Unset robot_query() character col type assumption

Also add col_types from readr::read_tsv() for management. To
reduce verbosity, show_col_types has been set to FALSE and
cannot be changed.

Tests (robot_wrappers): PASS

R/extract.R

@@ -465,7 +465,7 @@ 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.
-#' @inheritParams tidy_sparql
+#' @inheritParams robot_query
 #'
 #' @returns
 #' If `output` is specified, the path to the output file with the data.
@@ -482,7 +482,7 @@ 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") {
+                                  tidy_what = "everything", col_types = NULL) {
     if (isTRUE(as_skos)) {
         q_nm <- "mapping-ordo-skos.rq"
     } else {
@@ -494,7 +494,8 @@ extract_ordo_mappings <- function(ordo_path, as_skos = TRUE, output = NULL,
         input = ordo_path,
         query = q_file,
         output = output,
-        tidy_what = tidy_what
+        tidy_what = tidy_what,
+        col_types = col_types
     )
 
     out

R/robot_wrappers.R

@@ -51,6 +51,7 @@ convert_to_ofn <- function(path, out_path = NULL, gzip = FALSE,
 #' [ROBOT query](http://robot.obolibrary.org/query) formatted as described in
 #' [DO.utils::robot()].
 #' @inheritParams tidy_sparql
+#' @inheritParams readr::read_tsv
 #'
 #' @returns
 #' If `output` is specified, the path to the output file with the query result.
@@ -60,7 +61,7 @@ convert_to_ofn <- function(path, out_path = NULL, gzip = FALSE,
 #'
 #' @export
 robot_query <- function(input, query, output = NULL, ...,
-                        tidy_what = "nothing") {
+                        tidy_what = "nothing", col_types = NULL) {
     # load query, also ensure query in a file (required by ROBOT)
     query_is_file <- file.exists(query)
     if (query_is_file) {
@@ -121,7 +122,8 @@ robot_query <- function(input, query, output = NULL, ...,
     } else {
         out <- readr::read_tsv(
             output,
-            col_types = readr::cols(.default = readr::col_character())
+            col_types = col_types,
+            show_col_types = FALSE
         )
         out <- tidy_sparql(out, tidy_what)
     }