rename qenv (#733)

DESCRIPTION

@@ -91,6 +91,7 @@ Collate:
     'modules_debugging.R'
     'reporter_previewer_module.R'
     'show_rcode_modal.R'
+    'tdata.R'
     'teal.R'
     'utils.R'
     'validations.R'

NAMESPACE

@@ -1,5 +1,10 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(get_code,tdata)
+S3method(get_join_keys,default)
+S3method(get_join_keys,tdata)
+S3method(get_metadata,default)
+S3method(get_metadata,tdata)
 S3method(is_arg_used,"function")
 S3method(is_arg_used,default)
 S3method(is_arg_used,teal_module)
@@ -20,17 +25,21 @@ export(.log)
 export(bookmarkableShinyApp)
 export(default_filter)
 export(example_module)
+export(get_join_keys)
+export(get_metadata)
 export(get_rcode)
 export(get_rcode_srv)
 export(get_rcode_ui)
 export(init)
 export(log_app_usage)
 export(module)
 export(modules)
+export(new_tdata)
 export(reporter_previewer_module)
 export(root_modules)
 export(show_rcode_modal)
 export(srv_teal_with_splash)
+export(tdata2env)
 export(ui_teal_with_splash)
 export(validate_has_data)
 export(validate_has_elements)

NEWS.md

@@ -3,7 +3,7 @@
 ### Enhancements
 
 * Added option to choose which variables can be filtered in the filter panel by using the `filterable` attributes for the per-dataset lists in the `filter` argument of `init`. 
-* `teal_module` having `data` argument in its arguments will receive a list of reactive filter data with `"code"` and `"join_keys"` attributes.
+* `teal_module` having `data` argument in its arguments of type `tdata`. Modules receive this object (a list of reactive filtered datasets with `"code"` and `"join_keys"` attributes).
 * Updated the internals of `module_teal` to reflect changes in `teal.slice`.
 * `teal_module` having `filter_panel_api` argument in its arguments will receive a `FilterPanelAPI` object.
 

R/example_module.R

@@ -20,6 +20,7 @@ example_module <- function(label = "example teal module") {
   module(
     label,
     server = function(id, data) {
+      checkmate::assert_class(data, "tdata")
       moduleServer(id, function(input, output, session) {
         output$text <- renderPrint(data[[input$dataname]]())
       })

R/module_nested_tabs.R

@@ -228,9 +228,9 @@ srv_nested_tabs.teal_module <- function(id, datasets, modules, reporter) {
   reactive(modules)
 }
 
-#' Convert `FilteredData` to reactive list of data
+#' Convert `FilteredData` to reactive list of datasets of the `tdata` type.
 #'
-#' Converts `FilteredData` object to list of data containing datasets needed for specific module.
+#' Converts `FilteredData` object to `tdata` object containing datasets needed for a specific module.
 #' Please note that if module needs dataset which has a parent, then parent will be also returned.
 #'
 #' @param module (`teal_module`) module where needed filters are taken from
@@ -255,10 +255,13 @@ srv_nested_tabs.teal_module <- function(id, datasets, modules, reporter) {
     }
   )
 
-  # code from previous stages
-  attr(data, "code") <- get_datasets_code(datanames, datasets)
+  metadata <- lapply(datanames, datasets$get_metadata)
+  names(metadata) <- datanames
 
-  # join_keys
-  attr(data, "join_keys") <- datasets$get_join_keys()
-  data
+  new_tdata(
+    data,
+    reactive(get_datasets_code(datanames, datasets)),
+    datasets$get_join_keys(),
+    metadata
+  )
 }

R/modules_debugging.R

@@ -10,8 +10,6 @@
 #' and avoids session restarts!
 #'
 #' @param label `character` label of module
-#' @param active_datanames `character vector` datanames shown in filter panel;
-#'   can be `"all"` to mean all available datasets
 #' @keywords internal
 #'
 #' @examples
@@ -34,19 +32,19 @@
 #'   ),
 #'   header = "Simple teal app"
 #' )
-#' \dontrun{
-#' shinyApp(app$ui, app$server)
+#' if (interactive()) {
+#'   shinyApp(app$ui, app$server)
 #' }
-filter_calls_module <- function(label = "Filter Calls Module", active_datanames = "all") { # nolint
+filter_calls_module <- function(label = "Filter Calls Module") { # nolint
   checkmate::assert_string(label)
-  checkmate::check_character(active_datanames, min.len = 1, any.missing = FALSE)
 
   module(
     label = label,
-    server = function(input, output, session, datasets) {
+    server = function(input, output, session, data) {
+      checkmate::assert_class(data, "tdata")
+
       output$filter_calls <- renderText({
-        active_datanames <- datasets$handle_active_datanames(active_datanames)
-        teal.slice::get_filter_expr(datasets, datanames = active_datanames)
+        get_code(data)
       })
     },
     ui = function(id, ...) {
@@ -56,6 +54,6 @@ filter_calls_module <- function(label = "Filter Calls Module", active_datanames
         verbatimTextOutput(ns("filter_calls"))
       )
     },
-    filters = active_datanames
+    filters = "all"
   )
 }

