Merge pull request #160 from openpharma/jt-make_row_review_more_effic…

…ient

Improve row review a little

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: clinsight
 Title: ClinSight
-Version: 0.1.1.9020
+Version: 0.1.1.9021
 Authors@R: c(
     person("Leonard Daniël", "Samson", , "[email protected]", role = c("cre", "aut"),
            comment = c(ORCID = "0000-0002-6252-7639")),

R/mod_common_forms.R

@@ -97,58 +97,88 @@ mod_common_forms_server <- function(
   moduleServer( id, function(input, output, session){
     ns <- session$ns
 
-    common_form_data <- reactiveVal()
-    SAE_data <- reactiveVal()
-    observe({
-      df <- {
+    common_form_data <- reactive({
+      golem::cat_dev(form, "data computed \n")
+      shiny::validate(need(
+        !is.null(r$filtered_data[[form]]),
+        paste0("Warning: no data found in the database for the form '", form, "'.")
+      ))
+      df <-
+      dplyr::left_join(
+        r$filtered_data[[form]],
+        with(r$review_data, r$review_data[item_group == form, ]) |>
+          dplyr::select(-dplyr::all_of(c("edit_date_time", "event_date"))),
+        by = id_item
+      ) |>
+        dplyr::mutate(
+          item_value = ifelse(
+            reviewed == "No",
+            paste0("<b>", htmltools::htmlEscape(item_value), "*</b>"),
+            htmltools::htmlEscape(item_value)
+          )
+        ) |>
+        create_table(expected_columns = names(form_items)) |>
+        dplyr::mutate(o_reviewed = Map(\(x, y, z) append(x, list(
+          row_id = y, 
+          disabled = z,
+          updated = isolate(session$userData$update_checkboxes[[form]]))
+        ), 
+        o_reviewed, 
+        dplyr::row_number(),
+        subject_id != r$subject_id))
+      if(form == "Adverse events") {
+        df |>
+          dplyr::filter(!grepl("Yes", `Serious Adverse Event`)
+          ) |>
+          dplyr::select(-dplyr::starts_with("SAE"))
+      } else {
+        df
+      }
+    })
+
+    if (form == "Adverse events") {
+      SAE_data <- reactive({
         shiny::validate(need(
           !is.null(r$filtered_data[[form]]),
           paste0("Warning: no data found in the database for the form '", form, "'.")
         ))
+        golem::cat_dev("SAE data computed \n")
         dplyr::left_join(
           r$filtered_data[[form]],
-          with(r$review_data, r$review_data[item_group == form, ]) |> 
-            dplyr::select(-dplyr::all_of(c("edit_date_time", "event_date"))), 
+          with(r$review_data, r$review_data[item_group == form, ]) |>
+            dplyr::select(-dplyr::all_of(c("edit_date_time", "event_date"))),
           by = id_item
-        ) |> 
+        ) |>
           dplyr::mutate(
             item_value = ifelse(
-              reviewed == "No", 
-              paste0("<b>", htmltools::htmlEscape(item_value), "*</b>"), 
+              reviewed == "No",
+              paste0("<b>", htmltools::htmlEscape(item_value), "*</b>"),
               htmltools::htmlEscape(item_value)
             )
+          ) |>
+          create_table(expected_columns = names(form_items)) |>
+          dplyr::mutate(o_reviewed = Map(\(x, y, z) append(x, list(
+            row_id = y, 
+            disabled = z,
+            updated = isolate(session$userData$update_checkboxes[[form]]))
+          ), 
+          o_reviewed, 
+          dplyr::row_number(),
+          subject_id != r$subject_id)
           ) |> 
-          create_table(expected_columns = names(form_items)) |> 
-          dplyr::mutate(o_reviewed = Map(\(x, y, z) append(x, list(row_id = y, disabled = z)), 
-                                         o_reviewed, 
-                                         dplyr::row_number(),
-                                         subject_id != r$subject_id))
-      }
-      common_form_data({
-        if(form == "Adverse events") {
-          df |> 
-            dplyr::filter(!grepl("Yes", `Serious Adverse Event`)
-            ) |> 
-            dplyr::select(-dplyr::starts_with("SAE"))
-        } else {
-          df
-        }
+          dplyr::filter(grepl("Yes", `Serious Adverse Event`)) |>
+          dplyr::select(dplyr::any_of(
+            c("o_reviewed", "subject_id","form_repeat", "Name", "AESI",  "SAE Start date",
+              "SAE End date", "CTCAE severity", "Treatment related",
+              "Treatment action", "Other action", "SAE Category",
+              "SAE Awareness date", "SAE Date of death", "SAE Death reason")
+          )) |>
+          adjust_colnames("^SAE ")
       })
-      if (form == "Adverse events")
-        SAE_data({
-          df |>
-            dplyr::filter(grepl("Yes", `Serious Adverse Event`)) |>
-            dplyr::select(dplyr::any_of(
-              c("o_reviewed", "subject_id","form_repeat", "Name", "AESI",  "SAE Start date",
-                "SAE End date", "CTCAE severity", "Treatment related",
-                "Treatment action", "Other action", "SAE Category",
-                "SAE Awareness date", "SAE Date of death", "SAE Death reason")
-            )) |>
-            adjust_colnames("^SAE ")
-        })
-    })
+    }
+
     mod_review_form_tbl_server("review_form_tbl", r, common_form_data, form, reactive(input$show_all_data), table_names, form)
-    if (form == "Adverse events")
+    if (form == "Adverse events") 
       mod_review_form_tbl_server("review_form_SAE_tbl", r, SAE_data, form, reactive(input$show_all_data), table_names, "Serious Adverse Events")
 
