From c002ffa235cb990050ebd2cea25d6fef388f188b Mon Sep 17 00:00:00 2001
From: zitoa <zito.a@hotmail.com>
Date: Thu, 7 Aug 2025 16:31:32 +0200
Subject: [PATCH 01/23] wip

---
 .../R/upload_module_preview_counts.R          |   8 +-
 components/board.upload/R/upload_server.R     |  92 ++++++++++++--
 components/board.upload/R/upload_ui.R         | 116 +++++++++++++-----
 3 files changed, 169 insertions(+), 47 deletions(-)

diff --git a/components/board.upload/R/upload_module_preview_counts.R b/components/board.upload/R/upload_module_preview_counts.R
index e94c5b38e..4a097cd14 100644
--- a/components/board.upload/R/upload_module_preview_counts.R
+++ b/components/board.upload/R/upload_module_preview_counts.R
@@ -27,7 +27,8 @@ upload_table_preview_counts_server <- function(
     info.text,
     caption,
     upload_datatype,
-    is.olink
+    is.olink,
+    public_dataset_id
     ) {
 
   moduleServer(id, function(input, output, session) {
@@ -486,6 +487,11 @@ upload_table_preview_counts_server <- function(
       }
     })
 
+    observeEvent(input$counts_csv, {
+      dbg("-------MNT.K1: uploaded$counts.csv: ", dim(uploaded$counts.csv))
+      dbg("-------MNT.K2: uploaded$samples.csv: ", dim(uploaded$samples.csv))
+    })
+
     # pass counts to uploaded when uploaded
     observeEvent(input$counts_csv, {
       # check if counts is csv (necessary due to drag and drop of any file)
diff --git a/components/board.upload/R/upload_server.R b/components/board.upload/R/upload_server.R
index 536727c61..6713cf1dc 100644
--- a/components/board.upload/R/upload_server.R
+++ b/components/board.upload/R/upload_server.R
@@ -124,7 +124,39 @@ UploadBoard <- function(id,
         return(FALSE)
       }
     })
-    
+
+    observeEvent(input$start_search, {
+      if (input$dataset_identifier != "") {
+        ID <- input$dataset_identifier
+        is.valid.ID <- playbase::is.GEO.id.valid(ID)
+        if (!is.valid.ID) {
+          msg <- paste0(ID, " seems not a valid ID. Please use a valid dataset ID.")
+          shinyalert::shinyalert(text = msg, type = "error")
+        } else {
+          msg <- paste0("Searching ", ID, " in GEO and ReCount databases...")
+          shiny::withProgress(message = msg, value = 0.5, {
+            GEO <- tryCatch({ playbase::pgx.getGEOseries(id = ID, get.info = FALSE)},
+              error = function(w) { NULL } )
+          })
+          if (!is.null(GEO)) {
+            cm <- intersect(colnames(GEO[["counts"]]), rownames(GEO[["samples"]]))
+            uploaded$counts.csv <- GEO[["counts"]][, cm, drop = FALSE]
+            uploaded$samples.csv <- GEO[["samples"]][cm, , drop = FALSE]
+            msg <- paste0("Success! ", ID, " found in ", GEO[["source"]])
+            shinyalert::shinyalert(text = msg, type = "success")
+            rm(GEO)
+            new_upload(new_upload() + 1)
+          } else {
+            msg <- paste0(ID, " not found in ReCount and GEO. Please try a different ID.")
+            shinyalert::shinyalert(text = msg, type = "error")
+          }
+        }
+      } else {
+        msg <- paste0("Please add a dataset ID")
+        shinyalert::shinyalert(text = msg, type = "warning")
+      }
+    })
+
     ## ============================================================================
     ## ================== NEW DATA UPLOAD =========================================
     ## ============================================================================
@@ -134,10 +166,10 @@ UploadBoard <- function(id,
     uploaded_method <- NA
 
     shiny::observeEvent(input$upload_files_btn,
-      {
-        shinyjs::click(id = "upload_files")
-      },
-      ignoreNULL = TRUE
+    {
+      shinyjs::click(id = "upload_files")
+    },
+    ignoreNULL = TRUE
     )
 
     shiny::observeEvent(uploaded_pgx(), {
@@ -248,6 +280,8 @@ UploadBoard <- function(id,
       ## --------------------------------------------------------
       df0 <- uploaded$counts.csv
       if (is.null(df0)) return(NULL)
+
+      dbg("-------------------MNT1: dim(df0)=", dim(df0))
       
       checked_for_log(FALSE)
       res <- playbase::pgx.checkINPUT(df0, "COUNTS")
@@ -277,7 +311,7 @@ UploadBoard <- function(id,
       }
 
       return(list(res = res, olink = olink))
-
+      
     }
     )
 
@@ -291,7 +325,10 @@ UploadBoard <- function(id,
       res <- uploaded_counts()$res
       olink <- uploaded_counts()$olink
       if (is.null(res)) { return(list(status = "Missing counts.csv", matrix = NULL)) }
-      
+
+      dbg("-------------------MNT2: is.null(res)=", is.null(res))
+      dbg("-------------------MNT3: dim(res$df)=", dim(res$df))
+
       ## wait for dialog finished
       shiny::req(checked_for_log())
       
@@ -341,6 +378,10 @@ UploadBoard <- function(id,
         status <- "ERROR: incorrect counts matrix"
       }
 
+      ## HACK AZ
+      checked <- res$df
+      status <- "OK"
+
       ## --------------------------------------------------------
       ## check files: maximum samples allowed
       ## --------------------------------------------------------
@@ -367,7 +408,13 @@ UploadBoard <- function(id,
       if (is.null(checked)) {
         uploaded[["last_uploaded"]] <- setdiff(uploaded[["last_uploaded"]], "counts.csv")
       }
-      
+
+      dbg("-------------------MNT4: is.null(status)=", is.null(status))
+      dbg("-------------------MNT5: status=", status)
+      dbg("-------------------MNT6: is.null(checked)=", is.null(checked))
+      dbg("-------------------MNT7: class(checked)=", class(checked))
+      dbg("-------------------MNT8: dim(checked)=", dim(checked))
+
       if (check.e29) {
         if (isConfirmed) isConfirmed = TRUE
         if (is.null(isConfirmed)) isConfirmed = FALSE
@@ -392,6 +439,9 @@ UploadBoard <- function(id,
         df0 <- uploaded$samples.csv
         if (is.null(df0)) { return(list(status = "Missing samples.csv", matrix = NULL)) }
 
+        dbg("---------MNT9: dim(checked_counts()$matrix) = ", dim(checked_counts()$matrix))
+        dbg("---------MNT10: dim(uploaded$samples.csv)=", dim(uploaded$samples.csv))
+
         ## Single matrix counts check
         res <- playbase::pgx.checkINPUT(df0, "SAMPLES")
 
@@ -449,6 +499,9 @@ UploadBoard <- function(id,
           uploaded[["contrasts.csv"]] <<- NULL
         }
 
+        dbg("-------------------MNT11: dim(res_counts) = ", dim(res_counts))
+        dbg("-------------------MNT12: dim(res_samples) = ", dim(res_samples))
+
         list(status = status, SAMPLES = res_samples, COUNTS = res_counts)
       }
     )
@@ -464,9 +517,7 @@ UploadBoard <- function(id,
       {
         ## get uploaded counts
         df0 <- uploaded$contrasts.csv
-        if (is.null(df0)) {
-          return(list(status = "Missing contrasts.csv", matrix = NULL))
-        }
+        if (is.null(df0)) return(list(status = "Missing contrasts.csv", matrix = NULL))
 
         ## --------- Single matrix counts check----------
         res <- playbase::pgx.checkINPUT(df0, "CONTRASTS")
@@ -484,6 +535,18 @@ UploadBoard <- function(id,
         ## Check if samples.csv exists before uploading contrast.csv
         cc <- checked_samples_counts()
 
+        dbg("-------------------MNT13: is.null(cc$COUNTS) = ", is.null(cc$COUNTS))
+        dbg("-------------------MNT14: class(cc$COUNTS) = ", class(cc$COUNTS))
+        dbg("-------------------MNT15: dim(cc$COUNTS) = ", dim(cc$COUNTS))
+
+        dbg("-------------------MNT16: is.null(cc$SAMPLES) = ", is.null(cc$SAMPLES))
+        dbg("-------------------MNT17: class(cc$SAMPLES) = ", class(cc$SAMPLES))
+        dbg("-------------------MNT18: dim(cc$SAMPLES) = ", dim(cc$SAMPLES))
+
+        dbg("-------------------MNT19: is.null(checked) = ", is.null(checked))
+        dbg("-------------------MNT20: class(checked) = ", class(checked))
+        dbg("-------------------MNT21: dim(checked) = ", dim(checked))
+
         ## -------------- max contrast check ------------------
         MAXCONTRASTS <- as.integer(auth$options$MAX_COMPARISONS)
         if (!is.null(checked)) {
@@ -499,6 +562,10 @@ UploadBoard <- function(id,
           }
         }
 
