From aff0f350e58dd2272e94633ffe0f8ecf370571c4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Mon, 12 Feb 2024 14:28:10 +0100
Subject: [PATCH] revert export of resolve

---
 NAMESPACE      |   1 -
 R/resolve.R    |  70 +++++++--------------------------
 man/resolve.Rd | 104 +++++++++++++++++++++++--------------------------
 3 files changed, 61 insertions(+), 114 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 7cef7a44..49700e8d 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -58,7 +58,6 @@ export(merge_datasets)
 export(merge_expression_module)
 export(merge_expression_srv)
 export(no_selected_as_NULL)
-export(resolve)
 export(resolve_delayed)
 export(select_spec)
 export(select_spec.default)
diff --git a/R/resolve.R b/R/resolve.R
index fc82e837..91db8126 100644
--- a/R/resolve.R
+++ b/R/resolve.R
@@ -2,6 +2,9 @@
 #'
 #' `r lifecycle::badge("stable")`
 #'
+#' @note This is an internal function that is used by [resolve_delayed()].
+#' All the methods are used internally only.
+#'
 #' @param x (`delayed_data`) object to resolve.
 #' @param datasets (named `list` of `data.frame`) to use in evaluation.
 #' @param keys (named `list` of `character`) to be used as the keys for each dataset.
@@ -9,63 +12,7 @@
 #'
 #' @return Resolved object.
 #'
-#' @examples
-#' library(shiny)
-#' ADSL <- rADSL
-#'
-#' attr(ADSL, "keys") <- c("STUDYID", "USUBJID")
-#' data_list <- list(ADSL = reactive(ADSL))
-#' keys <- list(ADSL = attr(ADSL, "keys"))
-#' isolate({
-#'   # value_choices example
-#'   v1 <- value_choices("ADSL", "SEX", "SEX")
-#'   v1
-#'   resolve(v1, data_list, keys)
-#'
-#'   # variable_choices example
-#'   v2 <- variable_choices("ADSL", c("BMRKR1", "BMRKR2"))
-#'   v2
-#'   resolve(v2, data_list, keys)
-#'
-#'   # data_extract_spec example
-#'   adsl_filter <- filter_spec(
-#'     vars = variable_choices("ADSL", "SEX"),
-#'     sep = "-",
-#'     choices = value_choices("ADSL", "SEX", "SEX"),
-#'     selected = "F",
-#'     multiple = FALSE,
-#'     label = "Choose endpoint and Censor"
-#'   )
-#'
-#'   adsl_select <- select_spec(
-#'     label = "Select variable:",
-#'     choices = variable_choices("ADSL", c("BMRKR1", "BMRKR2")),
-#'     selected = "BMRKR1",
-#'     multiple = FALSE,
-#'     fixed = FALSE
-#'   )
-#'
-#'   adsl_de <- data_extract_spec(
-#'     dataname = "ADSL",
-#'     select = adsl_select,
-#'     filter = adsl_filter
-#'   )
-#'
-#'   resolve(adsl_filter, data_list, keys)
-#'   resolve(adsl_select, data_list, keys)
-#'   resolve(adsl_de, data_list, keys)
-#'
-#'   # nested list (arm_ref_comp)
-#'   arm_ref_comp <- list(
-#'     ARMCD = list(
-#'       ref = variable_choices("ADSL"),
-#'       comp = variable_choices("ADSL")
-#'     )
-#'   )
-#'
-#'   resolve(arm_ref_comp, data_list, keys)
-#' })
-#' @export
+#' @keywords internal
 #'
 resolve <- function(x, datasets, keys = NULL) {
   checkmate::assert_list(datasets, types = "reactive", min.len = 1, names = "named")
@@ -79,6 +26,7 @@ resolve <- function(x, datasets, keys = NULL) {
   UseMethod("resolve")
 }
 
+#' @describeIn resolve Call [variable_choices()] on the delayed `variable_choices` object.
 #' @export
 resolve.delayed_variable_choices <- function(x, datasets, keys) {
   if (is.null(x$key)) {
@@ -92,6 +40,7 @@ resolve.delayed_variable_choices <- function(x, datasets, keys) {
   do.call("variable_choices", x)
 }
 
+#' @describeIn resolve Call [value_choices()] on the delayed `value_choices` object.
 #' @export
 resolve.delayed_value_choices <- function(x, datasets, keys) {
   x$data <- datasets[[x$data]]()
@@ -102,6 +51,7 @@ resolve.delayed_value_choices <- function(x, datasets, keys) {
   do.call("value_choices", x)
 }
 
+#' @describeIn resolve Call [select_spec()] on the delayed `choices_selected` object.
 #' @export
 resolve.delayed_choices_selected <- function(x, datasets, keys) {
   if (inherits(x$selected, "delayed_data")) {
@@ -121,6 +71,7 @@ resolve.delayed_choices_selected <- function(x, datasets, keys) {
   do.call("choices_selected", x)
 }
 
+#' @describeIn resolve Call [select_spec()] on the delayed specification.
 #' @export
 resolve.delayed_select_spec <- function(x, datasets, keys) {
   x$choices <- resolve(x$choices, datasets = datasets, keys)
@@ -131,6 +82,7 @@ resolve.delayed_select_spec <- function(x, datasets, keys) {
   do.call("select_spec", x)
 }
 
+#' @describeIn resolve Call [filter_spec()] on the delayed specification.
 #' @export
 resolve.delayed_filter_spec <- function(x, datasets, keys) {
   if (inherits(x$vars_choices, "delayed_data")) {
@@ -149,6 +101,7 @@ resolve.delayed_filter_spec <- function(x, datasets, keys) {
   do.call("filter_spec_internal", x[intersect(names(x), methods::formalArgs(filter_spec_internal))])
 }
 