     mod_timeline_server(

R/mod_review_form_tbl.R

@@ -23,8 +23,8 @@ mod_review_form_tbl_ui <- function(id) {
 #'   `review_data` will be used to determine which rows will be displayed in
 #'   bold and, for the form Adverse events, which timeline data should be
 #'   highlighted.
-#' @param table_data Common reactive value. Used to manage the server data
-#'   displayed in the DataTable.
+#' @param reactive_table_data Common reactive value. Used to manage the server
+#'   data displayed in the DataTable.
 #' @param form A character string with the name of the form to display.
 #' @param show_all Common reactive value, a logical indicating whether all
 #'   records should be displayed.
@@ -41,36 +41,47 @@ mod_review_form_tbl_ui <- function(id) {
 mod_review_form_tbl_server <- function(
     id,
     r,
-    table_data,
+    reactive_table_data,
     form,
     show_all,
     table_names = NULL,
     title = NULL
 ){
   stopifnot(is.reactivevalues(r))
-  stopifnot(is.reactive(table_data))
+  stopifnot(is.reactive(reactive_table_data))
   stopifnot(is.character(form), length(form) == 1)
   stopifnot(is.reactive(show_all))
 
   moduleServer(id, function(input, output, session){
     ns <- session$ns
 
     reload_data <- reactiveVal(0)
-    datatable_rendered <- reactiveVal(FALSE)
+    datatable_rendered <- reactiveVal(NULL)
+    table_data <- reactiveVal()
 
     ############################### Observers: #################################
 
+    # table data manipulation code should ideally be here, then we can remove this.
+    # Alternatively, we can also pass this from the main module as a function argument
+
     observe({
+      golem::cat_dev(form, "| Resetting userData\n")
       reload_data(reload_data() + 1)
+      datatable_rendered(NULL)
       session$userData$update_checkboxes[[form]] <- NULL
       session$userData$review_records[[form]] <- data.frame(id = integer(), reviewed = character())
     }) |> 
-      bindEvent(r$subject_id, r$review_data)
+      bindEvent(r$subject_id, r$review_data, r$filtered_data[[form]])
+
+    observeEvent(datatable_rendered(), {
+      table_data(reactive_table_data())
+    }, ignoreInit = TRUE)
 
     observeEvent(session$userData$update_checkboxes[[form]], {
+      req(datatable_rendered())
+      golem::cat_dev(form, "| Updating checkboxes\n")
       reload_data(reload_data() + 1)
       checked <- session$userData$update_checkboxes[[form]]
-
       df <- table_data() |> 
         dplyr::mutate(o_reviewed = dplyr::if_else(subject_id == r$subject_id, 
                                                   lapply(o_reviewed, modifyList, list(updated = checked)),
@@ -79,6 +90,8 @@ mod_review_form_tbl_server <- function(
     })
 