+        dbg("-------------------MNT22: is.null(checked) = ", is.null(checked))
+        dbg("-------------------MNT23: class(checked) = ", class(checked))
+        dbg("-------------------MNT24: dim(checked) = ", dim(checked))
+
         ## -------------- cross-check with samples ------------------
         if (!is.null(checked) && !is.null(cc$SAMPLES)) {
           cross_check <- playbase::pgx.crosscheckINPUT(
@@ -1184,7 +1251,8 @@ UploadBoard <- function(id,
       info.text = "This is the uploaded counts data.",
       caption = "This is the uploaded counts data.",
       upload_datatype = upload_datatype,
-      is.olink = is.olink
+      is.olink = is.olink,
+      public_dataset_id = input$dataset_identifier
     )
 
     upload_table_preview_samples_server(
diff --git a/components/board.upload/R/upload_ui.R b/components/board.upload/R/upload_ui.R
index 6047bba23..055dbae19 100644
--- a/components/board.upload/R/upload_ui.R
+++ b/components/board.upload/R/upload_ui.R
@@ -12,47 +12,93 @@ UploadUI <- function(id) {
     bslib::layout_columns(
       fill = TRUE,
       div(
-        style = "display: flex; flex-direction: column; align-items: center; gap: 20px; margin-bottom: 150px; margin-top: 120px;",
+        style = "display: flex; flex-direction: column; align-items: flex-start; gap: 20px; margin-bottom: 150px; margin-top: 250px;",
+
         div(
-          style = "width: 60%;",
-          bs_alert("To upload your own data, you should prepare at least two CSV files: an <b>counts.csv</b> file (containing your experiment data) and a <b>samples.csv</b> file (containing your sample information). A third <b>contrasts.csv</b> file (describing your comparisons) is optional. Read more about data preparation <a href='https://omicsplayground.readthedocs.io/en/latest/dataprep/dataprep/'><u>here</u></a>.", closable = FALSE, translate = TRUE, html = TRUE)
+          style = "display: flex; flex-direction: row; align-items: center; gap: 20px;",
+          shiny::conditionalPanel(
+            condition = sprintf("input['%s'] <= 0", ns("public_data_opts")),
+            shiny::actionButton(ns("show_upload_opts"), "Upload your data", class = "btn-primary upload-btn-large")
+          ),
+          shiny::conditionalPanel(
+            condition = sprintf("input['%s'] <= 0", ns("show_upload_opts")),
+            shiny::actionButton(ns("public_data_opts"), "Retrieve public data", class = "btn-primary upload-btn-large")
+          )
         ),
         br(),
-        div(
-          p("Data type:", style = "text-align: left; margin: 0 0 2px 0; font-weight: bold;"),
-          shiny::selectInput(
-            ns("selected_datatype"), NULL,
-            choices = c(
-              "RNA-seq",
-              "mRNA microarray",
-              "proteomics",
-              "scRNA-seq",
-              "metabolomics (beta)" = "metabolomics",
-              "multi-omics (beta)" = "multi-omics"
+
+        tags$style(HTML("
+          .upload-btn-large {
+            font-size: 1.6em;
+            padding: 20px 45px;
+            min-width: 260px;
+            border-radius: 8px;
+            margin-left: 20vw;
+            display: block;
+            box-shadow: 0 2px 16px rgba(0,0,0,0.13);
+          }
+          .upload-btn-wrapper {
+            width: 100%;
+            display: flex;
+            justify-content: flex-start;
+            margin: 60px 5vw 0 0;
+          }
+        ")),
+
+        shiny::conditionalPanel(
+          condition = sprintf("input['%s'] > 0", ns("show_upload_opts")),
+          div(
+            style = "display: flex; flex-direction: column; align-items: center; gap: 20px; margin-bottom: 150px; margin-top: 120px;",
+            div(
+              style = "width: 60%;",
+              bs_alert("To upload your own data, you should prepare at least two CSV files: an <b>counts.csv</b> file (containing your experiment data) and a <b>samples.csv</b> file (containing your sample information). A third <b>contrasts.csv</b> file (describing your comparisons) is optional. Read more about data preparation <a href='https://omicsplayground.readthedocs.io/en/latest/dataprep/dataprep/'><u>here</u></a>.",
+                closable = FALSE, translate = TRUE, html = TRUE)
             ),
-            selected = DEFAULTS$datatype,
-            width = "400px"
-          ),
-          shiny::uiOutput(ns("proteomics_subtype_ui"))
-        ),
-        div(
-          p("Organism:", style = "text-align: left; margin: 0 0 2px 0; font-weight: bold;"),
-          shiny::selectInput(
-            inputId = ns("selected_organism"),
-            label = NULL,
-            choices = NULL,
-            multiple = FALSE,
-            width = "400px"
+            br(),
+            div(
+              p("Data type:", style = "text-align: left; margin: 0 0 2px 0; font-weight: bold;"),
+              shiny::selectInput(
+                ns("selected_datatype"), NULL,
+                choices = c("RNA-seq", "mRNA microarray", "proteomics", "scRNA-seq",
+                  "metabolomics (beta)" = "metabolomics", "multi-omics (beta)" = "multi-omics"),
+                selected = DEFAULTS$datatype,
+                width = "400px"
+              )
+            ),
+            div(
+              p("Organism:", style = "text-align: left; margin: 0 0 2px 0; font-weight: bold;"),
+              shiny::selectInput(
+                inputId = ns("selected_organism"), label = NULL,
+                choices = NULL, multiple = FALSE, width = "400px"
+              )
+            ),
+            br(),
+            shiny::actionButton(ns("start_upload"), "Start upload", class = "btn-primary"),
+            br()
           )
         ),
-        br(),
-        shiny::actionButton(
-          ns("start_upload"),
-          "Start upload",
-          class = "btn-primary"
+        
+        shiny::conditionalPanel(
+          condition = sprintf("input['%s'] > 0", ns("public_data_opts")),
+          div(
+            style = "display: flex; flex-direction: column; align-items: center; gap: 20px; margin-bottom: 150px; margin-top: 120px;",
+            div(
+              style = "width: 60%;",
+              bs_alert("The 'Retrieve public data' functionality in OPG allows to query large repositories of publically available data to retrieve a specific dataset. You will need the dataset's unique identifier, such as the GEO ID. At the moment, GEO, ReCount, and ArrayExpress repositories are queried.",
+                closable = FALSE, translate = TRUE, html = TRUE)
+            ),
+            br(),
+            div(
+              p("Dataset identifier:", style = "text-align: left; margin: 0 0 2px 0; font-weight: bold;"),
+              shiny::textInput(ns("dataset_identifier"), label = NULL, width = "400px")
+            ),
+            br(),
+            shiny::actionButton(ns("start_search"), "Start search & download", class = "btn-primary"),
+            br()
+          )
         ),
-        br()
-      )
+
+        )
     )
   )
 
@@ -61,5 +107,7 @@ UploadUI <- function(id) {
     uiOutput(ns("upload_wizard")),
     body
   )
+
   return(ui)
+
 }

From f066a2171d6d173ca89322837b080ba37b54ceb8 Mon Sep 17 00:00:00 2001
From: zitoa <zito.a@hotmail.com>
Date: Fri, 8 Aug 2025 09:36:24 +0200
Subject: [PATCH 02/23] wip

---
 components/board.upload/R/upload_module_preview_counts.R | 3 +++
 components/board.upload/R/upload_server.R                | 7 ++++---
 components/board.upload/R/upload_ui.R                    | 4 ++++
 3 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/components/board.upload/R/upload_module_preview_counts.R b/components/board.upload/R/upload_module_preview_counts.R
index 4a097cd14..3230c7fa1 100644
--- a/components/board.upload/R/upload_module_preview_counts.R
+++ b/components/board.upload/R/upload_module_preview_counts.R
@@ -37,6 +37,7 @@ upload_table_preview_counts_server <- function(
     table_data <- shiny::reactive({
       shiny::req(!is.null(uploaded$counts.csv))
       dt <- uploaded$counts.csv      
+      dbg("-----------MNT1: public_dataset_id=",public_dataset_id)
       nrow0 <- nrow(dt)
       ncol0 <- ncol(dt)
       MAXROW <- 1000
@@ -533,6 +534,8 @@ upload_table_preview_counts_server <- function(
         )
       }
 
+      dbg("-----------public_dataset_id = ", public_dataset_id)
+
       ##---counts---##
       sel <- grep("count|expression|abundance|concentration", tolower(input$counts_csv$name))
       if (length(sel)) {
diff --git a/components/board.upload/R/upload_server.R b/components/board.upload/R/upload_server.R
index 6713cf1dc..95af817b6 100644
--- a/components/board.upload/R/upload_server.R
+++ b/components/board.upload/R/upload_server.R
@@ -101,7 +101,8 @@ UploadBoard <- function(id,
       names(all_species)[all_species=="No organism"] <- "<custom organism>"
       shiny::updateSelectizeInput(session, "selected_organism", choices = all_species, server = TRUE)
     })
-    
+
+    ## AZ: 7/8/2025: disappeared!!!! Tell Xavier.
     output$proteomics_subtype_ui <- shiny::renderUI({
       if (upload_datatype() == "proteomics") {
         shiny::selectInput(
@@ -132,6 +133,8 @@ UploadBoard <- function(id,
         if (!is.valid.ID) {
           msg <- paste0(ID, " seems not a valid ID. Please use a valid dataset ID.")
           shinyalert::shinyalert(text = msg, type = "error")
+          ID <- ""
+          dbg("-----------------ID=",ID)
         } else {
           msg <- paste0("Searching ", ID, " in GEO and ReCount databases...")
           shiny::withProgress(message = msg, value = 0.5, {
@@ -506,7 +509,6 @@ UploadBoard <- function(id,
       }
     )
 
-
     ## --------------------------------------------------------
     ## Check contrast matrix
     ## --------------------------------------------------------
@@ -1231,7 +1233,6 @@ UploadBoard <- function(id,
       }
     )
 
-
     ## =====================================================================
     ## ======================== MODULES SERVERS ============================
     ## =====================================================================
diff --git a/components/board.upload/R/upload_ui.R b/components/board.upload/R/upload_ui.R
index 055dbae19..31f12f561 100644
--- a/components/board.upload/R/upload_ui.R
+++ b/components/board.upload/R/upload_ui.R
@@ -17,10 +17,12 @@ UploadUI <- function(id) {
         div(
           style = "display: flex; flex-direction: row; align-items: center; gap: 20px;",
           shiny::conditionalPanel(
+            #condition = sprintf("input.%s <= 0", ns("public_data_opts")),
             condition = sprintf("input['%s'] <= 0", ns("public_data_opts")),
             shiny::actionButton(ns("show_upload_opts"), "Upload your data", class = "btn-primary upload-btn-large")
           ),
           shiny::conditionalPanel(
+            #condition = sprintf("input.%s <= 0", ns("show_upload_opts")),
             condition = sprintf("input['%s'] <= 0", ns("show_upload_opts")),
             shiny::actionButton(ns("public_data_opts"), "Retrieve public data", class = "btn-primary upload-btn-large")
           )
@@ -46,6 +48,7 @@ UploadUI <- function(id) {
         ")),
 
         shiny::conditionalPanel(
+          #condition = sprintf("input.%s > 0", ns("show_upload_opts")),
           condition = sprintf("input['%s'] > 0", ns("show_upload_opts")),
           div(
             style = "display: flex; flex-direction: column; align-items: center; gap: 20px; margin-bottom: 150px; margin-top: 120px;",
@@ -79,6 +82,7 @@ UploadUI <- function(id) {
         ),
         
         shiny::conditionalPanel(
+          #condition = sprintf("input.%s > 0", ns("public_data_opts")),
           condition = sprintf("input['%s'] > 0", ns("public_data_opts")),
           div(
             style = "display: flex; flex-direction: column; align-items: center; gap: 20px; margin-bottom: 150px; margin-top: 120px;",

From 9049df948375edac61276296755599de98f07a0c Mon Sep 17 00:00:00 2001
From: zitoa <zito.a@hotmail.com>
Date: Fri, 8 Aug 2025 10:12:23 +0200
Subject: [PATCH 03/23] improve upload UI

