Merge 9be50ff into b36c67e

R/adtteSpec.R

@@ -263,6 +263,8 @@ adtteSpecServer <- function(id, # nolint
   checkmate::assert_class(shiny::isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
+    ns <- session$ns
+
     # Join ADTTE with gene data.
     adtte_joined <- reactive({
       experiment_data <- experiment_data()
@@ -305,7 +307,7 @@ adtteSpecServer <- function(id, # nolint
     # Start by disabling selection, will be overriden if there are valid choices.
     session$sendCustomMessage(
       "toggle_dropdown",
-      list(input_id = session$ns("paramcd"), disabled = TRUE)
+      list(input_id = ns("paramcd"), disabled = TRUE)
     )
 
     # Once available endpoints change, we update choices (and also the selection
@@ -326,12 +328,11 @@ adtteSpecServer <- function(id, # nolint
       updateSelectizeInput(
         "paramcd",
         choices = paramcd_choices,
-        selected = new_selected,
-        session = session
+        selected = restoreInput(ns("paramcd"), new_selected)
       )
       session$sendCustomMessage(
         "toggle_dropdown",
-        list(input_id = session$ns("paramcd"), disabled = (length(paramcd_choices) == 0))
+        list(input_id = ns("paramcd"), disabled = (length(paramcd_choices) == 0))
       )
     })
 

R/assaySpec.R

@@ -106,6 +106,8 @@ assaySpecServer <- function(id, # nolint
   assert_character(exclude_assays, any.missing = FALSE)
 
   moduleServer(id, function(input, output, session) {
+    ns <- session$ns
+
     # When the assay names change, update the choices for assay.
     choices <- reactive({
       assays <- assays()
@@ -131,7 +133,7 @@ assaySpecServer <- function(id, # nolint
       updateSelectizeInput(session, "name", choices = choices)
       session$sendCustomMessage(
         "toggle_dropdown",
-        list(input_id = session$ns("name"), disabled = (length(choices) == 0))
+        list(input_id = ns("name"), disabled = (length(choices) == 0))
       )
     })
 

R/barplot.R

@@ -132,8 +132,10 @@ srv_g_barplot <- function(id,
   checkmate::assert_class(shiny::isolate(data()), "teal_data")
   assert_flag(.test)
   moduleServer(id, function(input, output, session) {
+    ns <- session$ns
+
     output$experiment_ui <- renderUI({
-      experimentSpecInput(session$ns("experiment"), data, mae_name)
+      experimentSpecInput(ns("experiment"), data, mae_name)
     })
     experiment <- experimentSpecServer(
       "experiment",

R/boxplot.R

@@ -128,8 +128,10 @@ srv_g_boxplot <- function(id,
   checkmate::assert_class(shiny::isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
+    ns <- session$ns
+
     output$experiment_ui <- renderUI({
-      experimentSpecInput(session$ns("experiment"), data, mae_name)
+      experimentSpecInput(ns("experiment"), data, mae_name)
     })
     experiment <- experimentSpecServer(
       "experiment",

R/forestplot.R

@@ -155,8 +155,10 @@ srv_g_forest_tte <- function(id,
   checkmate::assert_class(shiny::isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
+    ns <- session$ns
+
     output$experiment_ui <- renderUI({
-      experimentSpecInput(session$ns("experiment"), data, mae_name)
+      experimentSpecInput(ns("experiment"), data, mae_name)
     })
     experiment <- experimentSpecServer(
       "experiment",

R/geneSpec.R

@@ -156,8 +156,8 @@ h_update_gene_selection <- function(session,
   updateSelectizeInput(
     session = session,
     inputId = inputId,
-    selected = selected[is_new_selected],
     choices = stats::setNames(choices$id, choices$name),
+    selected = restoreInput(session$ns(inputId), selected[is_new_selected]),
     server = TRUE
   )
 
@@ -300,6 +300,8 @@ geneSpecServer <- function(id, # nolint
   assert_character(label_modal_footer)
 
   moduleServer(id, function(input, output, session) {
+    ns <- session$ns
+
     # The `reactiveValues` object for storing current gene text input.
     # This will also be a data frame with id and name columns.
     parsed_genes <- reactiveVal(NULL, label = "Parsed genes")
@@ -380,14 +382,14 @@ geneSpecServer <- function(id, # nolint
     dataModal <- function(example_list) { # nolint
       modalDialog(
         textInput(
-          session$ns("gene_text"),
+          ns("gene_text"),
           label = label_modal_title,
           placeholder = example_list
         ),
         do.call("span", as.list(label_modal_footer)),
         footer = tagList(
           modalButton("Cancel"),
-          actionButton(session$ns("ok_button"), "OK")
+          actionButton(ns("ok_button"), "OK")
         )
       )
     }

R/km.R

@@ -159,8 +159,10 @@ srv_g_km <- function(id,
   checkmate::assert_class(shiny::isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
+    ns <- session$ns
+
     output$experiment_ui <- renderUI({
-      experimentSpecInput(session$ns("experiment"), data, mae_name)
+      experimentSpecInput(ns("experiment"), data, mae_name)
     })
     experiment <- experimentSpecServer(
       "experiment",

