Rename tidy_sparql() what arg to tidy_what

To make it easier to implement and document in other functions.
Also update robot_query() and extract_ordo_mappings() with
these changes.

Tests (robot_wrappers): PASS

R/extract.R

@@ -465,7 +465,8 @@ extract_as_tidygraph <- function(x, query = NULL, collapse_method = "first",
 #'
 #' @param output The path where output will be written, as a string, or `NULL`
 #' (default) to load data directly.
-#' @inheritDotParams tidy_sparql -query_res
+#' @inheritParams tidy_sparql
+#'
 #' @returns
 #' If `output` is specified, the path to the output file with the data.
 #' Otherwise, the data as a [tibble](tibble::tibble).
@@ -481,15 +482,20 @@ extract_as_tidygraph <- function(x, query = NULL, collapse_method = "first",
 #'
 #' @export
 extract_ordo_mappings <- function(ordo_path, as_skos = TRUE, output = NULL,
-                                  ...) {
+                                  tidy_what = "everything") {
     if (isTRUE(as_skos)) {
         q_nm <- "mapping-ordo-skos.rq"
     } else {
         q_nm <- "mapping-ordo.rq"
     }
 
     q_file <- system.file("sparql", q_nm, package = "DO.utils", mustWork = TRUE)
-    out <- robot_query(input = ordo_path, query = q_file, output)
-    out <- tidy_sparql(out, ...)
+    out <- robot_query(
+        input = ordo_path,
+        query = q_file,
+        output = output,
+        tidy_what = tidy_what
+    )
+
     out
 }

R/robot_wrappers.R

@@ -50,9 +50,7 @@ convert_to_ofn <- function(path, out_path = NULL, gzip = FALSE,
 #' @param ... Additional arguments to
 #' [ROBOT query](http://robot.obolibrary.org/query) formatted as described in
 #' [DO.utils::robot()].
-#' @param tidy_what The elements of a SELECT query to tidy, as a character
-#' vector. Ignored when `output` is specified. See [tidy_sparql()] `what` for
-#' options (default: `"nothing"`).
+#' @inheritParams tidy_sparql
 #'
 #' @returns
 #' If `output` is specified, the path to the output file with the query result.
@@ -125,7 +123,7 @@ robot_query <- function(input, query, output = NULL, ...,
             output,
             col_types = readr::cols(.default = readr::col_character())
         )
-        out <- tidy_sparql(out, what = tidy_what)
+        out <- tidy_sparql(out, tidy_what)
     }
     out
 }

R/tidy.R

@@ -5,15 +5,15 @@ utils::globalVariables("where")
 
 #' Tidy SPARQL Query
 #'
-#' Tidies SPARQL query results according to desired specifications (see `what`
-#' param for details).
+#' Tidies SPARQL query results according to desired specifications (see
+#' `tidy_what` parameter for details).
 #'
 #' @param query_res The results of a SPARQL query, as a data.frame (usually
 #'     produced by [owl_xml()]$query() or similar from [DOrepo()], but can also
 #'     be used to tidy results of [robot("query", ...)][robot] loaded with
 #'     `readr`).
-#' @param what The elements of the query to tidy, as a character vector. One or
-#' more of the following:
+#' @param tidy_what The elements of a SPARQL-created data.frame to tidy, as a
+#' character vector. One or more of the following:
 #'
 #' * `"everything"` to apply all tidy operations (has precedence over
 #' `"nothing"`).
@@ -27,41 +27,41 @@ utils::globalVariables("where")
 #' @inheritDotParams to_curie -x
 #'
 #' @export
-tidy_sparql <- function(query_res, what = "everything", ...) {
+tidy_sparql <- function(query_res, tidy_what = "everything", ...) {
     what_opts <- c("header", "unnest", "uri_to_curie", "lgl_NA_FALSE",
                           "as_tibble")
-    what <- match.arg(
-        what,
+    tidy_what <- match.arg(
+        tidy_what,
         choices = c(what_opts, "everything", "nothing"),
         several.ok = TRUE
     )
-    if ("everything" %in% what) what <- what_opts
-    if ("nothing" %in% what) return(query_res)
+    if ("everything" %in% tidy_what) tidy_what <- what_opts
+    if ("nothing" %in% tidy_what) return(query_res)
 
     res <- query_res
-    if ("header" %in% what) {
+    if ("header" %in% tidy_what) {
         names(res) <- stringr::str_remove(names(res), "^\\?")
     }
 
-    if ("unnest" %in% what) {
+    if ("unnest" %in% tidy_what) {
         res <- DO.utils::unnest_cross(res, where(is.list), keep_empty = TRUE)
     }
 
-    if ("uri_to_curie" %in% what) {
+    if ("uri_to_curie" %in% tidy_what) {
         res <- dplyr::mutate(
             res,
             dplyr::across(dplyr::where(is.character), ~ to_curie(.x, ...))
         )
     }
 
-    if ("lgl_NA_FALSE" %in% what) {
+    if ("lgl_NA_FALSE" %in% tidy_what) {
         res <- dplyr::mutate(
             res,
             dplyr::across(dplyr::where(is.logical), ~ replace_na(.x, FALSE))
         )
     }
 
-    if ("as_tibble" %in% what) {
+    if ("as_tibble" %in% tidy_what) {
         res <- tibble::as_tibble(query_res)
     }