---
 components/board.upload/R/upload_ui.R | 37 +++++++++++++++++++--------
 1 file changed, 26 insertions(+), 11 deletions(-)

diff --git a/components/board.upload/R/upload_ui.R b/components/board.upload/R/upload_ui.R
index 31f12f561..4f8d46ce0 100644
--- a/components/board.upload/R/upload_ui.R
+++ b/components/board.upload/R/upload_ui.R
@@ -17,13 +17,8 @@ UploadUI <- function(id) {
         div(
           style = "display: flex; flex-direction: row; align-items: center; gap: 20px;",
           shiny::conditionalPanel(
-            #condition = sprintf("input.%s <= 0", ns("public_data_opts")),
-            condition = sprintf("input['%s'] <= 0", ns("public_data_opts")),
-            shiny::actionButton(ns("show_upload_opts"), "Upload your data", class = "btn-primary upload-btn-large")
-          ),
-          shiny::conditionalPanel(
-            #condition = sprintf("input.%s <= 0", ns("show_upload_opts")),
-            condition = sprintf("input['%s'] <= 0", ns("show_upload_opts")),
+            condition = sprintf("input['%s'] == 0 && input['%s'] == 0", ns("public_data_opts"), ns("show_upload_opts")),
+            shiny::actionButton(ns("show_upload_opts"), "Upload your data", class = "btn-primary upload-btn-large"),
             shiny::actionButton(ns("public_data_opts"), "Retrieve public data", class = "btn-primary upload-btn-large")
           )
         ),
@@ -48,7 +43,6 @@ UploadUI <- function(id) {
         ")),
 
         shiny::conditionalPanel(
-          #condition = sprintf("input.%s > 0", ns("show_upload_opts")),
           condition = sprintf("input['%s'] > 0", ns("show_upload_opts")),
           div(
             style = "display: flex; flex-direction: column; align-items: center; gap: 20px; margin-bottom: 150px; margin-top: 120px;",
@@ -58,16 +52,17 @@ UploadUI <- function(id) {
                 closable = FALSE, translate = TRUE, html = TRUE)
             ),
             br(),
+
             div(
               p("Data type:", style = "text-align: left; margin: 0 0 2px 0; font-weight: bold;"),
               shiny::selectInput(
                 ns("selected_datatype"), NULL,
                 choices = c("RNA-seq", "mRNA microarray", "proteomics", "scRNA-seq",
                   "metabolomics (beta)" = "metabolomics", "multi-omics (beta)" = "multi-omics"),
-                selected = DEFAULTS$datatype,
-                width = "400px"
+                selected = DEFAULTS$datatype, width = "400px"
               )
             ),
+
             div(
               p("Organism:", style = "text-align: left; margin: 0 0 2px 0; font-weight: bold;"),
               shiny::selectInput(
@@ -76,13 +71,13 @@ UploadUI <- function(id) {
               )
             ),
             br(),
+
             shiny::actionButton(ns("start_upload"), "Start upload", class = "btn-primary"),
             br()
           )
         ),
         
         shiny::conditionalPanel(
-          #condition = sprintf("input.%s > 0", ns("public_data_opts")),
           condition = sprintf("input['%s'] > 0", ns("public_data_opts")),
           div(
             style = "display: flex; flex-direction: column; align-items: center; gap: 20px; margin-bottom: 150px; margin-top: 120px;",
@@ -91,11 +86,31 @@ UploadUI <- function(id) {
               bs_alert("The 'Retrieve public data' functionality in OPG allows to query large repositories of publically available data to retrieve a specific dataset. You will need the dataset's unique identifier, such as the GEO ID. At the moment, GEO, ReCount, and ArrayExpress repositories are queried.",
                 closable = FALSE, translate = TRUE, html = TRUE)
             ),
+            br(),
+
+            div(
+              p("Data type:", style = "text-align: left; margin: 0 0 2px 0; font-weight: bold;"),
+              shiny::selectInput(
+                ns("selected_datatype"), NULL,
+                choices = c("Transcriptomics", "Proteomics"),
+                selected = "Transcriptomics", width = "400px"
+              )
+            ),
+
+            div(
+              p("Organism:", style = "text-align: left; margin: 0 0 2px 0; font-weight: bold;"),
+              shiny::selectInput(
+                inputId = ns("selected_organism"), label = NULL,
+                choices = playbase::SPECIES_TABLE$species_name, multiple = FALSE, width = "400px"
+              )
+            ),
+
             br(),
             div(
               p("Dataset identifier:", style = "text-align: left; margin: 0 0 2px 0; font-weight: bold;"),
               shiny::textInput(ns("dataset_identifier"), label = NULL, width = "400px")
             ),
+
             br(),
             shiny::actionButton(ns("start_search"), "Start search & download", class = "btn-primary"),
             br()

From 0e69c2403ea78b1e88bfd4027dd1769dfb4cba5a Mon Sep 17 00:00:00 2001
From: zitoa <zito.a@hotmail.com>
Date: Tue, 12 Aug 2025 09:26:05 +0200
Subject: [PATCH 04/23] refactoring and polishing

---
 .../R/upload_module_preview_counts.R          | 359 ++++++++++++------
 components/board.upload/R/upload_server.R     | 104 ++---
 2 files changed, 270 insertions(+), 193 deletions(-)

diff --git a/components/board.upload/R/upload_module_preview_counts.R b/components/board.upload/R/upload_module_preview_counts.R
index 3230c7fa1..b0c3a14cf 100644
--- a/components/board.upload/R/upload_module_preview_counts.R
+++ b/components/board.upload/R/upload_module_preview_counts.R
@@ -13,31 +13,98 @@ upload_table_preview_counts_ui <- function(id) {
 }
 
 upload_table_preview_counts_server <- function(
-    id,
-    create_raw_dir,
-    auth,
-    uploaded,
-    checked_matrix,
-    is_logscale,
-    checklist,
-    scrollY,
-    width,
-    height,
-    title,
-    info.text,
-    caption,
-    upload_datatype,
-    is.olink,
-    public_dataset_id
-    ) {
+                                               id,
+                                               create_raw_dir,
+                                               auth,
+                                               uploaded,
+                                               checked_matrix,
+                                               is_logscale,
+                                               checklist,
+                                               scrollY,
+                                               width,
+                                               height,
+                                               title,
+                                               info.text,
+                                               caption,
+                                               upload_datatype,
+                                               is.olink,
+                                               public_dataset_id
+                                               ) {
 
   moduleServer(id, function(input, output, session) {
+
     ns <- session$ns
 
+    GEO_alert_shown <- reactiveVal(FALSE)
+
+    shiny::insertUI(
+      selector = "head",
+      where = "beforeEnd",
+      ui = list(
+        tags$style(HTML("
+        #custom-progress-modal {
+          position: fixed;
+          top: 50% !important;
+          left: 50% !important;
+          transform: translate(-50%, -50%);
+          background-color: #ffffff;
+          color: black;
+          padding: 30px 50px;
+          font-size: 20px;
+          font-weight: bold;
+          border-radius: 10px;
+          z-index: 1050;
+          text-align: center;
+        }
+        #custom-progress-bar {
+          height: 15px;
+          background-color: #007bff;
+          width: 40%;
+          transition: width 0.3s ease;
+          color: white;
+          font-weight: bold;
+          line-height: 25px;
+          animation: pulse-blue 2s infinite;
+          transform-origin: center;
+        }
+       @keyframes pulse-blue {
+          0% { box-shadow: 0 0 8px 2px #007bff;
+            transform: scale(1.2); }
+          50% { box-shadow: 0 0 18px 8px #3399ff;
+            transform: scale(1.4); }
+          100% { box-shadow: 0 0 8px 2px #007bff;
+            transform: scale(1); }
+       }
+        #custom-progress-container {
+          width: 100%;
+          background-color: #e9ecef;
+          border-radius: 0.25rem;
+          overflow: hidden;
+          margin-top: 15px;
+        }
+        .shiny-notification{ display: none !important; }
+      ")),
+      tags$script(HTML("
+          Shiny.addCustomMessageHandler('updateProgressBar', function(message) {
+            var val = message.value;
+            var pb = document.getElementById('custom-progress-bar');
+            if(pb) {
+              pb.style.width = val + '%';
+              pb.textContent = val + '%';
+            }
+          });
+        "))
+      )
+    )
+    
     table_data <- shiny::reactive({
       shiny::req(!is.null(uploaded$counts.csv))
-      dt <- uploaded$counts.csv      
-      dbg("-----------MNT1: public_dataset_id=",public_dataset_id)
+      dt <- uploaded$counts.csv
+
+      dbg("---------class(public_dataset_id) = ", class(public_dataset_id))
+      dbg("---------public_dataset_id = ", public_dataset_id())
+      dbg("---------class(upload_datatype) = ", class(upload_datatype))
+
       nrow0 <- nrow(dt)
       ncol0 <- ncol(dt)
       MAXROW <- 1000
@@ -60,10 +127,8 @@ upload_table_preview_counts_server <- function(
     table.RENDER <- function() {
       dt <- table_data()
       req(!is.null(dt))
-
       is.integer <- is.integer(dt) || all(round(dt) == dt, na.rm = TRUE)
       digits <- ifelse(is.integer, 0, 2)
-
       DT::datatable(dt,
         class = "compact hover",
         rownames = TRUE,
@@ -84,6 +149,7 @@ upload_table_preview_counts_server <- function(
     }
 
     output$table_counts <- shiny::renderUI({
+
       action_buttons <- div(
         style = "display: flex; justify-content: left; margin: 8px;",
         if (is.null(uploaded$counts.csv)) {
@@ -117,95 +183,31 @@ upload_table_preview_counts_server <- function(
         )
       )
 
