delim, na = c("", "NA"), col_types = NULL,
+                           col_select = NULL, channels = "values", ...) {
+
+  channels <- channel_opt_standardize(channels)
+
+  if (is.null(col_select)) {
+    selected_col_types <- col_types
+  } else {
+     selected_col_types <- col_types[tidyselect::eval_select(
+      rlang::enquo(col_select),
+      col_types,
+    )]
+  }
+
+  string_df <- readr::read_delim(
+    file,
+    delim,
+    col_select = {{col_select}},
+    col_types = readr::cols(.default=readr::col_character()),
+    ...
+  )
+
+  result <- NULL
+
+  if ("values" %in% names(channels)) {
+    # Commenting out because https://github.com/tidyverse/readr/issues/1526
+    #values_df <- string_df |>
+    #  readr::type_convert(
+    #    col_types=selected_col_types,
+    #    na=na,
+    #  ) |>
+    #  dplyr::rename_with(\(x) paste0(x, channels[["values"]]))
+
+    # Until the issue is fixed, let's just re-read the csv...
+    values_df <- readr::read_delim(
+        file,
+        delim,
+        col_types=selected_col_types,
+        col_select = {{col_select}},
+        na=na,
+        ...
+      ) |>
+      dplyr::rename_with(\(x) paste0(x, channels[["values"]]))
+
+    result <- dplyr::bind_cols(result, values_df)
+  }
+
+  if ("missing" %in% names(channels)) {
+    missing_df <- string_df |>
+      dplyr::mutate(
+        dplyr::across(
+          dplyr::everything(),
+          \(x) dplyr::if_else(x %in% na, x, NA_character_)
+        )
+      ) |>
+      dplyr::rename_with(\(x) paste0(x, channels[["missing"]]))
+    result <- dplyr::bind_cols(result, values_df)
+  }
+  result
+}