Refactor input page and handle preset errors

R/input_page.R

@@ -0,0 +1,102 @@
+#' Create the UI for the input page.
+#' @noRd
+input_page_ui <- function(id) {
+    sidebarLayout(
+        sidebarPanel(
+            width = 3,
+            preset_editor_ui(NS(id, "preset_editor")),
+            tabsetPanel(
+                id = NS(id, "apply_panel"),
+                type = "hidden",
+                tabPanelBody(value = "hide"),
+                tabPanelBody(
+                    value = "show",
+                    actionButton(
+                        NS(id, "apply_button"),
+                        "Perform analysis",
+                        class = "btn-primary",
+                        style = "margin-top: 16px; margin-bottom: 16px"
+                    )
+                )
+            ),
+            comparison_editor_ui(NS(id, "comparison_editor"))
+        ),
+        mainPanel(
+            width = 9,
+            plotly::plotlyOutput(
+                NS(id, "positions_plot"),
+                width = "100%",
+                height = "600px"
+            )
+        )
+    )
+}
+
+#' Application logic for the input page.
+#'
+#' @param id ID for namespacing the inputs and outputs.
+#' @return A list containing two reactives: the `preset` for the analysis and
+#'   the `comparison_gene_ids`.
+#'
+#' @noRd
+input_page_server <- function(id) {
+    moduleServer(id, function(input, output, session) {
+        current_preset <- reactiveVal(
+            geposan::preset(genes[verified | suggested == TRUE, id])
+        )
+
+        potential_preset <- preset_editor_server("preset_editor")
+
+        comparison_gene_ids <- comparison_editor_server(
+            "comparison_editor",
+            current_preset
+        )
+
+        output$positions_plot <- plotly::renderPlotly({
+            preset <- potential_preset()
+
+            if (is.null(preset)) {
+                NULL
+            } else {
+                gene_sets <- list("Reference genes" = preset$reference_gene_ids)
+                comparison_gene_ids <- comparison_gene_ids()
+
+                if (length(comparison_gene_ids) >= 1) {
+                    gene_sets <- c(
+                        gene_sets,
+                        list("Comparison genes" = comparison_gene_ids)
+                    )
+                }
+
+                geposan::plot_positions(preset$species_ids, gene_sets)
+            }
+        })
+
+        observe({
+            if (is.null(potential_preset()) |
+                rlang::hash(potential_preset()) ==
+                    rlang::hash(current_preset())) {
+                updateTabsetPanel(
+                    session,
+                    "apply_panel",
+                    selected = "hide"
+                )
+            } else {
+                updateTabsetPanel(
+                    session,
+                    "apply_panel",
+                    selected = "show"
+                )
+            }
+        })
+
+        observe({
+            current_preset(potential_preset())
+        }) |> bindEvent(input$apply_button)
+
+        list(
+            preset = current_preset,
+            comparison_gene_ids = comparison_gene_ids
+        )
+    })
+}

R/preset_editor.R

@@ -1,4 +1,9 @@
-# Create a preset editor.
+#' Create the UI for a preset editor.
+#'
+#' @param id ID for namespacing.
+#' @return The UI elements.
+#'
+#' @noRd
 preset_editor_ui <- function(id) {
     verticalLayout(
         h3("Inputs"),
@@ -47,29 +52,17 @@ preset_editor_ui <- function(id) {
                 label = "Enter reference genes",
                 height = "250px"
             )
-        ),
-        tabsetPanel(
-            id = NS(id, "apply_panel"),
-            type = "hidden",
-            tabPanelBody(value = "hide"),
-            tabPanelBody(
-                value = "show",
-                actionButton(
-                    NS(id, "apply_button"),
-                    "Perform analysis",
-                    class = "btn-primary",
-                    style = "margin-top: 16px; margin-bottom: 16px"
-                )
-            )
         )
     )
 }
 
-# Create a server for the preset editor.
+#' Application logic for the preset editor.
-#
+#'
-# @param id ID for namespacing the inputs and outputs.
+#' @param id ID for namespacing the inputs and outputs.
-#
+#' @return A reactive containing the preset or `NULL`, if the input data doesn't
-# @return A reactive containing the preset.
+#'   result in a valid one.
+#'
+#' @noRd
 preset_editor_server <- function(id) {
     moduleServer(id, function(input, output, session) {
         species_choices <- geposan::species$id
@@ -82,17 +75,12 @@ preset_editor_server <- function(id) {
             server = TRUE
         )
 