-      div(
-        bslib::as_fill_carrier(),
-        style = "width: 100%; display: flex; ",
-        if (is.null(uploaded$counts.csv)) {
-          if (upload_datatype() == "proteomics") {
-            msg <- "The counts file (counts.csv) contains the gene counts for all samples. For proteomics data types other than Olink NPX, the file should be a tabular text file (.csv), where each row corresponds to a feature (i.e. genes) and each column corresponds to a sample. For Olink NPX, the uploaded file needs to be the standard Olink format."
-          } else {
-            msg <- "The counts file (counts.csv) contains the gene counts for all samples. The file should be a tabular text file (.csv), where each row corresponds to a feature (i.e. genes) and each column corresponds to a sample."
+      if (public_dataset_id() != "") {
+
+        ID <- public_dataset_id()
+        msg <- paste0("Retrieving ", ID, " from GEO or ReCount databases...")
+        showModal(modalDialog(
+          div(id = "custom-progress-modal", msg,
+            div(id = "custom-progress-container",
+              div(id = "custom-progress-bar"))),
+          footer = NULL, fade = FALSE))
+        progress <- shiny::Progress$new(session, min = 0, max = 100)
+        GEO <- tryCatch({ playbase::pgx.getGEOseries(id = ID, get.info = FALSE)},
+          error = function(w) { NULL })
+        removeModal()
+
+        if (!is.null(GEO)) {
+          if (!GEO_alert_shown()) {
+            msg <- paste0("Success! ", ID, " found in ", GEO[["source"]])
+            shinyalert::shinyalert(text = msg, type = "success")            
+            GEO_alert_shown(TRUE)
           }
-            bslib::layout_columns(
-              col_widths = c(-3, 6, -3),
-              row_heights = list("auto", 8, 1, 2),
-              gap = "0.5rem",
-              bslib::as_fill_carrier(bs_alert(tspan(msg), closable = FALSE, translate_js = FALSE)),
-              bslib::card(
-              if (upload_datatype() == "multi-omics") {
-                shiny::radioButtons(
-                  ns("data_source"),
-                  label = "Select input files from:",
-                  choices = c("multi-csv", "pgx", "single-csv"),
-                  selected = "multi-csv",
-                  inline = TRUE
-                )
-              },
-              if (upload_datatype() == "multi-omics") {
-                shiny::conditionalPanel(
-                  condition = sprintf("input['%s'] == 'pgx'", ns("data_source")),
-                  div(
-                    div(
-                      style = "margin-bottom: 15px;",
-                      shiny::radioButtons(
-                        ns("data_processing"),
-                        label = "Select data processing level:",
-                        choices = c("Raw" = "raw", "Normalized (also batch corrected if selected on computation)" = "normalized"),
-                        selected = "raw",
-                        inline = TRUE
-                      )
-                    ),
-                    div(
-                      style = "display: flex; align-items: center; gap: 10px; margin-bottom: 10px;",
-                      span("Selected:", style = "font-weight: bold;"),
-                      textOutput(ns("selected_rows_text")),
-                    ),
-                    div(
-                      style = "height: 350px; overflow-y: auto;",
-                      DT::DTOutput(ns("available_data_table"))
-                    ),
-                    style = "width: 100%; max-height: 400px; overflow-y: auto;"
-                  ),
-                  selection = "multiple",
-                  options = list(pageLength = 5, dom = "tp", scrollY = TRUE)
-                )
-              },
-
-              if (upload_datatype() == "multi-omics") {
-                shiny::conditionalPanel(
-                  condition = sprintf("input['%s'] == 'multi-csv'", ns("data_source")),
-                  shiny::uiOutput(ns("dynamic_file_inputs"))#,
-                )
-              },
-
-              if (upload_datatype() == "multi-omics") {
-                shiny::conditionalPanel(
-                  condition = sprintf("input['%s'] == 'single-csv'", ns("data_source")),
-                  fileInputArea(
-                    ns("counts_csv"),
-                    shiny::h4(tspan("Upload counts.csv", js = FALSE), class = "mb-0"),
-                    multiple = FALSE,
-                    accept = c(".csv"),
-                    width = "100%"
-                  )
-                )
-              },
-
-              if (upload_datatype() != "multi-omics") {
-                fileInputArea(
-                  ns("counts_csv"),
-                  shiny::h4(tspan("Upload counts.csv", js = FALSE), class = "mb-0"),
-                  multiple = FALSE,
-                  accept = c(".csv"),
-                  width = "100%"
-                )
-              },
-              style = "background-color: aliceblue; border: 0.07rem dashed steelblue;"
-            ),
-            action_buttons,
-            br()
-          )
-        },
+          uploaded$counts.csv <- GEO[["counts"]]
+          uploaded$samples.csv <- GEO[["samples"]]
+          GEO <- NULL
+        }
+        
         if (!is.null(uploaded$counts.csv)) {
           bslib::layout_columns(
             col_widths = 12,
@@ -229,8 +231,129 @@ upload_table_preview_counts_server <- function(
             ),
             bslib::layout_columns(action_buttons, br(), uiOutput(ns("error_summary")))
           )
-        } ## end of if-else
-      ) ## end of div
+        } else {
+          div("No counts data available for this public dataset.")
+        }
+
+      } else {
+
+        div(
+          bslib::as_fill_carrier(),
+          style = "width: 100%; display: flex; ",
+          if (is.null(uploaded$counts.csv)) {
+            if (upload_datatype() == "proteomics") {
+              msg <- "The counts file (counts.csv) contains the gene counts for all samples. For proteomics data types other than Olink NPX, the file should be a tabular text file (.csv), where each row corresponds to a feature (i.e. genes) and each column corresponds to a sample. For Olink NPX, the uploaded file needs to be the standard Olink format."
+            } else {
+              msg <- "The counts file (counts.csv) contains the gene counts for all samples. The file should be a tabular text file (.csv), where each row corresponds to a feature (i.e. genes) and each column corresponds to a sample."
+            }
+            bslib::layout_columns(
+              col_widths = c(-3, 6, -3),
+              row_heights = list("auto", 8, 1, 2),
+              gap = "0.5rem",
+              bslib::as_fill_carrier(bs_alert(tspan(msg), closable = FALSE, translate_js = FALSE)),
+              bslib::card(
+                if (upload_datatype() == "multi-omics") {
+                  shiny::radioButtons(
+                    ns("data_source"),
+                    label = "Select input files from:",
+                    choices = c("multi-csv", "pgx", "single-csv"),
+                    selected = "multi-csv",
+                    inline = TRUE
+                  )
+                },
+                if (upload_datatype() == "multi-omics") {
+                  shiny::conditionalPanel(
+                    condition = sprintf("input['%s'] == 'pgx'", ns("data_source")),
+                    div(
+                      div(
+                        style = "margin-bottom: 15px;",
+                        shiny::radioButtons(
+                          ns("data_processing"),
+                          label = "Select data processing level:",
+                          choices = c("Raw" = "raw", "Normalized (also batch corrected if selected on computation)" = "normalized"),
+                          selected = "raw",
+                          inline = TRUE
+                        )
+                      ),
+                      div(
+                        style = "display: flex; align-items: center; gap: 10px; margin-bottom: 10px;",
+                        span("Selected:", style = "font-weight: bold;"),
+                        textOutput(ns("selected_rows_text")),
+                        ),
+                      div(
+                        style = "height: 350px; overflow-y: auto;",
+                        DT::DTOutput(ns("available_data_table"))
+                      ),
+                      style = "width: 100%; max-height: 400px; overflow-y: auto;"
+                    ),
+                    selection = "multiple",
+                    options = list(pageLength = 5, dom = "tp", scrollY = TRUE)
+                  )
+                },
+
+                if (upload_datatype() == "multi-omics") {
+                  shiny::conditionalPanel(
+                    condition = sprintf("input['%s'] == 'multi-csv'", ns("data_source")),
+                    shiny::uiOutput(ns("dynamic_file_inputs"))#,
+                  )
+                },
+
+                if (upload_datatype() == "multi-omics") {
+                  shiny::conditionalPanel(
+                    condition = sprintf("input['%s'] == 'single-csv'", ns("data_source")),
+                    fileInputArea(
+                      ns("counts_csv"),
+                      shiny::h4(tspan("Upload counts.csv", js = FALSE), class = "mb-0"),
+                      multiple = FALSE,
+                      accept = c(".csv"),
+                      width = "100%"
+                    )
+                  )
+                },
+
+                if (upload_datatype() != "multi-omics") {
+                  fileInputArea(
+                    ns("counts_csv"),
+                    shiny::h4(tspan("Upload counts.csv", js = FALSE), class = "mb-0"),
+                    multiple = FALSE,
+                    accept = c(".csv"),
+                    width = "100%"
+                  )
+                },
+                
+                style = "background-color: aliceblue; border: 0.07rem dashed steelblue;"
+              ),
+              action_buttons,
+              br()
+            )
+          },
+          if (!is.null(uploaded$counts.csv)) {
+            bslib::layout_columns(
+              col_widths = 12,
+              bslib::layout_columns(
+                col_widths = c(8, 4),
+                TableModuleUI(
+                  ns("counts_datasets"),
+                  width = width,
+                  height = height,
+                  title = title,
+                  info.text = info.text,
+                  caption = caption,
+                  label = "",
+                  show.maximize = FALSE,
+                  translate_js = FALSE
+                ),
+                bslib::navset_card_pill(
+                  bslib::nav_panel(title = "Histogram", br(), plotOutput(ns("histogram"))),
+                  bslib::nav_panel(title = "Box plots", br(), plotOutput(ns("boxplots")))
+                )
+              ),
+              bslib::layout_columns(action_buttons, br(), uiOutput(ns("error_summary")))
+            )
+          } ## end of if-else
+        ) ## end of div
+      }
+      
     })
 
     output$selected_rows_text <- renderText({
@@ -487,12 +610,7 @@ upload_table_preview_counts_server <- function(
         shinyalert::shinyalert(title = "Warning", text = err.html, html = TRUE)
       }
     })
-
-    observeEvent(input$counts_csv, {
-      dbg("-------MNT.K1: uploaded$counts.csv: ", dim(uploaded$counts.csv))
-      dbg("-------MNT.K2: uploaded$samples.csv: ", dim(uploaded$samples.csv))
-    })
-
+      
     # pass counts to uploaded when uploaded
     observeEvent(input$counts_csv, {
       # check if counts is csv (necessary due to drag and drop of any file)
@@ -533,9 +651,7 @@ upload_table_preview_counts_server <- function(
           overwrite = TRUE
         )
       }
-
-      dbg("-----------public_dataset_id = ", public_dataset_id)
-
+      
       ##---counts---##
       sel <- grep("count|expression|abundance|concentration", tolower(input$counts_csv$name))
       if (length(sel)) {
@@ -581,7 +697,7 @@ upload_table_preview_counts_server <- function(
       if (upload_datatype() == "proteomics" && is.olink() && !is.null(df.samples)) {
         uploaded$samples.csv <- df.samples
       }
-      
+
       ## ##---samples---##
       ## sel <- grep("samples", tolower(input$counts_csv$name))
       ## if (length(sel)) {
@@ -679,3 +795,4 @@ upload_table_preview_counts_server <- function(
     )
   }) ## end of moduleServer
 } ## end of server
+                                                                                                        
diff --git a/components/board.upload/R/upload_server.R b/components/board.upload/R/upload_server.R
index 95af817b6..3385617c5 100644
--- a/components/board.upload/R/upload_server.R
+++ b/components/board.upload/R/upload_server.R
@@ -27,6 +27,7 @@ UploadBoard <- function(id,
     upload_name <- reactiveVal(NULL)
     upload_description <- reactiveVal(NULL)
     upload_datatype <- reactiveVal(NULL)
+    public_dataset_id <- reactiveVal(NULL)
     upload_gset_methods <- reactiveVal(NULL)
     upload_gx_methods <- reactiveVal(NULL)
     process_counter <- reactiveVal(0)
@@ -127,39 +128,21 @@ UploadBoard <- function(id,
     })
 
