Add big file diann

DESCRIPTION

@@ -25,10 +25,11 @@ Authors@R: c(
 License: Artistic-2.0
 Depends: R (>= 4.2)
 Imports: shiny, shinyBS, shinyjs, shinybusy, dplyr, ggplot2, plotly, data.table, Hmisc, shinyFiles,
-  MSstats,MSstatsBig, MSstatsTMT, MSstatsPTM, MSstatsConvert, gplots, marray, DT, readxl,
+  MSstats, MSstatsTMT, MSstatsPTM, MSstatsConvert, gplots, marray, DT, readxl,
   ggrepel, uuid, utils, stats, htmltools, methods, tidyr, grDevices, graphics, mockery, MSstatsBioNet,
   shinydashboard, arrow, tools, MSstatsResponse
-Suggests: 
+Suggests:
+    MSstatsBig,
     rmarkdown,
     tinytest,
     sessioninfo,

R/module-loadpage-server.R

@@ -20,31 +20,37 @@ loadpageServer <- function(id, parent_session, is_web_server = FALSE) {
     # Define volumes for the file selection.
     if (!is_web_server) {
       volumes <- shinyFiles::getVolumes()()
-
-      # Server-side logic for the shinyFiles button
-      shinyFiles::shinyFileChoose(input, "big_file_browse", roots = volumes, session = session)
-
-      # Reactive to parse and store the full file information (path, name, etc.)
-      # This is efficient because parseFilePaths is only called once.
-      local_file_info <- reactive({
-        req(is.list(input$big_file_browse))
-        shinyFiles::parseFilePaths(volumes, input$big_file_browse)
-      })
-
-      # Reactive to get just the full datapath, for use in backend processing.
-      local_big_file_path <- reactive({
-        path_info <- local_file_info()
-        if (nrow(path_info) > 0) path_info$datapath else NULL
-      })
-
-      # Render just the filename for user feedback in the UI.
-      output$specdata_big_path <- renderPrint({
-        req(nrow(local_file_info()) > 0)
-        cat(local_file_info()$name)
-      })
-    } 
+
+      # Register one shinyFiles pipeline per filetype so DIANN and Spectronaut
+      # selections can't leak across when the user switches filetypes mid-session.
+      make_big_file_path <- function(id_suffix) {
+        browse_id <- paste0("big_file_browse_", id_suffix)
+        path_id   <- paste0("big_file_path_", id_suffix)
+
+        shinyFiles::shinyFileChoose(input, browse_id, roots = volumes, session = session)
+
+        file_info <- reactive({
+          req(is.list(input[[browse_id]]))
+          shinyFiles::parseFilePaths(volumes, input[[browse_id]])
+        })
+
+        output[[path_id]] <- renderPrint({
+          req(nrow(file_info()) > 0)
+          cat(file_info()$name)
+        })
+
+        reactive({
+          info <- file_info()
+          if (nrow(info) > 0) info$datapath else NULL
+        })
+      }
+
+      local_big_file_path_spec  <- make_big_file_path("spec")
+      local_big_file_path_diann <- make_big_file_path("diann")
+    }
     else {
-      local_big_file_path <- reactive({ NULL })
+      local_big_file_path_spec  <- reactive({ NULL })
+      local_big_file_path_diann <- reactive({ NULL })
     }
 
     output$spectronaut_header_ui <- renderUI({
@@ -72,6 +78,51 @@ loadpageServer <- function(id, parent_session, is_web_server = FALSE) {
       tagList(ui_elements, create_separator_buttons(session$ns, "sep_specdata"))
     })
 