     observeEvent(input$table_review_selection, {
+      golem::cat_dev(form, "| table review selection changed to:\n")
+      golem::print_dev(input$table_review_selection[c("id", "reviewed")])
       # Update review values for session's user data
       session$userData$update_checkboxes[[form]] <- NULL
       session$userData$review_records[[form]] <-
@@ -103,6 +116,7 @@ mod_review_form_tbl_server <- function(
     observe({
       req(!is.null(show_all()))
       req(table_data(), datatable_rendered())
+      golem::cat_dev(form, "| renewing datatable server data\n")
       DT::dataTableAjax(table_proxy$session, 
                         subset(table_data(), show_all() | subject_id == r$subject_id), 
                         rownames = FALSE,
@@ -114,19 +128,16 @@ mod_review_form_tbl_server <- function(
     observeEvent(reload_data(), {
       req(!is.null(show_all()))
       req(table_data(), datatable_rendered())
+      golem::cat_dev(form, "| reload_data() triggered\n")
       DT::reloadData(table_proxy)
     }, ignoreInit = TRUE)
 
-    observeEvent(r$subject_id, {
-      req(table_data())
-      reload_data(reload_data() + 1)
-      df <- table_data() |> 
-        dplyr::mutate(o_reviewed = Map(\(x, y) modifyList(x, list(updated = NULL, disabled = y)), o_reviewed, subject_id != r$subject_id))
-      table_data(df)
-    })
-
     observeEvent(show_all(), {
       req(table_data(), datatable_rendered())
+      golem::cat_dev(
+        form, "| show_all() trigger changed. Incrementing reload_data()",
+        "and toggle showing subject_id column \n"
+      )
       reload_data(reload_data() + 1)
       index <- match("subject_id", colnames(table_data())) - 1
       if (show_all()) {
@@ -139,10 +150,9 @@ mod_review_form_tbl_server <- function(
     ############################### Outputs: ###################################
 
     output[["table"]] <- DT::renderDT({
-      req(r$filtered_data[[form]])
       datatable_rendered(TRUE)
       datatable_custom(
-        isolate(subset(table_data(), show_all() | subject_id == r$subject_id)), 
+        subset(reactive_table_data(), isolate(show_all() | subject_id == r$subject_id)), 
         rename_vars = c("Review Status" = "o_reviewed", table_names), 
         rownames= FALSE,
         title = title,

R/mod_review_forms.R

@@ -137,6 +137,7 @@ mod_review_forms_server <- function(
       bindEvent(active_form(), session$userData$review_records[[active_form()]])
 
     observeEvent(r$subject_id, {
+      golem::cat_dev("mod_review_forms | Reset review records\n")
       session$userData$update_checkboxes[[active_form()]] <- NULL
       session$userData$review_records[[active_form()]] <- data.frame(id = integer(), reviewed = character())
     })
@@ -158,8 +159,6 @@ mod_review_forms_server <- function(
     observeEvent(c(active_form(), r$subject_id), {
       cat("Update confirm review button\n\n\n")
       req(r$review_data)
-      golem::cat_dev("review_data_active:\n")
-      golem::print_dev(review_data_active())
       review_indeterminate(FALSE)
       if(nrow(review_data_active()) == 0){ 
         cat("No review data found for Subject id: ", r$subject_id, 
@@ -270,10 +269,12 @@ mod_review_forms_server <- function(
           status      = ifelse(reviewed == "Yes", "old", "new")
         ) 
 
-      golem::cat_dev("review records to add:\n")
-      golem::print_dev(review_records)
+      golem::cat_dev(
+        active_form(), "|", "Adjusting review status for", 
+        length(unique(review_records$id)), "ids\n" 
+      )
 
-      cat("write review progress to database\n")
+      cat("Writing review progress to database\n")
       db_save_review(
         review_records, 
         db_path = db_path,