     observeEvent(input$start_search, {
+      dbg("-------public_dataset_id = ", public_dataset_id())
       if (input$dataset_identifier != "") {
-        ID <- input$dataset_identifier
-        is.valid.ID <- playbase::is.GEO.id.valid(ID)
-        if (!is.valid.ID) {
-          msg <- paste0(ID, " seems not a valid ID. Please use a valid dataset ID.")
-          shinyalert::shinyalert(text = msg, type = "error")
-          ID <- ""
-          dbg("-----------------ID=",ID)
+        ID <- public_dataset_id()
+        valid.ID <- playbase::is.GEO.id.valid(ID)
+        if (!valid.ID) {
+          msg <- paste0(ID, " seems not valid. Please use a valid dataset ID.")
+          shinyalert::shinyalert(text = msg, type = "error")           
         } else {
-          msg <- paste0("Searching ", ID, " in GEO and ReCount databases...")
-          shiny::withProgress(message = msg, value = 0.5, {
-            GEO <- tryCatch({ playbase::pgx.getGEOseries(id = ID, get.info = FALSE)},
-              error = function(w) { NULL } )
-          })
-          if (!is.null(GEO)) {
-            cm <- intersect(colnames(GEO[["counts"]]), rownames(GEO[["samples"]]))
-            uploaded$counts.csv <- GEO[["counts"]][, cm, drop = FALSE]
-            uploaded$samples.csv <- GEO[["samples"]][cm, , drop = FALSE]
-            msg <- paste0("Success! ", ID, " found in ", GEO[["source"]])
-            shinyalert::shinyalert(text = msg, type = "success")
-            rm(GEO)
-            new_upload(new_upload() + 1)
-          } else {
-            msg <- paste0(ID, " not found in ReCount and GEO. Please try a different ID.")
-            shinyalert::shinyalert(text = msg, type = "error")
-          }
+          new_upload(new_upload() + 1)
         }
       } else {
-        msg <- paste0("Please add a dataset ID")
-        shinyalert::shinyalert(text = msg, type = "warning")
+        shinyalert::shinyalert(text = "Please enter a dataset ID", type = "error")           
       }
     })
-
+    
     ## ============================================================================
     ## ================== NEW DATA UPLOAD =========================================
     ## ============================================================================
@@ -284,8 +267,6 @@ UploadBoard <- function(id,
       df0 <- uploaded$counts.csv
       if (is.null(df0)) return(NULL)
 
-      dbg("-------------------MNT1: dim(df0)=", dim(df0))
-      
       checked_for_log(FALSE)
       res <- playbase::pgx.checkINPUT(df0, "COUNTS")
       write_check_output(res$checks, "COUNTS", raw_dir())
@@ -328,10 +309,7 @@ UploadBoard <- function(id,
       res <- uploaded_counts()$res
       olink <- uploaded_counts()$olink
       if (is.null(res)) { return(list(status = "Missing counts.csv", matrix = NULL)) }
-
-      dbg("-------------------MNT2: is.null(res)=", is.null(res))
-      dbg("-------------------MNT3: dim(res$df)=", dim(res$df))
-
+      
       ## wait for dialog finished
       shiny::req(checked_for_log())
       
@@ -343,7 +321,6 @@ UploadBoard <- function(id,
       isConfirmed <- input$logCorrectCounts
       if (is.null(isConfirmed)) isConfirmed = FALSE
 
-      ## RESTORE AVERAGE RANK PLOT.
       if (olink) {
         res$checks[["e29"]] <- NULL
         check.e29 = TRUE
@@ -381,10 +358,6 @@ UploadBoard <- function(id,
         status <- "ERROR: incorrect counts matrix"
       }
 
-      ## HACK AZ
-      checked <- res$df
-      status <- "OK"
-
       ## --------------------------------------------------------
       ## check files: maximum samples allowed
       ## --------------------------------------------------------
@@ -412,12 +385,6 @@ UploadBoard <- function(id,
         uploaded[["last_uploaded"]] <- setdiff(uploaded[["last_uploaded"]], "counts.csv")
       }
 
-      dbg("-------------------MNT4: is.null(status)=", is.null(status))
-      dbg("-------------------MNT5: status=", status)
-      dbg("-------------------MNT6: is.null(checked)=", is.null(checked))
-      dbg("-------------------MNT7: class(checked)=", class(checked))
-      dbg("-------------------MNT8: dim(checked)=", dim(checked))
-
       if (check.e29) {
         if (isConfirmed) isConfirmed = TRUE
         if (is.null(isConfirmed)) isConfirmed = FALSE
@@ -442,9 +409,6 @@ UploadBoard <- function(id,
         df0 <- uploaded$samples.csv
         if (is.null(df0)) { return(list(status = "Missing samples.csv", matrix = NULL)) }
 
-        dbg("---------MNT9: dim(checked_counts()$matrix) = ", dim(checked_counts()$matrix))
-        dbg("---------MNT10: dim(uploaded$samples.csv)=", dim(uploaded$samples.csv))
-
         ## Single matrix counts check
         res <- playbase::pgx.checkINPUT(df0, "SAMPLES")
 
@@ -502,10 +466,8 @@ UploadBoard <- function(id,
           uploaded[["contrasts.csv"]] <<- NULL
         }
 
-        dbg("-------------------MNT11: dim(res_counts) = ", dim(res_counts))
-        dbg("-------------------MNT12: dim(res_samples) = ", dim(res_samples))
-
-        list(status = status, SAMPLES = res_samples, COUNTS = res_counts)
+        LL <- list(status = status, SAMPLES = res_samples, COUNTS = res_counts)
+        return(LL)
       }
     )
 
@@ -537,18 +499,6 @@ UploadBoard <- function(id,
         ## Check if samples.csv exists before uploading contrast.csv
         cc <- checked_samples_counts()
 
-        dbg("-------------------MNT13: is.null(cc$COUNTS) = ", is.null(cc$COUNTS))
-        dbg("-------------------MNT14: class(cc$COUNTS) = ", class(cc$COUNTS))
-        dbg("-------------------MNT15: dim(cc$COUNTS) = ", dim(cc$COUNTS))
-
-        dbg("-------------------MNT16: is.null(cc$SAMPLES) = ", is.null(cc$SAMPLES))
-        dbg("-------------------MNT17: class(cc$SAMPLES) = ", class(cc$SAMPLES))
-        dbg("-------------------MNT18: dim(cc$SAMPLES) = ", dim(cc$SAMPLES))
-
-        dbg("-------------------MNT19: is.null(checked) = ", is.null(checked))
-        dbg("-------------------MNT20: class(checked) = ", class(checked))
-        dbg("-------------------MNT21: dim(checked) = ", dim(checked))
-
         ## -------------- max contrast check ------------------
         MAXCONTRASTS <- as.integer(auth$options$MAX_COMPARISONS)
         if (!is.null(checked)) {
@@ -564,10 +514,6 @@ UploadBoard <- function(id,
           }
         }
 
-        dbg("-------------------MNT22: is.null(checked) = ", is.null(checked))
-        dbg("-------------------MNT23: class(checked) = ", class(checked))
-        dbg("-------------------MNT24: dim(checked) = ", dim(checked))
-
         ## -------------- cross-check with samples ------------------
         if (!is.null(checked) && !is.null(cc$SAMPLES)) {
           cross_check <- playbase::pgx.crosscheckINPUT(
@@ -602,6 +548,7 @@ UploadBoard <- function(id,
 
     ## Dynamic render of appropriate wizard
     output$upload_wizard <- shiny::renderUI({
+
       counts_ui <- wizardR::wizard_step(
         step_title = tspan("Step 1: Upload counts", js = FALSE),
         step_id = "step_counts",
@@ -616,10 +563,10 @@ UploadBoard <- function(id,
         step_id = "step_samples",
         server = TRUE,
         upload_table_preview_samples_ui(
-            ns("samples_preview")
+          ns("samples_preview")
         )
       )
-
+      
       contrasts_ui <- wizardR::wizard_step(
         step_title = "Step 3: Create comparisons",
         step_id = "step_comparisons",
@@ -787,6 +734,11 @@ UploadBoard <- function(id,
       upload_organism(input$selected_organism)
     })
 
+    ## NEW AZ
+    observeEvent(input$dataset_identifier, {
+      public_dataset_id(input$dataset_identifier)
+    })
+
     observeEvent(input$start_upload, {
       recompute_pgx(NULL) ## need to reset ???
     })
@@ -1237,6 +1189,16 @@ UploadBoard <- function(id,
     ## ======================== MODULES SERVERS ============================
     ## =====================================================================
 
+    shiny::observeEvent(uploaded$counts.csv, {
+      dbg("-----------------------------")
+      dbg("-------FINAL CHECKS----------")
+      dbg("----dim(checked_counts()$matrix) = ", dim(checked_counts()$matrix))
+      dbg("----dim(uploaded$counts.csv) = ", dim(uploaded$counts.csv))
+      dbg("----all.equal = ", all.equal(uploaded$counts.csv, checked_counts()$matrix))
+      dbg("----public_dataset_id = ", public_dataset_id())
+      dbg("-------------------------------------")
+    })
+
     upload_table_preview_counts_server(
       id = "counts_preview",
       create_raw_dir = create_raw_dir,
@@ -1253,7 +1215,7 @@ UploadBoard <- function(id,
       caption = "This is the uploaded counts data.",
       upload_datatype = upload_datatype,
       is.olink = is.olink,
-      public_dataset_id = input$dataset_identifier
+      public_dataset_id = public_dataset_id
     )
 
     upload_table_preview_samples_server(
@@ -1373,8 +1335,6 @@ UploadBoard <- function(id,
       probetype = probetype
     )
 
-
-
     ## ------------------------------------------------
     ## Board return object
     ## ------------------------------------------------