-        current_preset <- reactiveVal(geposan::preset(
+        reactive({
-            genes[suggested | verified == TRUE, id]
+            reference_gene_ids <- if (input$reference_genes == "tpeold") {
-        ))
-
-        # Reactive containing the latest valid set of reference genes.
-        reference_gene_ids <- reactiveVal(
                 genes[verified | suggested == TRUE, id]
-        )
+            } else if (input$reference_genes == "verified") {
-
+                genes[verified == TRUE, id]
-        observeEvent(c(input$reference_genes, input$custom_reference_genes), {
+            } else {
-            if (input$reference_genes == "custom") {
                 inputs <- strsplit(input$custom_reference_genes, "\\s+")[[1]]
 
                 gene_ids <- if (input$identifier_type == "hgnc") {
@@ -100,20 +88,8 @@ preset_editor_server <- function(id) {
                 } else {
                     geposan::genes[id %chin% inputs, id]
                 }
-
-                if (length(gene_ids) >= 5) {
-                    reference_gene_ids(gene_ids)
             }
-            } else {
-                reference_gene_ids(if (input$reference_genes == "tpeold") {
-                    genes[verified | suggested == TRUE, id]
-                } else if (input$reference_genes == "verified") {
-                    genes[verified == TRUE, id]
-                })
-            }
-        })
 
-        new_preset <- reactive({
             species_ids <- if (input$species == "replicative") {
                 species_ids_replicative
             } else if (input$species == "all") {
@@ -122,41 +98,13 @@ preset_editor_server <- function(id) {
                 input$custom_species
             }
 
+            tryCatch(
                 geposan::preset(
-                reference_gene_ids(),
+                    reference_gene_ids,
-                methods = methods,
+                    species_ids = species_ids
-                species_ids = species_ids,
+                ),
-                gene_ids = genes$id
+                error = function(err) NULL
             )
         })
-
-        observeEvent(
-            { # nolint
-                current_preset()
-                new_preset()
-            },
-            { # nolint
-                if (rlang::hash(new_preset()) !=
-                    rlang::hash(current_preset())) {
-                    updateTabsetPanel(
-                        session,
-                        "apply_panel",
-                        selected = "show"
-                    )
-                } else {
-                    updateTabsetPanel(
-                        session,
-                        "apply_panel",
-                        selected = "hide"
-                    )
-                }
-            }
-        )
-
-        observeEvent(input$apply_button, {
-            current_preset(new_preset())
-        })
-
-        current_preset
     })
 }

R/server.R

@@ -8,7 +8,9 @@ js_link <- DT::JS("function(row, data) {
 }")
 
 server <- function(input, output, session) {
-    preset <- preset_editor_server("preset_editor")
+    input_reactives <- input_page_server("input_page")
+    preset <- input_reactives$preset
+    comparison_gene_ids <- input_reactives$comparison_gene_ids
 
     # Compute the results according to the preset.
     analysis <- reactive({
@@ -48,23 +50,6 @@ server <- function(input, output, session) {
     # Server for the detailed results panel.
     results_server("results", results_filtered)
 
-    comparison_gene_ids <- comparison_editor_server("comparison_editor", preset)
-
-    output$scatter <- plotly::renderPlotly({
-        preset <- preset()
-        gene_sets <- list("Reference genes" = preset$reference_gene_ids)
-        comparison_gene_ids <- comparison_gene_ids()
-
-        if (length(comparison_gene_ids) >= 1) {
-            gene_sets <- c(
-                gene_sets,
-                list("Comparison genes" = comparison_gene_ids)
-            )
-        }
-
-        geposan::plot_positions(preset$species_ids, gene_sets)
-    })
-
     output$rank_plot <- plotly::renderPlotly({
         preset <- preset()
         gene_sets <- list("Reference genes" = preset$reference_gene_ids)

R/ui.R

@@ -11,21 +11,7 @@ ui <- div(
         selected = "Results",
         tabPanel(
             "Input data",
-            sidebarLayout(
+            input_page_ui("input_page")
-                sidebarPanel(
-                    width = 3,
-                    preset_editor_ui("preset_editor"),
-                    comparison_editor_ui("comparison_editor")
-                ),
-                mainPanel(
-                    width = 9,
-                    plotly::plotlyOutput(
-                        "scatter",
-                        width = "100%",
-                        height = "600px"
-                    )
-                )
-            ),
         ),
         tabPanel(
             "Results",