Fixes failing "Add to Report" for modules that have DT table visualization (#1411)

# Pull Request

- Fixes #1404

### Changes description

- Reverts changes from #1350
- Decorated objects are `rlistings` or `rtables`, module output is `DT`
- Adds documentation explicitly saying what is being decorated
- Uses a pattern of `table_r` that contains 2 elements (report and html)

---------

Signed-off-by: André Veríssimo <[email protected]>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

Author: averissimo

NEWS.md

@@ -2,12 +2,16 @@
 
 ### Enhancements
 * Added argument `conf_type` to module `tm_g_km` to allow users to set a confidence interval type for median survival time estimation.
-
-### Enhancements
 * Added `denom` argument in `tm_t_binary_outcome` module.
 
 ### Bug fixes
 * Fixed bug in `tm_t_events` to return sorted table (#1393).
+* Fixed "Add to Report" failures in `tm_g_pp_adverse_events`, `tm_g_pp_therapy`, `tm_t_pp_basic_info`, `tm_t_pp_laboratory` and `tm_t_pp_prior_medication` modules (#1404).
+
+### Breaking changes
+
+* Removed the `table` object decoration in `tm_g_pp_adverse_events`, `tm_g_pp_therapy` (#1404).
+* Deprecated the `decorators` argument in `tm_t_pp_basic_info`, `tm_t_pp_laboratory` and `tm_t_pp_prior_medication` (#1404).
 
 # teal.modules.clinical 0.10.0
 

R/tm_g_pp_adverse_events.R

@@ -58,7 +58,6 @@ template_adverse_events <- function(dataname = "ANL",
               dplyr::where(~ inherits(., what = "difftime")), ~ as.double(., units = "auto")
             )
           )
-        table_output <- DT::datatable(table_data)
       },
       env = list(
         dataname = as.name(dataname),
@@ -183,7 +182,6 @@ template_adverse_events <- function(dataname = "ANL",
 #'
 #' This module generates the following objects, which can be modified in place using decorators::
 #' - `plot` (`ggplot`)
-#' - `table` (`datatables` - output of `DT::datatable()`)
 #'
 #' A Decorator is applied to the specific output using a named list of `teal_transform_module` objects.
 #' The name of this list corresponds to the name of the output to which the decorator is applied.
@@ -193,8 +191,7 @@ template_adverse_events <- function(dataname = "ANL",
 #' tm_g_pp_adverse_events(
 #'    ..., # arguments for module
 #'    decorators = list(
-#'      plot = teal_transform_module(...), # applied only to `plot` output
-#'      table = teal_transform_module(...) # applied only to `table` output
+#'      plot = teal_transform_module(...) # applied only to `plot` output
 #'    )
 #' )
 #' ```
@@ -310,7 +307,7 @@ tm_g_pp_adverse_events <- function(label,
   checkmate::assert_class(pre_output, classes = "shiny.tag", null.ok = TRUE)
   checkmate::assert_class(post_output, classes = "shiny.tag", null.ok = TRUE)
   checkmate::assert_class(ggplot2_args, "ggplot2_args")
-  assert_decorators(decorators, names = c("plot", "table"))
+  assert_decorators(decorators, names = "plot")
 
   args <- as.list(environment())
   data_extract_list <- list(
@@ -432,7 +429,6 @@ ui_g_adverse_events <- function(id, ...) {
           is_single_dataset = is_single_dataset_value
         )
       ),
-      ui_decorate_teal_data(ns("d_table"), decorators = select_decorators(ui_args$decorators, "table")),
       ui_decorate_teal_data(ns("d_plot"), decorators = select_decorators(ui_args$decorators, "plot")),
       bslib::accordion_panel(
         title = "Plot settings",
@@ -594,36 +590,26 @@ srv_g_adverse_events <- function(id,
     # Allow for the table and plot qenv to be joined
     table_q <- reactive({
       req(all_q())
-      teal.code::eval_code(all_q(), "table <- table_output")
+      within(all_q(), {
+        table <- rtables::df_to_tt(table_data)
+        table
+      })
     })
     plot_q <- reactive({
       req(all_q())
-      teal.code::eval_code(all_q(), "plot <- plot_output")
+      within(all_q(), plot <- plot_output)
     })
 
-    decorated_all_q_table <- srv_decorate_teal_data(
-      "d_table",
-      data = table_q,
-      decorators = select_decorators(decorators, "table"),
-      expr = table
-    )
-
     decorated_all_q_plot <- srv_decorate_teal_data(
       "d_plot",
       data = plot_q,
       decorators = select_decorators(decorators, "plot"),
       expr = plot
     )
 
-    table_r <- reactive({
-      req(decorated_all_q_table())
-
-      decorated_all_q_table()[["table"]]
-    })
-
     plot_r <- reactive({
       req(iv_r()$is_valid(), decorated_all_q_plot())
-      decorated_all_q_plot()[["plot"]]
+      req(decorated_all_q_plot())[["plot"]]
     })
 
     pws <- teal.widgets::plot_with_settings_srv(
@@ -633,13 +619,22 @@ srv_g_adverse_events <- function(id,
       width = plot_width
     )
 
-    output$table <- DT::renderDataTable(
-      expr = table_r(),
-      options = list(pageLength = input$table_rows)
-    )
+    table_r <- reactive({
+      q <- req(table_q())
+
+      list(
+        html = DT::datatable(
+          data = q[["table_data"]],
+          options = list(pageLength = input$table_rows)
+        ),
+        report = q[["table"]]
+      )
+    })
+
+    output$table <- DT::renderDataTable(table_r()[["html"]])
 
     decorated_all_q <- reactive(
-      c(decorated_all_q_table(), decorated_all_q_plot())
+      c(table_q(), decorated_all_q_plot())
     )
 