From 8b439988a7ae98b011f21f7a19e495474988a1a1 Mon Sep 17 00:00:00 2001
From: zitoa <zito.a@hotmail.com>
Date: Wed, 13 Aug 2025 14:54:39 +0200
Subject: [PATCH 05/23] refactoring and polishing

---
 .../R/upload_module_preview_counts.R          | 13 ++++--------
 components/board.upload/R/upload_server.R     | 20 ++++---------------
 2 files changed, 8 insertions(+), 25 deletions(-)

diff --git a/components/board.upload/R/upload_module_preview_counts.R b/components/board.upload/R/upload_module_preview_counts.R
index b0c3a14cf..e7163b1e4 100644
--- a/components/board.upload/R/upload_module_preview_counts.R
+++ b/components/board.upload/R/upload_module_preview_counts.R
@@ -100,11 +100,6 @@ upload_table_preview_counts_server <- function(
     table_data <- shiny::reactive({
       shiny::req(!is.null(uploaded$counts.csv))
       dt <- uploaded$counts.csv
-
-      dbg("---------class(public_dataset_id) = ", class(public_dataset_id))
-      dbg("---------public_dataset_id = ", public_dataset_id())
-      dbg("---------class(upload_datatype) = ", class(upload_datatype))
-
       nrow0 <- nrow(dt)
       ncol0 <- ncol(dt)
       MAXROW <- 1000
@@ -186,20 +181,20 @@ upload_table_preview_counts_server <- function(
       if (public_dataset_id() != "") {
 
         ID <- public_dataset_id()
-        msg <- paste0("Retrieving ", ID, " from GEO or ReCount databases...")
+        msg <- paste0("Retrieving ", ID, " from GEO, ReCount, or ArrayExpress...<br>", "May take up to 20 minutes...")
         showModal(modalDialog(
-          div(id = "custom-progress-modal", msg,
+          div(id = "custom-progress-modal", HTML(msg),
             div(id = "custom-progress-container",
               div(id = "custom-progress-bar"))),
           footer = NULL, fade = FALSE))
         progress <- shiny::Progress$new(session, min = 0, max = 100)
-        GEO <- tryCatch({ playbase::pgx.getGEOseries(id = ID, get.info = FALSE)},
+        GEO <- tryCatch({ playbase::pgx.getGEOseries(accession = ID, get.info = FALSE)},
           error = function(w) { NULL })
         removeModal()
 
         if (!is.null(GEO)) {
           if (!GEO_alert_shown()) {
-            msg <- paste0("Success! ", ID, " found in ", GEO[["source"]])
+            msg <- paste0("Success! ", ID, " found in ", GEO[["source"]], ".\nWe're preparing it...")
             shinyalert::shinyalert(text = msg, type = "success")            
             GEO_alert_shown(TRUE)
           }
diff --git a/components/board.upload/R/upload_server.R b/components/board.upload/R/upload_server.R
index 3385617c5..600e0b7e5 100644
--- a/components/board.upload/R/upload_server.R
+++ b/components/board.upload/R/upload_server.R
@@ -128,18 +128,17 @@ UploadBoard <- function(id,
     })
 
     observeEvent(input$start_search, {
-      dbg("-------public_dataset_id = ", public_dataset_id())
-      if (input$dataset_identifier != "") {
-        ID <- public_dataset_id()
+      ID <- public_dataset_id()
+      if (ID != "") {
         valid.ID <- playbase::is.GEO.id.valid(ID)
         if (!valid.ID) {
           msg <- paste0(ID, " seems not valid. Please use a valid dataset ID.")
-          shinyalert::shinyalert(text = msg, type = "error")           
+          shinyalert::shinyalert(text = msg, type = "error")
         } else {
           new_upload(new_upload() + 1)
         }
       } else {
-        shinyalert::shinyalert(text = "Please enter a dataset ID", type = "error")           
+        shinyalert::shinyalert(text = "Please enter a dataset ID", type = "error")
       }
     })
     
@@ -734,7 +733,6 @@ UploadBoard <- function(id,
       upload_organism(input$selected_organism)
     })
 
-    ## NEW AZ
     observeEvent(input$dataset_identifier, {
       public_dataset_id(input$dataset_identifier)
     })
@@ -1189,16 +1187,6 @@ UploadBoard <- function(id,
     ## ======================== MODULES SERVERS ============================
     ## =====================================================================
 
-    shiny::observeEvent(uploaded$counts.csv, {
-      dbg("-----------------------------")
-      dbg("-------FINAL CHECKS----------")
-      dbg("----dim(checked_counts()$matrix) = ", dim(checked_counts()$matrix))
-      dbg("----dim(uploaded$counts.csv) = ", dim(uploaded$counts.csv))
-      dbg("----all.equal = ", all.equal(uploaded$counts.csv, checked_counts()$matrix))
-      dbg("----public_dataset_id = ", public_dataset_id())
-      dbg("-------------------------------------")
-    })
-
     upload_table_preview_counts_server(
       id = "counts_preview",
       create_raw_dir = create_raw_dir,

From 5a682fad84a9b43c3e51b28032d521ff92dd4393 Mon Sep 17 00:00:00 2001
From: zitoa <zito.a@hotmail.com>
Date: Wed, 13 Aug 2025 15:23:04 +0200
Subject: [PATCH 06/23] Only transcriptomics for now

---
 components/board.upload/R/upload_ui.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/components/board.upload/R/upload_ui.R b/components/board.upload/R/upload_ui.R
index 4f8d46ce0..e10f7a8c1 100644
--- a/components/board.upload/R/upload_ui.R
+++ b/components/board.upload/R/upload_ui.R
@@ -92,8 +92,8 @@ UploadUI <- function(id) {
               p("Data type:", style = "text-align: left; margin: 0 0 2px 0; font-weight: bold;"),
               shiny::selectInput(
                 ns("selected_datatype"), NULL,
-                choices = c("Transcriptomics", "Proteomics"),
-                selected = "Transcriptomics", width = "400px"
+                choices = c("RNA-seq", "mRNA microarray"),
+                selected = "RNA-seq", width = "400px"
               )
             ),
 

From bb8597b1cf1715d706d9c00d52849b5d8afff3e8 Mon Sep 17 00:00:00 2001
From: zitoa <zito.a@hotmail.com>
Date: Thu, 14 Aug 2025 16:29:29 +0200
Subject: [PATCH 07/23] refactor proteomics type box && cleaning

---
 .../board.upload/R/upload_module_preview_counts.R |  2 +-
 components/board.upload/R/upload_server.R         | 15 ---------------
 components/board.upload/R/upload_ui.R             |  9 +++++++++
 3 files changed, 10 insertions(+), 16 deletions(-)

diff --git a/components/board.upload/R/upload_module_preview_counts.R b/components/board.upload/R/upload_module_preview_counts.R
index e7163b1e4..78d37bc87 100644
--- a/components/board.upload/R/upload_module_preview_counts.R
+++ b/components/board.upload/R/upload_module_preview_counts.R
@@ -181,7 +181,7 @@ upload_table_preview_counts_server <- function(
       if (public_dataset_id() != "") {
 
         ID <- public_dataset_id()
-        msg <- paste0("Retrieving ", ID, " from GEO, ReCount, or ArrayExpress...<br>", "May take up to 20 minutes...")
+        msg <- paste0("Retrieving ", ID, " from GEO, ReCount, or ArrayExpress...<br>", "Please wait. Most datasets take 2-3 mins.")
         showModal(modalDialog(
           div(id = "custom-progress-modal", HTML(msg),
             div(id = "custom-progress-container",
diff --git a/components/board.upload/R/upload_server.R b/components/board.upload/R/upload_server.R
index 600e0b7e5..4c352fa39 100644
--- a/components/board.upload/R/upload_server.R
+++ b/components/board.upload/R/upload_server.R
@@ -103,21 +103,6 @@ UploadBoard <- function(id,
       shiny::updateSelectizeInput(session, "selected_organism", choices = all_species, server = TRUE)
     })
 
-    ## AZ: 7/8/2025: disappeared!!!! Tell Xavier.
-    output$proteomics_subtype_ui <- shiny::renderUI({
-      if (upload_datatype() == "proteomics") {
-        shiny::selectInput(
-          ns("proteomics_type"),
-          label = "Proteomics type:",
-          choices = c("MS", "Olink NPX"),
-          selected = "MS",
-          width = "150px"
-        )
-      } else {
-        NULL
-      }
-    })
-
     is.olink <- shiny::reactive({
       req(upload_datatype())
       if (upload_datatype() == "proteomics" && !is.null(input$proteomics_type)) {
diff --git a/components/board.upload/R/upload_ui.R b/components/board.upload/R/upload_ui.R
index e10f7a8c1..608bd3b91 100644
--- a/components/board.upload/R/upload_ui.R
+++ b/components/board.upload/R/upload_ui.R
@@ -63,6 +63,15 @@ UploadUI <- function(id) {
               )
             ),
 
+            shiny::conditionalPanel(
+              condition = sprintf("input['%s'] == 'proteomics'", ns("selected_datatype")),
+              div(style = "width: 22%;",
+                shiny::selectInput(ns("proteomics_type"),
+                  label = tags$b("Proteomics type:"), choices = c("MS", "Olink NPX"),
+                  selected = "MS", width = "150px")
+              )
+            ),
+            
             div(
               p("Organism:", style = "text-align: left; margin: 0 0 2px 0; font-weight: bold;"),
               shiny::selectInput(

From 5b0703f8af49797bb339d35cfba16cbb484ebff8 Mon Sep 17 00:00:00 2001
From: zitoa <zito.a@hotmail.com>
Date: Thu, 14 Aug 2025 16:48:19 +0200
Subject: [PATCH 08/23] add timer to success box

---
 components/board.upload/R/upload_module_preview_counts.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/components/board.upload/R/upload_module_preview_counts.R b/components/board.upload/R/upload_module_preview_counts.R
index 78d37bc87..aa8e9e83e 100644
--- a/components/board.upload/R/upload_module_preview_counts.R
+++ b/components/board.upload/R/upload_module_preview_counts.R
@@ -195,7 +195,7 @@ upload_table_preview_counts_server <- function(
         if (!is.null(GEO)) {
           if (!GEO_alert_shown()) {
             msg <- paste0("Success! ", ID, " found in ", GEO[["source"]], ".\nWe're preparing it...")
-            shinyalert::shinyalert(text = msg, type = "success")            
+            shinyalert::shinyalert(text = msg, type = "success", timer = 4000)            
             GEO_alert_shown(TRUE)
           }
           uploaded$counts.csv <- GEO[["counts"]]

