Merge pull request #28 from Boehringer-Ingelheim/303774-app_creator_vignette

Review functionality vignette

Author: zsigmas

.git-blame-ignore-revs

@@ -0,0 +1,3 @@
+# formatting
+23b125d3d44eda8230e873fcbd88f2a20175d087
+a5a5d133ad5ef0df7fd40be2ec4f9cd22ab0fa9d

.lintr.R

@@ -9,6 +9,7 @@ linters <- lintr::modify_defaults(
   , object_length_linter = NULL               # we don't type long var names just because
   , pipe_continuation_linter = NULL           # wickham being overly prescriptive
   , trailing_blank_lines_linter = NULL        # natural extension of trailing_whitespace_linter, present on the template
+  , semicolon_linter = NULL                   # used to highlight checks that lead to the early out on a function
 )
 
 if(identical(Sys.getenv('CI'), "true")){

R/mock_listings.R

@@ -130,7 +130,7 @@ mock_listings_mm <- function() {
   )
 }
 
-mock_cqm <- function() {
+mock_review <- function() {
   ae <- safetyData::sdtm_ae
   dm <- safetyData::sdtm_dm
 
@@ -247,7 +247,7 @@ mock_cqm <- function() {
 
   # Step 5 - Run app
   dv.manager::run_app(
-    data = list("CQM_AE_list" = data_list),
+    data = list("AE_list_review" = data_list),
     module_list = list(
       "Listing" = listing,
       "Signal receiver" = mod_receiver(module_id = "papo", sender_id = "listing")

R/mod_listings.R

@@ -217,6 +217,11 @@ listings_UI <- function(module_id) { # nolint
 #' @param on_sbj_click `[function()]`
 #'
 #' Function to invoke when a subject ID is clicked in a listing
+#' 
+#' @param review `[list()]`
+#'
+#' Configuration of the experimental data review feature. 
+#' For more details, please refer to `vignette("data_review")`.
 #'
 #' @export
 listings_server <- function(module_id,
@@ -389,7 +394,7 @@ listings_server <- function(module_id,
       "clear_filters",
       # NOTE(miguel): Added here for easier merge with other branches
       # TODO(miguel): Move elsewhere after merging 
-      REV_UI(ns = ns, roles = review[["roles"]])[["input_ids_to_exclude_from_bookmarking"]]
+      REV_UI(ns = ns, roles = character(0))[["input_ids_to_exclude_from_bookmarking"]]
     ))
 
     # Bookmarking (end)
@@ -429,6 +434,10 @@ listings_server <- function(module_id,
       } else {
         fs_client <- fs_init(fs_callbacks, review[["store_path"]])
       }
+      
+      # Overly restrictive sanitization of role strings, as they will be used for file names:
+      # TODO: Consider adapting https://github.com/r-lib/fs/blob/main/R/sanitize.R instead to allow alternative charsets
+      review[["roles"]] <- gsub("[^a-zA-Z0-9 _.-]", "", review[["roles"]]) # Accepts alpha+num+space+'.'+'_'+'-'
 
       output[[TBL$REVIEW_UI_ID]] <- shiny::renderUI(
         shinyWidgets::dropdownButton(
@@ -919,12 +928,12 @@ check_mod_listings <- function(afmm, datasets, module_id, dataset_names,
           ) &&
           CM$assert(
             container = err,
-            cond = (checkmate::test_character(info[["tracked_vars"]], min.chars = 1, unique = TRUE) &&
+            cond = (checkmate::test_character(info[["tracked_vars"]], min.chars = 1, min.len = 3, unique = TRUE) &&
                       checkmate::test_subset(info[["tracked_vars"]], names(dataset))),
             msg = sprintf(
               paste(
-                "`review$datasets$%s$tracked_vars` should be a character vector listing a subset of the columns",
-                "available in dataset `%s`"
+                "`review$datasets$%s$tracked_vars` should be a character vector listing a subset of",
+                " at least three columns available in dataset `%s`"
               ), domain, domain
             )
           )

R/review.R

@@ -69,7 +69,7 @@ REV_include_review_info <- function(annotation_info, data, col_names, extra_col_
 }
 
 REV_UI <- function(ns, roles) {
-  choices <- setNames(c("", roles), c("<select reviewer role>", make.names(roles)))
+  choices <- setNames(c("", roles), c("<select reviewer role>", roles))
 
   res <- list()
   res[["ui"]] <- shiny::tagList(
@@ -108,8 +108,6 @@ REV_load_annotation_info <- function(folder_contents, review, dataset_lists) {
     folder_IO_plan <<- c(folder_IO_plan, list(action))
   }
 
-  review[["roles"]] <- make.names(review[["roles"]])
-
   for (dataset_lists_name in names(dataset_lists)) {
     sub_res <- list()
     dataset_list <- dataset_lists[[dataset_lists_name]]
@@ -590,7 +588,7 @@ REV_logic_2 <- function(ns, state, input, review, datasets, selected_dataset_lis
       SH$double_to_raw(timestamp)
     )
 
-    fname <- paste0(dataset_name, "_", make.names(role), ".review")
+    fname <- paste0(dataset_name, "_", role, ".review")
 
     IO_plan <- list(
       list(