+    output$diann_header_ui <- renderUI({
+      req(input$filetype == 'diann', input$BIO != 'PTM')
+      create_diann_header()
+    })
+
+    output$diann_file_selection_ui <- renderUI({
+      req(input$filetype == 'diann', input$BIO != 'PTM')
+
+      ui_elements <- tagList()
+
+      if (!is_web_server) {
+        ui_elements <- tagList(ui_elements, create_diann_mode_selector(session$ns, isTRUE(input$big_file_diann)))
+
+        if (isTRUE(input$big_file_diann)) {
+          ui_elements <- tagList(ui_elements, create_diann_large_file_ui(session$ns))
+        } else {
+          ui_elements <- tagList(ui_elements, create_diann_standard_ui(session$ns))
+        }
+      } else {
+        ui_elements <- tagList(ui_elements, create_diann_standard_ui(session$ns))
+      }
+
+      tagList(ui_elements, create_separator_buttons(session$ns, "sep_dianndata"))
+    })
+
+    output$diann_options_ui <- renderUI({
+      req(input$filetype == 'diann', input$BIO != 'PTM')
+
+      if (!is_web_server && isTRUE(input$big_file_diann)) {
+        mbr_def <- if (is.null(input$diann_MBR)) TRUE else input$diann_MBR
+
+        max_feature_def <- if (is.null(input$max_feature_count)) 100 else input$max_feature_count
+        unique_peps_def <- if (is.null(input$filter_unique_peptides)) FALSE else input$filter_unique_peptides
+        agg_psms_def <- if (is.null(input$aggregate_psms)) FALSE else input$aggregate_psms
+        few_obs_def <- if (is.null(input$filter_few_obs)) FALSE else input$filter_few_obs
+
+        tagList(
+          create_diann_large_filter_options(session$ns, mbr_def),
+          create_diann_large_bottom_ui(session$ns, max_feature_def, unique_peps_def, agg_psms_def, few_obs_def)
+        )
+      } else {
+        NULL
+      }
+    })
+
     output$spectronaut_options_ui <- renderUI({
       req(input$filetype == 'spec', input$BIO != 'PTM')
 
@@ -186,7 +237,7 @@ loadpageServer <- function(id, parent_session, is_web_server = FALSE) {
               }
             } else if (input$filetype == "spec") {
               spec_regular_file_ok <- !isTRUE(input$big_file_spec) && !is.null(input$specdata)
-              spec_big_file_ok <- isTRUE(input$big_file_spec) && length(local_big_file_path()) > 0
+              spec_big_file_ok <- isTRUE(input$big_file_spec) && length(local_big_file_path_spec()) > 0
               if((spec_regular_file_ok || spec_big_file_ok) && !is.null(input$sep_specdata)) {
                 enable("proceed1")
               }
@@ -195,7 +246,9 @@ loadpageServer <- function(id, parent_session, is_web_server = FALSE) {
                 enable("proceed1")
               }
             } else if (input$filetype == "diann") {
-              if(!is.null(input$dianndata) && !is.null(input$sep_dianndata)) { # && !is.null(input$annot)
+              diann_regular_file_ok <- !isTRUE(input$big_file_diann) && !is.null(input$dianndata)
+              diann_big_file_ok <- isTRUE(input$big_file_diann) && length(local_big_file_path_diann()) > 0
+              if((diann_regular_file_ok || diann_big_file_ok) && !is.null(input$sep_dianndata)) {
                 enable("proceed1")
               }
             }
@@ -305,7 +358,11 @@ loadpageServer <- function(id, parent_session, is_web_server = FALSE) {
 
 
     get_data = eventReactive(input$proceed1, {
-      getData(input)
+      getData(
+        input,
+        big_file_path_spec  = local_big_file_path_spec(),
+        big_file_path_diann = local_big_file_path_diann()
+      )
     })
 
 

R/module-loadpage-ui.R

@@ -271,11 +271,10 @@ create_skyline_uploads <- function(ns) {
 #' Create DIANN file uploads
 #' @noRd
 create_diann_uploads <- function(ns) {
-  conditionalPanel(
-    condition = "input['loadpage-filetype'] == 'diann' && input['loadpage-BIO'] != 'PTM'",
-    h4("4. Upload MSstats report from DIANN"),
-    fileInput(ns('dianndata'), "", multiple = FALSE, accept = NULL),
-    create_separator_buttons(ns, "sep_dianndata")
+  tagList(
+    uiOutput(ns("diann_header_ui")),
+    uiOutput(ns("diann_file_selection_ui")),
+    uiOutput(ns("diann_options_ui"))
   )
 }
 