From 38ee72ee0a002deb4fc774bb3a297320a2b07983 Mon Sep 17 00:00:00 2001
From: zitoa <zito.a@hotmail.com>
Date: Thu, 14 Aug 2025 17:08:58 +0200
Subject: [PATCH 09/23] polishing

---
 components/board.upload/R/upload_module_preview_counts.R | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/components/board.upload/R/upload_module_preview_counts.R b/components/board.upload/R/upload_module_preview_counts.R
index aa8e9e83e..a105c5c9a 100644
--- a/components/board.upload/R/upload_module_preview_counts.R
+++ b/components/board.upload/R/upload_module_preview_counts.R
@@ -182,16 +182,17 @@ upload_table_preview_counts_server <- function(
 
         ID <- public_dataset_id()
         msg <- paste0("Retrieving ", ID, " from GEO, ReCount, or ArrayExpress...<br>", "Please wait. Most datasets take 2-3 mins.")
+        
         showModal(modalDialog(
           div(id = "custom-progress-modal", HTML(msg),
             div(id = "custom-progress-container",
               div(id = "custom-progress-bar"))),
           footer = NULL, fade = FALSE))
-        progress <- shiny::Progress$new(session, min = 0, max = 100)
+        progress <- shiny::Progress$new(session, min = 0, max = 100)          
         GEO <- tryCatch({ playbase::pgx.getGEOseries(accession = ID, get.info = FALSE)},
-          error = function(w) { NULL })
+        error = function(w) { NULL })
         removeModal()
-
+        
         if (!is.null(GEO)) {
           if (!GEO_alert_shown()) {
             msg <- paste0("Success! ", ID, " found in ", GEO[["source"]], ".\nWe're preparing it...")

From c40d9b8f7309a664ce6768da53a62515850c9b38 Mon Sep 17 00:00:00 2001
From: zitoa <zito.a@hotmail.com>
Date: Mon, 18 Aug 2025 18:07:43 +0200
Subject: [PATCH 10/23] add specification

---
 components/board.upload/R/upload_server.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/components/board.upload/R/upload_server.R b/components/board.upload/R/upload_server.R
index 8627bfeb4..cb85df052 100644
--- a/components/board.upload/R/upload_server.R
+++ b/components/board.upload/R/upload_server.R
@@ -1194,7 +1194,7 @@ UploadBoard <- function(id,
       caption = "This is the uploaded counts data.",
       upload_datatype = upload_datatype,
       is.olink = is.olink,
-      public_dataset_id = public_dataset_id
+      public_dataset_id = public_dataset_id ## accession ID
     )
 
     upload_table_preview_samples_server(

From 9c04425bdf4029ee3ca4156c9a91110dc6a3d9d5 Mon Sep 17 00:00:00 2001
From: zitoa <zito.a@hotmail.com>
Date: Tue, 19 Aug 2025 16:12:39 +0200
Subject: [PATCH 11/23] fixes to display public metadata

---
 .../R/upload_module_preview_counts.R          | 10 ++--
 .../R/upload_module_preview_samples.R         | 54 +++++++++++++++----
 components/board.upload/R/upload_server.R     |  4 +-
 3 files changed, 54 insertions(+), 14 deletions(-)

diff --git a/components/board.upload/R/upload_module_preview_counts.R b/components/board.upload/R/upload_module_preview_counts.R
index a105c5c9a..703e55375 100644
--- a/components/board.upload/R/upload_module_preview_counts.R
+++ b/components/board.upload/R/upload_module_preview_counts.R
@@ -189,8 +189,8 @@ upload_table_preview_counts_server <- function(
               div(id = "custom-progress-bar"))),
           footer = NULL, fade = FALSE))
         progress <- shiny::Progress$new(session, min = 0, max = 100)          
-        GEO <- tryCatch({ playbase::pgx.getGEOseries(accession = ID, get.info = FALSE)},
-        error = function(w) { NULL })
+        GEO <- tryCatch({ playbase::pgx.getGEOseries(accession = ID, archs.h5 = NULL, get.info = FALSE)},
+          error = function(w) { NULL })
         removeModal()
         
         if (!is.null(GEO)) {
@@ -199,9 +199,13 @@ upload_table_preview_counts_server <- function(
             shinyalert::shinyalert(text = msg, type = "success", timer = 4000)            
             GEO_alert_shown(TRUE)
           }
+          dbg("-----------------MNT1: source = ", GEO[["source"]])
+          dbg("-----------------MNT2: dim(samples) = ", dim(GEO[["samples"]]))
+          dbg("-----------------MNT3: colnames(samples) = ", colnames(GEO[["samples"]]))
           uploaded$counts.csv <- GEO[["counts"]]
           uploaded$samples.csv <- GEO[["samples"]]
-          GEO <- NULL
+          dbg("-----------------MNT4: dim(uploaded$samples.csv) = ", dim(uploaded$samples.csv))
+          #GEO <- NULL
         }
         
         if (!is.null(uploaded$counts.csv)) {
diff --git a/components/board.upload/R/upload_module_preview_samples.R b/components/board.upload/R/upload_module_preview_samples.R
index b60156bf7..c61ae756d 100644
--- a/components/board.upload/R/upload_module_preview_samples.R
+++ b/components/board.upload/R/upload_module_preview_samples.R
@@ -21,15 +21,31 @@ upload_table_preview_samples_server <- function(
     title,
     info.text,
     caption,
-    upload_datatype) {
+    upload_datatype,
+    public_dataset_id
+    ) {
 
   moduleServer(id, function(input, output, session) {
 
     ns <- session$ns
 
+    public_metadata_full <- shiny::reactiveVal(NULL)
+    shiny::observe({
+      if (public_dataset_id() != "" && !is.null(uploaded$samples.csv)) {
+        orig_sample_matrix(uploaded$samples.csv)
+        if (is.null(public_metadata_full())) {
+          public_metadata_full(orig_sample_matrix())
+        }
+      }
+    })
+
     table_data <- shiny::reactive({
       shiny::req(!is.null(uploaded$samples.csv))
-      dt <- orig_sample_matrix()
+      dt <- if (public_dataset_id() != "" && !is.null(public_metadata_full())) {
+        public_metadata_full()
+      } else {
+        orig_sample_matrix()
+      }      
       nrow0 <- nrow(dt)
       ncol0 <- ncol(dt)
       MAXSHOW <- 100
@@ -50,25 +66,43 @@ upload_table_preview_samples_server <- function(
       dt <- dt[, vars_selected, drop = FALSE]
       uploaded$samples.csv <- dt
       loaded_samples(TRUE)
-      dt
+      return(dt)
     })
 
     shiny::observeEvent(input$vars_selected, {
-      if (all(input$vars_selected %in% colnames(orig_sample_matrix()))) {
+      dt_cols <- if (public_dataset_id() != "" && !is.null(public_metadata_full())) {
+        colnames(public_metadata_full())
+      } else {
+        colnames(orig_sample_matrix())
+      }
+      if (all(input$vars_selected %in% dt_cols)) {
         vars_selected(input$vars_selected)
       }
     })
-
-    shiny::observeEvent(orig_sample_matrix(), {
-      vars_selected(colnames(orig_sample_matrix()))
+   
+    shiny::observe({
+      cols <- if (public_dataset_id() != "" && !is.null(public_metadata_full())) {
+        colnames(public_metadata_full())
+      } else {
+        colnames(orig_sample_matrix())
+      }
+      current_selected <- vars_selected()
+      if (is.null(current_selected) || length(current_selected) == 0 || !all(current_selected %in% cols)) {
+        vars_selected(cols)
+      }
     })
 
     output$col_sel <- renderUI({
+      choices <- if (public_dataset_id() != "" && !is.null(public_metadata_full())) {
+        colnames(public_metadata_full())
+      } else {
+        colnames(orig_sample_matrix())
+      }
       shiny::checkboxGroupInput(
         ns("vars_selected"),
         label = "Retain variable:",
-        choices = colnames(orig_sample_matrix()),
-        selected = colnames(orig_sample_matrix()),
+        choices = choices,
+        selected = vars_selected(),
         inline = TRUE
       )
     })
@@ -125,7 +159,7 @@ upload_table_preview_samples_server <- function(
 
       div(
         bslib::as_fill_carrier(),
-        if (!loaded_samples()) {
+        if (!loaded_samples() && public_dataset_id() == "") {
           bslib::layout_columns(
             col_widths = c(-3, 6, -3),
             row_heights = list("auto", 8, 1, 2),
diff --git a/components/board.upload/R/upload_server.R b/components/board.upload/R/upload_server.R
index cb85df052..a24f080a3 100644
--- a/components/board.upload/R/upload_server.R
+++ b/components/board.upload/R/upload_server.R
@@ -394,6 +394,7 @@ UploadBoard <- function(id,
       {
         ## get uploaded counts
         df0 <- uploaded$samples.csv
+
         if (is.null(df0)) { return(list(status = "Missing samples.csv", matrix = NULL)) }
 
         ## Single matrix counts check
@@ -1210,7 +1211,8 @@ UploadBoard <- function(id,
       title = "Uploaded Samples",
       info.text = "This is the uploaded samples data.",
       caption = "This is the uploaded samples data.",
-      upload_datatype = upload_datatype
+      upload_datatype = upload_datatype,
+      public_dataset_id = public_dataset_id ## accession ID
     )
 
     modified_ct <- upload_table_preview_contrasts_server(

From 56e5b86e26b3a90792751b46961c2421439288b8 Mon Sep 17 00:00:00 2001
From: zitoa <zito.a@hotmail.com>
Date: Tue, 19 Aug 2025 16:54:58 +0200
Subject: [PATCH 12/23] polishing

---
 components/board.upload/R/upload_module_preview_counts.R | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/components/board.upload/R/upload_module_preview_counts.R b/components/board.upload/R/upload_module_preview_counts.R
index 703e55375..3548f34c3 100644
--- a/components/board.upload/R/upload_module_preview_counts.R
+++ b/components/board.upload/R/upload_module_preview_counts.R
@@ -199,12 +199,8 @@ upload_table_preview_counts_server <- function(
             shinyalert::shinyalert(text = msg, type = "success", timer = 4000)            
             GEO_alert_shown(TRUE)
           }
-          dbg("-----------------MNT1: source = ", GEO[["source"]])
-          dbg("-----------------MNT2: dim(samples) = ", dim(GEO[["samples"]]))
-          dbg("-----------------MNT3: colnames(samples) = ", colnames(GEO[["samples"]]))
           uploaded$counts.csv <- GEO[["counts"]]
           uploaded$samples.csv <- GEO[["samples"]]
-          dbg("-----------------MNT4: dim(uploaded$samples.csv) = ", dim(uploaded$samples.csv))
           #GEO <- NULL
         }
         