+#' @describeIn resolve Call [data_extract_spec()] on the delayed specification.
 #' @export
 resolve.delayed_data_extract_spec <- function(x, datasets, keys) {
   x$select <- `if`(
@@ -165,12 +118,15 @@ resolve.delayed_data_extract_spec <- function(x, datasets, keys) {
   do.call("data_extract_spec", x)
 }
 
+#' @describeIn resolve Iterates over elements of the list and recursively calls
+#' `resolve`.
 #' @export
 resolve.list <- function(x, datasets, keys) {
   # If specified explicitly, return it unchanged. Otherwise if delayed, resolve.
   lapply(x, resolve, datasets = datasets, keys = keys)
 }
 
+#' @describeIn resolve Default method that does nothing and returns `x` itself.
 #' @export
 resolve.default <- function(x, datasets, keys) {
   x
diff --git a/man/resolve.Rd b/man/resolve.Rd
index 41d46996..104962f1 100644
--- a/man/resolve.Rd
+++ b/man/resolve.Rd
@@ -2,9 +2,33 @@
 % Please edit documentation in R/resolve.R
 \name{resolve}
 \alias{resolve}
+\alias{resolve.delayed_variable_choices}
+\alias{resolve.delayed_value_choices}
+\alias{resolve.delayed_choices_selected}
+\alias{resolve.delayed_select_spec}
+\alias{resolve.delayed_filter_spec}
+\alias{resolve.delayed_data_extract_spec}
+\alias{resolve.list}
+\alias{resolve.default}
 \title{Resolve delayed inputs by evaluating the code within the provided datasets}
 \usage{
 resolve(x, datasets, keys = NULL)
+
+\method{resolve}{delayed_variable_choices}(x, datasets, keys)
+
+\method{resolve}{delayed_value_choices}(x, datasets, keys)
+
+\method{resolve}{delayed_choices_selected}(x, datasets, keys)
+
+\method{resolve}{delayed_select_spec}(x, datasets, keys)
+
+\method{resolve}{delayed_filter_spec}(x, datasets, keys)
+
+\method{resolve}{delayed_data_extract_spec}(x, datasets, keys)
+
+\method{resolve}{list}(x, datasets, keys)
+
+\method{resolve}{default}(x, datasets, keys)
 }
 \arguments{
 \item{x}{(\code{delayed_data}) object to resolve.}
@@ -20,60 +44,28 @@ Resolved object.
 \description{
 \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
 }
-\examples{
-library(shiny)
-ADSL <- rADSL
-
-attr(ADSL, "keys") <- c("STUDYID", "USUBJID")
-data_list <- list(ADSL = reactive(ADSL))
-keys <- list(ADSL = attr(ADSL, "keys"))
-isolate({
-  # value_choices example
-  v1 <- value_choices("ADSL", "SEX", "SEX")
-  v1
-  resolve(v1, data_list, keys)
-
-  # variable_choices example
-  v2 <- variable_choices("ADSL", c("BMRKR1", "BMRKR2"))
-  v2
-  resolve(v2, data_list, keys)
-
-  # data_extract_spec example
-  adsl_filter <- filter_spec(
-    vars = variable_choices("ADSL", "SEX"),
-    sep = "-",
-    choices = value_choices("ADSL", "SEX", "SEX"),
-    selected = "F",
-    multiple = FALSE,
-    label = "Choose endpoint and Censor"
-  )
-
-  adsl_select <- select_spec(
-    label = "Select variable:",
-    choices = variable_choices("ADSL", c("BMRKR1", "BMRKR2")),
-    selected = "BMRKR1",
-    multiple = FALSE,
-    fixed = FALSE
-  )
-
-  adsl_de <- data_extract_spec(
-    dataname = "ADSL",
-    select = adsl_select,
-    filter = adsl_filter
-  )
-
-  resolve(adsl_filter, data_list, keys)
-  resolve(adsl_select, data_list, keys)
-  resolve(adsl_de, data_list, keys)
-
-  # nested list (arm_ref_comp)
-  arm_ref_comp <- list(
-    ARMCD = list(
-      ref = variable_choices("ADSL"),
-      comp = variable_choices("ADSL")
-    )
-  )
-
-  resolve(arm_ref_comp, data_list, keys)
-})
+\section{Methods (by class)}{
+\itemize{
+\item \code{resolve(delayed_variable_choices)}: Call \code{\link[=variable_choices]{variable_choices()}} on the delayed \code{variable_choices} object.
+
+\item \code{resolve(delayed_value_choices)}: Call \code{\link[=value_choices]{value_choices()}} on the delayed \code{value_choices} object.
+
+\item \code{resolve(delayed_choices_selected)}: Call \code{\link[=select_spec]{select_spec()}} on the delayed \code{choices_selected} object.
+
+\item \code{resolve(delayed_select_spec)}: Call \code{\link[=select_spec]{select_spec()}} on the delayed specification.
+
+\item \code{resolve(delayed_filter_spec)}: Call \code{\link[=filter_spec]{filter_spec()}} on the delayed specification.
+
+\item \code{resolve(delayed_data_extract_spec)}: Call \code{\link[=data_extract_spec]{data_extract_spec()}} on the delayed specification.
+
+\item \code{resolve(list)}: Iterates over elements of the list and recursively calls
+\code{resolve}.
+
+\item \code{resolve(default)}: Default method that does nothing and returns \code{x} itself.
+
+}}
+\note{
+This is an internal function that is used by \code{\link[=resolve_delayed]{resolve_delayed()}}.
+All the methods are used internally only.
 }
+\keyword{internal}