R/pca.R

@@ -168,8 +168,10 @@ srv_g_pca <- function(id,
   checkmate::assert_class(shiny::isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
+    ns <- session$ns
+
     output$experiment_ui <- renderUI({
-      experimentSpecInput(session$ns("experiment"), data, mae_name)
+      experimentSpecInput(ns("experiment"), data, mae_name)
     })
     experiment <- experimentSpecServer(
       "experiment",
@@ -201,9 +203,8 @@ srv_g_pca <- function(id,
       if (filter_top) {
         n_top <- input$n_top
         updateSliderInput(
-          session = session,
           inputId = "n_top",
-          value = min(n_top, n_genes),
+          value = restoreInput(ns("n_top"), min(n_top, n_genes)),
           max = n_genes
         )
       }
@@ -238,10 +239,9 @@ srv_g_pca <- function(id,
       id_names <- c("x_var", "y_var")
       for (i in seq_along(id_names)) {
         updateSelectizeInput(
-          session,
-          id_names[i],
+          inputId = id_names[i],
           choices = pc_choices,
-          selected = pc_choices[i]
+          selected = restoreInput(ns(id_names[i]), pc_choices[i])
         )
       }
     })

R/quality.R

@@ -211,8 +211,10 @@ srv_g_quality <- function(id,
   checkmate::assert_class(shiny::isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
+    ns <- session$ns
+
     output$experiment_ui <- renderUI({
-      experimentSpecInput(session$ns("experiment"), data, mae_name)
+      experimentSpecInput(ns("experiment"), data, mae_name)
     })
     experiment <- experimentSpecServer(
       "experiment",
@@ -250,24 +252,21 @@ srv_g_quality <- function(id,
       properties <- experiment_properties()
 
       teal.widgets::updateOptionalSelectInput(
-        session,
-        "annotate",
+        inputId = "annotate",
         choices = properties$annotations,
-        selected = "WidthBP"
+        selected = restoreInput(ns("annotate"), "WidthBP")
       )
       updateSliderInput(
-        session,
-        "min_cpm",
+        inputId = "min_cpm",
         min = properties$min_cpm_calc,
         max = properties$max_cpm_calc,
-        value = properties$min_cpm_calc
+        value = restoreInput(ns("min_cpm"), properties$min_cpm_calc)
       )
       updateSliderInput(
-        session,
-        "min_depth_continuous",
+        inputId = "min_depth_continuous",
         min = properties$min_depth_calc,
         max = properties$max_depth_calc,
-        value = properties$min_depth_calc
+        value = restoreInput(ns("min_depth_continuous"), properties$min_depth_calc)
       )
     })
 

R/sampleVarSpec.R

@@ -288,6 +288,8 @@ sampleVarSpecServer <- function(id, # nolint
   assert_string(label_modal_title)
 
   moduleServer(id, function(input, output, session) {
+    ns <- session$ns
+
     to_observe <- reactive({
       list(experiment_name(), original_data())
     })
@@ -320,10 +322,9 @@ sampleVarSpecServer <- function(id, # nolint
       sel <- intersect(input$sample_var, col_data_vars)
 
       teal.widgets::updateOptionalSelectInput(
-        session,
-        "sample_var",
+        inputId = "sample_var",
         choices = col_data_vars,
-        selected = sel
+        selected = restoreInput(ns("sample_var"), sel)
       )
     })
 
@@ -383,7 +384,7 @@ sampleVarSpecServer <- function(id, # nolint
       }
       modalDialog(
         shinyRadioMatrix::radioMatrixInput(
-          session$ns("comb_assignment"),
+          ns("comb_assignment"),
           rowIDs = sample_var_levels,
           rowIDsName = "Original levels",
           rowLLabels = rep("", length = length(sample_var_levels)),
@@ -393,7 +394,7 @@ sampleVarSpecServer <- function(id, # nolint
         tags$span(label_modal_title),
         footer = tagList(
           modalButton("Cancel"),
-          actionButton(session$ns("ok"), "OK")
+          actionButton(ns("ok"), "OK")
         ),
         include_js_files("checkbox.js")
       )

R/scatterplot.R

@@ -130,8 +130,10 @@ srv_g_scatterplot <- function(id,
   checkmate::assert_class(shiny::isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
+    ns <- session$ns
+
     output$experiment_ui <- renderUI({
-      experimentSpecInput(session$ns("experiment"), data, mae_name)
+      experimentSpecInput(ns("experiment"), data, mae_name)
     })
     experiment <- experimentSpecServer(
       "experiment",

R/volcanoplot.R

@@ -116,8 +116,10 @@ srv_g_volcanoplot <- function(id,
   checkmate::assert_class(shiny::isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
+    ns <- session$ns
+
     output$experiment_ui <- renderUI({
-      experimentSpecInput(session$ns("experiment"), data, mae_name)
+      experimentSpecInput(ns("experiment"), data, mae_name)
     })
     experiment_data <- experimentSpecServer(
       "experiment",