     # Render R code
@@ -660,7 +655,7 @@ srv_g_adverse_events <- function(id,
           filter_panel_api = filter_panel_api
         )
         card$append_text("Table", "header3")
-        card$append_table(table_r())
+        card$append_table(table_r()[["report"]])
         card$append_text("Plot", "header3")
         card$append_plot(plot_r(), dim = pws$dim())
         if (!comment == "") {

R/tm_g_pp_therapy.R

@@ -65,7 +65,7 @@ template_therapy <- function(dataname = "ANL",
 
       dataname[setdiff(cols_to_include, names(dataname))] <- NA
 
-      table <- dataname %>%
+      table_data <- dataname %>%
         dplyr::filter(atirel %in% c("CONCOMITANT", "PRIOR")) %>% # removed PRIOR_CONCOMITANT
         dplyr::select(dplyr::all_of(cols_to_include)) %>%
         dplyr::filter(!is.na(cmdecod)) %>%
@@ -84,8 +84,8 @@ template_therapy <- function(dataname = "ANL",
           teal.data::col_labels(dataname, fill = TRUE)[c(cmindc_char, cmdecod_char)], "Dosage",
           teal.data::col_labels(dataname, fill = TRUE)[c(cmstdy_char, cmendy_char)]
         ))
-
-      table <- DT::datatable(table)
+      table <- rtables::df_to_tt(table_data)
+      table
     }, env = list(
       dataname = as.name(dataname),
       atirel = as.name(atirel),
@@ -244,8 +244,7 @@ template_therapy <- function(dataname = "ANL",
 #'
 #' This module generates the following objects, which can be modified in place using decorators::
 #' - `plot` (`ggplot`)
-#' - `table` (`datatables` - output of `DT::datatable()`)
-#'
+
 #' A Decorator is applied to the specific output using a named list of `teal_transform_module` objects.
 #' The name of this list corresponds to the name of the output to which the decorator is applied.
 #' See code snippet below:
@@ -254,8 +253,7 @@ template_therapy <- function(dataname = "ANL",
 #' tm_g_pp_therapy(
 #'    ..., # arguments for module
 #'    decorators = list(
-#'      plot = teal_transform_module(...), # applied only to `plot` output
-#'      table = teal_transform_module(...) # applied only to `table` output
+#'      plot = teal_transform_module(...) # applied only to `plot` output
 #'    )
 #' )
 #' ```
@@ -396,7 +394,7 @@ tm_g_pp_therapy <- function(label,
   checkmate::assert_class(pre_output, classes = "shiny.tag", null.ok = TRUE)
   checkmate::assert_class(post_output, classes = "shiny.tag", null.ok = TRUE)
   checkmate::assert_class(ggplot2_args, "ggplot2_args")
-  assert_decorators(decorators, names = c("plot", "table"))
+  assert_decorators(decorators, names = "plot")
 
   args <- as.list(environment())
   data_extract_list <- list(
@@ -535,7 +533,6 @@ ui_g_therapy <- function(id, ...) {
         data_extract_spec = ui_args$cmendy,
         is_single_dataset = is_single_dataset_value
       ),
-      ui_decorate_teal_data(ns("d_table"), decorators = select_decorators(ui_args$decorators, "table")),
       ui_decorate_teal_data(ns("d_plot"), decorators = select_decorators(ui_args$decorators, "plot")),
       bslib::accordion_panel(
         title = "Plot settings",
@@ -701,30 +698,30 @@ srv_g_therapy <- function(id,
       paste("<h5><b>Patient ID:", all_q()[["pt_id"]], "</b></h5>")
     })
 
-    decorated_all_q_table <- srv_decorate_teal_data(
-      "d_table",
-      data = all_q,
-      decorators = select_decorators(decorators, "table"),
-      expr = table
-    )
+    table_r <- reactive({
+      q <- req(all_q())
 
-    output$therapy_table <- DT::renderDataTable(
-      expr = {
-        decorated_all_q_table()[["table"]]
-      },
-      options = list(pageLength = input$therapy_table_rows)
-    )
+      list(
+        html = DT::datatable(
+          data = q[["table_data"]],
+          options = list(pageLength = input$therapy_table_rows)
+        ),
+        report = q[["table"]]
+      )
+    })
+
+    output$therapy_table <- DT::renderDataTable(table_r()[["html"]])
 
     decorated_all_q_plot <- srv_decorate_teal_data(
       "d_plot",
-      data = decorated_all_q_table,
+      data = all_q,
       decorators = select_decorators(decorators, "plot"),
       expr = plot
     )
 
     plot_r <- reactive({
       req(iv_r()$is_valid())
-      decorated_all_q_plot()[["plot"]]
+      req(decorated_all_q_plot())[["plot"]]
     })
 
     pws <- teal.widgets::plot_with_settings_srv(
@@ -752,7 +749,7 @@ srv_g_therapy <- function(id,
           filter_panel_api = filter_panel_api
         )
         card$append_text("Table", "header3")
-        card$append_table(all_q()[["table"]])
+        card$append_table(table_r()[["report"]])
         card$append_text("Plot", "header3")
         card$append_plot(plot_r(), dim = pws$dim())
         if (!comment == "") {