R/mod_study_forms.R

@@ -163,35 +163,37 @@ mod_study_forms_server <- function(
         dplyr::mutate(item_name = factor(item_name, levels = names(form_items)))
     })
 
-    table_data <- reactiveVal()
-    observe({
-      df <- {
-        validate(need(
-          r$filtered_data[[form]],
-          paste0("Warning: no data found in database for the form '", form, "'")
-        ))
-        dplyr::left_join(
-          r$filtered_data[[form]],
-          with(r$review_data, r$review_data[item_group == form, ]) |> 
-            dplyr::select(-dplyr::all_of(c("edit_date_time", "event_date"))), 
-          by = id_item
+    study_form_data <- reactive({
+      cat(form, "data computed \n")
+      validate(need(
+        r$filtered_data[[form]],
+        paste0("Warning: no data found in database for the form '", form, "'")
+      ))
+      dplyr::left_join(
+        r$filtered_data[[form]],
+        with(r$review_data, r$review_data[item_group == form, ]) |> 
+          dplyr::select(-dplyr::all_of(c("edit_date_time", "event_date"))), 
+        by = id_item
+      ) |> 
+        dplyr::mutate(
+          item_value = ifelse(
+            reviewed == "No", 
+            paste0("<b>", htmltools::htmlEscape(item_value), "*</b>"), 
+            htmltools::htmlEscape(item_value)
+          )
         ) |> 
-          dplyr::mutate(
-            item_value = ifelse(
-              reviewed == "No", 
-              paste0("<b>", htmltools::htmlEscape(item_value), "*</b>"), 
-              htmltools::htmlEscape(item_value)
-            )
-          ) |> 
-          create_table(expected_columns = names(form_items)) |> 
-          dplyr::mutate(o_reviewed = Map(\(x, y, z) append(x, list(row_id = y, disabled = z)), 
-                                         o_reviewed, 
-                                         dplyr::row_number(),
-                                         subject_id != r$subject_id))
-      }
-      table_data(df)
+        create_table(expected_columns = names(form_items)) |> 
+        dplyr::mutate(o_reviewed = Map(\(x, y, z) append(x, list(
+          row_id = y, 
+          disabled = z,
+          updated = isolate(session$userData$update_checkboxes[[form]]))
+        ), 
+        o_reviewed, 
+        dplyr::row_number(),
+        subject_id != r$subject_id))
     })
-    mod_review_form_tbl_server("review_form_tbl", r, table_data, form, reactive(input$show_all), table_names)
+
+    mod_review_form_tbl_server("review_form_tbl", r, study_form_data, form, reactive(input$show_all), table_names)
 
     scaling_data <- reactive({
       cols <- c("item_scale", "use_unscaled_limits")
@@ -229,7 +231,7 @@ mod_study_forms_server <- function(
 
     if(form %in% c("Vital signs", "Vitals adjusted")){
       shiny::exportTestValues(
-        table_data = subset(table_data(), input$show_all | subject_id == r$subject_id),
+        table_data = subset(study_form_data(), input$show_all | subject_id == r$subject_id),
         fig_data = fig_data()
       )
     } 

inst/golem-config.yml

@@ -1,6 +1,6 @@
 default:
   golem_name: clinsight
-  golem_version: 0.1.1.9020
+  golem_version: 0.1.1.9021
   app_prod: no
   user_identification: test_user
   study_data: !expr clinsight::clinsightful_data

tests/testthat/_snaps/app_feature_04.md

@@ -28,8 +28,8 @@
       # A tibble: 2 x 11
         o_reviewed       subject_id event_name `Systolic blood pressure`
         <list>           <chr>      <chr>      <chr>                    
-      1 <named list [4]> 9600-002   Screening  <b>99*</b> mmHg          
-      2 <named list [4]> 9600-002   Visit 2    <b>99*</b> mmHg          
+      1 <named list [5]> 9600-002   Screening  <b>99*</b> mmHg          
+      2 <named list [5]> 9600-002   Visit 2    <b>99*</b> mmHg          
         `Diastolic blood pressure` Pulse                Resp                 
         <chr>                      <chr>                <chr>                
       1 <b>77*</b> mmHg            <b>77*</b> beats/min <b>9*</b> breaths/min