R/tdata.R

@@ -0,0 +1,131 @@
+#' Create a new `tdata` object which contains
+#'
+#' - `data` a `reactive` list of data.frames (or `MultiAssayExperiment`) with attributes
+#' i) `code` (`reactive`) containing code used to generate the data
+#' and ii) join_keys (`JoinKeys`) containing the relationships between
+#' the data iii) metadata (`named list`) containing any metadata associated with
+#' the data frames
+#'
+#' @param data A `named list` of `data.frames` (or `MultiAssayExperiment`)
+#'  which optionally can be `reactive`.
+#'   Inside this object all of these items will be made `reactive`.
+#' @param code A `character` (or `reactive` which evaluates to a `character`) containing
+#'   the code used to generate the data. This should be `reactive` if the code is changing
+#'   during a reactive context (e.g. if filtering changes the code). Inside this
+#'   object `code` will be made reactive
+#' @param join_keys A `teal.data::JoinKeys` object containing relationships between the
+#'   datasets.
+#' @param metadata A `named list` each element contains a list of metadata about the named data.frame
+#' Each element of these list should be atomic and length one.
+#' @return A `tdata` object
+#' @examples
+#'
+#' data <- new_tdata(
+#'   data = list(iris = iris, mtcars = reactive(mtcars), dd = data.frame(x = 1:10)),
+#'   code = "iris <- iris
+#'     mtcars <- mtcars
+#'     dd <- data.frame(x = 1:10)",
+#'   metadata = list(dd = list(author = "NEST"), iris = list(version = 1))
+#' )
+#'
+#' # Extract a data.frame
+#' isolate(data[["iris"]]())
+#'
+#' @export
+new_tdata <- function(data, code = "", join_keys = NULL, metadata = NULL) {
+  checkmate::assert_list(
+    data,
+    any.missing = FALSE, names = "unique",
+    types = c("data.frame", "reactive", "MultiAssayExperiment")
+  )
+  checkmate::assert_class(join_keys, "JoinKeys", null.ok = TRUE)
+  checkmate::assert_multi_class(code, c("character", "reactive"))
+
+  checkmate::assert_list(metadata, names = "unique", null.ok = TRUE)
+  checkmate::assert_subset(names(metadata), names(data))
+  for (m in metadata) teal.data::validate_metadata(m)
+
+  if (is.reactive(code)) {
+    isolate(checkmate::assert_class(code(), "character"))
+  }
+
+  #create reactive data.frames
+  for (x in names(data)) {
+    if (!is.reactive(data[[x]])) {
+      data[[x]] <- do.call(reactive, list(as.name(x)), envir = list2env(data[x]))
+    } else {
+      isolate(checkmate::assert_multi_class(data[[x]](), c("data.frame", "MultiAssayExperiment")))
+    }
+  }
+
+  # set attributes
+  attr(data, "code") <- if (is.reactive(code)) code else reactive(code)
+  attr(data, "join_keys") <- join_keys
+  attr(data, "metadata") <- metadata
+
+  # set class
+  class(data) <- c("tdata", class(data))
+  data
+}
+
+#' Function to convert a `tdata` object to an `environment`
+#' Any `reactives` inside `tdata` are first evaluated
+#' @param `data` a `tdata` object
+#' @return an `environment`
+#' @examples
+#'
+#' data <- new_tdata(
+#'   data = list(iris = iris, mtcars = reactive(mtcars)),
+#'   code = "iris <- iris
+#'     mtcars = mtcars"
+#' )
+#'
+#' my_env <- isolate(tdata2env(data))
+#'
+#' @export
+tdata2env <- function(data) { # nolint
+  checkmate::assert_class(data, "tdata")
+  list2env(lapply(data, function(x) if (is.reactive(x)) x() else x))
+}
+
+#' @export
+get_code.tdata <- function(data) {
+  # note teal.data which teal depends on defines the get_code method
+  attr(data, "code")()
+}
+
+#' @export
+get_join_keys <- function(data) {
+  UseMethod("get_join_keys", data)
+}
+
+
+#' @export
+get_join_keys.tdata <- function(data) {
+  attr(data, "join_keys")
+}
+
+#' @export
+get_join_keys.default <- function(data) {
+  stop("get_join_keys function not implemented for this object")
+}
+
+#' @export
+get_metadata <- function(data, dataname) {
+  checkmate::assert_string(dataname)
+  UseMethod("get_metadata", data)
+}
+
+#' @export
+get_metadata.tdata <- function(data, dataname) {
+  metadata <- attr(data, "metadata")
+  if (is.null(metadata)) {
+    return(NULL)
+  }
+  metadata[[dataname]]
+}
+
+#' @export
+get_metadata.default <- function(data, dataname) {
+  stop("get_metadata function not implemented for this object")
+}

tests/testthat/test-module_nested_tabs.R

@@ -311,7 +311,7 @@ testthat::test_that(".datasets_to_data returns required attributes", {
 
   # code
   testthat::expect_equal(
-    attr(data, "code")[1],
+    isolate(attr(data, "code")()[1]),
     "d1 <- data.frame(id = 1:5, pk = c(2, 3, 2, 1, 4), val = 1:5)\nd2 <- data.frame(id = 1:5, value = 1:5)\n\n"
   )
 })