@@ -295,24 +294,51 @@ create_spectronaut_header <- function() {
   h4("4. Upload MSstats scheme output from Spectronaut")
 }
 
+#' Create DIANN header
+#' @noRd
+create_diann_header <- function() {
+  h4("4. Upload MSstats report from DIANN")
+}
+
 #' Create Spectronaut mode selector (Local only)
 #' @noRd
 create_spectronaut_mode_selector <- function(ns, selected = FALSE) {
   checkboxInput(ns("big_file_spec"), "Large file mode", value = selected)
 }
 
+#' Create DIANN mode selector (Local only)
+#' @noRd
+create_diann_mode_selector <- function(ns, selected = FALSE) {
+  checkboxInput(ns("big_file_diann"), "Large file mode", value = selected)
+}
+
 #' Create Spectronaut standard file input
 #' @noRd
 create_spectronaut_standard_ui <- function(ns) {
   fileInput(ns('specdata'), "", multiple = FALSE, accept = NULL)
 }
 
+#' Create DIANN standard file input
+#' @noRd
+create_diann_standard_ui <- function(ns) {
+  fileInput(ns('dianndata'), "", multiple = FALSE, accept = NULL)
+}
+
 #' Create Spectronaut large file selection UI
 #' @noRd
 create_spectronaut_large_file_ui <- function(ns) {
   tagList(
-    shinyFiles::shinyFilesButton(ns("big_file_browse"), "Browse for local file...", "Please select a file", multiple = FALSE),
-    verbatimTextOutput(ns("specdata_big_path"))
+    shinyFiles::shinyFilesButton(ns("big_file_browse_spec"), "Browse for local file...", "Please select a file", multiple = FALSE),
+    verbatimTextOutput(ns("big_file_path_spec"))
+  )
+}
+
+#' Create DIANN large file selection UI
+#' @noRd
+create_diann_large_file_ui <- function(ns) {
+  tagList(
+    shinyFiles::shinyFilesButton(ns("big_file_browse_diann"), "Browse for local file...", "Please select a file", multiple = FALSE),
+    verbatimTextOutput(ns("big_file_path_diann"))
   )
 }
 
@@ -328,6 +354,16 @@ create_spectronaut_large_filter_options <- function(ns, excluded_def = FALSE, id
   )
 }
 
+#' Create DIANN large file filter options
+#' @noRd
+create_diann_large_filter_options <- function(ns, mbr_def = TRUE) {
+  tagList(
+    tags$hr(),
+    h4("Options for large file processing"),
+    checkboxInput(ns("diann_MBR"), "MBR Enabled", value = mbr_def)
+  )
+}
+
 #' Create Spectronaut Q-value cutoff input
 #' @noRd
 create_spectronaut_qvalue_cutoff_ui <- function(ns, cutoff_def = 0.01) {
@@ -345,6 +381,17 @@ create_spectronaut_large_bottom_ui <- function(ns, max_feature_def = 20, unique_
   )
 }
 
+#' Create DIANN large file options (Bottom part)
+#' @noRd
+create_diann_large_bottom_ui <- function(ns, max_feature_def = 100, unique_peps_def = FALSE, agg_psms_def = FALSE, few_obs_def = FALSE) {
+  tagList(
+    numericInput(ns("max_feature_count"), "Max feature count", value = max_feature_def, min = 1),
+    checkboxInput(ns("filter_unique_peptides"), "Use unique peptides", value = unique_peps_def),
+    checkboxInput(ns("aggregate_psms"), "Aggregate PSMs to peptides", value = agg_psms_def),
+    checkboxInput(ns("filter_few_obs"), "Filter features with few observations", value = few_obs_def)
+  )
+}
+
 #' Create PTM FragPipe uploads
 #' @noRd
 create_ptm_fragpipe_uploads <- function(ns) {