From 47f3a804db0c358995008e4024a0be25d893ea6a Mon Sep 17 00:00:00 2001
From: zitoa <zito.a@hotmail.com>
Date: Tue, 19 Aug 2025 17:09:24 +0200
Subject: [PATCH 13/23] polishing and set GEO NULL

---
 components/board.upload/R/upload_module_preview_counts.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/components/board.upload/R/upload_module_preview_counts.R b/components/board.upload/R/upload_module_preview_counts.R
index 3548f34c3..95680ad2a 100644
--- a/components/board.upload/R/upload_module_preview_counts.R
+++ b/components/board.upload/R/upload_module_preview_counts.R
@@ -201,7 +201,8 @@ upload_table_preview_counts_server <- function(
           }
           uploaded$counts.csv <- GEO[["counts"]]
           uploaded$samples.csv <- GEO[["samples"]]
-          #GEO <- NULL
+          cm <- intersect(colnames(GEO[["counts"]]), rownames(GEO[["samples"]]))
+          GEO <- NULL
         }
         
         if (!is.null(uploaded$counts.csv)) {

From ca65631daaa4e7731bb1fb5ce8f6373431fb4a2a Mon Sep 17 00:00:00 2001
From: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: Wed, 20 Aug 2025 15:57:55 +0200
Subject: [PATCH 14/23] remove unneded alerts

---
 components/board.upload/R/upload_module_preview_counts.R | 2 --
 1 file changed, 2 deletions(-)

diff --git a/components/board.upload/R/upload_module_preview_counts.R b/components/board.upload/R/upload_module_preview_counts.R
index 95680ad2a..8c714db7e 100644
--- a/components/board.upload/R/upload_module_preview_counts.R
+++ b/components/board.upload/R/upload_module_preview_counts.R
@@ -188,7 +188,6 @@ upload_table_preview_counts_server <- function(
             div(id = "custom-progress-container",
               div(id = "custom-progress-bar"))),
           footer = NULL, fade = FALSE))
-        progress <- shiny::Progress$new(session, min = 0, max = 100)          
         GEO <- tryCatch({ playbase::pgx.getGEOseries(accession = ID, archs.h5 = NULL, get.info = FALSE)},
           error = function(w) { NULL })
         removeModal()
@@ -196,7 +195,6 @@ upload_table_preview_counts_server <- function(
         if (!is.null(GEO)) {
           if (!GEO_alert_shown()) {
             msg <- paste0("Success! ", ID, " found in ", GEO[["source"]], ".\nWe're preparing it...")
-            shinyalert::shinyalert(text = msg, type = "success", timer = 4000)            
             GEO_alert_shown(TRUE)
           }
           uploaded$counts.csv <- GEO[["counts"]]

From 63ec8a811aa6a6a4dd4422abb517da86849022ea Mon Sep 17 00:00:00 2001
From: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: Wed, 20 Aug 2025 15:58:28 +0200
Subject: [PATCH 15/23] remove inserted html/move style to scss

---
 .../R/upload_module_preview_counts.R          | 60 -------------------
 scss/components/_progress.scss                | 43 +++++++++++++
 2 files changed, 43 insertions(+), 60 deletions(-)

diff --git a/components/board.upload/R/upload_module_preview_counts.R b/components/board.upload/R/upload_module_preview_counts.R
index 8c714db7e..8438fdd6a 100644
--- a/components/board.upload/R/upload_module_preview_counts.R
+++ b/components/board.upload/R/upload_module_preview_counts.R
@@ -37,66 +37,6 @@ upload_table_preview_counts_server <- function(
 
     GEO_alert_shown <- reactiveVal(FALSE)
 
-    shiny::insertUI(
-      selector = "head",
-      where = "beforeEnd",
-      ui = list(
-        tags$style(HTML("
-        #custom-progress-modal {
-          position: fixed;
-          top: 50% !important;
-          left: 50% !important;
-          transform: translate(-50%, -50%);
-          background-color: #ffffff;
-          color: black;
-          padding: 30px 50px;
-          font-size: 20px;
-          font-weight: bold;
-          border-radius: 10px;
-          z-index: 1050;
-          text-align: center;
-        }
-        #custom-progress-bar {
-          height: 15px;
-          background-color: #007bff;
-          width: 40%;
-          transition: width 0.3s ease;
-          color: white;
-          font-weight: bold;
-          line-height: 25px;
-          animation: pulse-blue 2s infinite;
-          transform-origin: center;
-        }
-       @keyframes pulse-blue {
-          0% { box-shadow: 0 0 8px 2px #007bff;
-            transform: scale(1.2); }
-          50% { box-shadow: 0 0 18px 8px #3399ff;
-            transform: scale(1.4); }
-          100% { box-shadow: 0 0 8px 2px #007bff;
-            transform: scale(1); }
-       }
-        #custom-progress-container {
-          width: 100%;
-          background-color: #e9ecef;
-          border-radius: 0.25rem;
-          overflow: hidden;
-          margin-top: 15px;
-        }
-        .shiny-notification{ display: none !important; }
-      ")),
-      tags$script(HTML("
-          Shiny.addCustomMessageHandler('updateProgressBar', function(message) {
-            var val = message.value;
-            var pb = document.getElementById('custom-progress-bar');
-            if(pb) {
-              pb.style.width = val + '%';
-              pb.textContent = val + '%';
-            }
-          });
-        "))
-      )
-    )
-    
     table_data <- shiny::reactive({
       shiny::req(!is.null(uploaded$counts.csv))
       dt <- uploaded$counts.csv
diff --git a/scss/components/_progress.scss b/scss/components/_progress.scss
index f0b9ae0f1..49f1ca82a 100644
--- a/scss/components/_progress.scss
+++ b/scss/components/_progress.scss
@@ -34,4 +34,47 @@ html {
     display: block;
   }
 
+  #custom-progress-modal {
+    position: fixed;
+    top: 50% !important;
+    left: 50% !important;
+    transform: translate(-50%, -50%);
+    background-color: #ffffff;
+    color: black;
+    padding: 30px 50px;
+    font-size: 20px;
+    font-weight: bold;
+    border-radius: 10px;
+    z-index: 1050;
+    text-align: center;
+  }
+
+  #custom-progress-bar {
+    height: 15px;
+    background-color: #007bff;
+    width: 40%;
+    transition: width 0.3s ease;
+    color: white;
+    font-weight: bold;
+    line-height: 25px;
+    animation: pulse-blue 2s infinite;
+    transform-origin: center;
+  }
+
+  @keyframes pulse-blue {
+     0% { box-shadow: 0 0 8px 2px #007bff;
+       transform: scale(1.2); }
+     50% { box-shadow: 0 0 18px 8px #3399ff;
+       transform: scale(1.4); }
+     100% { box-shadow: 0 0 8px 2px #007bff;
+       transform: scale(1); }
+  }
+
+  #custom-progress-container {
+    width: 100%;
+    background-color: #e9ecef;
+    border-radius: 0.25rem;
+    overflow: hidden;
+    margin-top: 15px;
+  }
 }
\ No newline at end of file

From 6fa743d63caff1bcf01994aa6698566aa46fce93 Mon Sep 17 00:00:00 2001
From: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: Wed, 20 Aug 2025 15:58:41 +0200
Subject: [PATCH 16/23] open sidebar on data upload

---
 components/modules/WelcomeBoard.R | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/components/modules/WelcomeBoard.R b/components/modules/WelcomeBoard.R
index 7dd56ee9d..cd8d8ba48 100644
--- a/components/modules/WelcomeBoard.R
+++ b/components/modules/WelcomeBoard.R
@@ -169,6 +169,8 @@ WelcomeBoard <- function(id, auth, load_example, new_upload) {
         input$btn_upload_new
       },
       {
+        bigdash.openSettings(lock = TRUE)
+        bigdash.openSidebar()
         bigdash.selectTab(session, selected = "upload-tab")
       }
     )

From 2f041104b9c70dede6584f9710e57e4c911bc110 Mon Sep 17 00:00:00 2001
From: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: Wed, 20 Aug 2025 16:02:29 +0200
Subject: [PATCH 17/23] handle public data selectors

---
 components/board.upload/R/upload_server.R | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/components/board.upload/R/upload_server.R b/components/board.upload/R/upload_server.R
index a24f080a3..0be5ab003 100644
--- a/components/board.upload/R/upload_server.R
+++ b/components/board.upload/R/upload_server.R
@@ -104,6 +104,7 @@ UploadBoard <- function(id,
       names(all_species) <- paste0(all_species," (",common_name,")")
       names(all_species)[all_species=="No organism"] <- "<custom organism>"
       shiny::updateSelectizeInput(session, "selected_organism", choices = all_species, server = TRUE)
+      shiny::updateSelectizeInput(session, "selected_organism_public", choices = all_species, server = TRUE)
     })
 
     is.olink <- shiny::reactive({
@@ -722,6 +723,16 @@ UploadBoard <- function(id,
       upload_organism(input$selected_organism)
     })
 
+    observeEvent(input$selected_datatype_public, {
+      upload_datatype(input$selected_datatype_public)
+      updateSelectInput(session, "selected_datatype", selected = input$selected_datatype_public)
+    })
+
+    observeEvent(input$selected_organism_public, {
+      upload_organism(input$selected_organism_public)
+      updateSelectInput(session, "selected_organism", selected = input$selected_organism_public)
+    })
+
     observeEvent(input$dataset_identifier, {
       public_dataset_id(input$dataset_identifier)
     })

From 357edde4820d61483012f5f632ee47b7fa0b2193 Mon Sep 17 00:00:00 2001
From: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: Wed, 20 Aug 2025 16:02:34 +0200
Subject: [PATCH 18/23] reshufle public data upload UI

---
 components/board.upload/R/upload_ui.R | 218 +++++++++++++-------------
 1 file changed, 105 insertions(+), 113 deletions(-)

diff --git a/components/board.upload/R/upload_ui.R b/components/board.upload/R/upload_ui.R
index 608bd3b91..fcb0fc3c5 100644
--- a/components/board.upload/R/upload_ui.R
+++ b/components/board.upload/R/upload_ui.R
@@ -12,121 +12,115 @@ UploadUI <- function(id) {
     bslib::layout_columns(
       fill = TRUE,
       div(
-        style = "display: flex; flex-direction: column; align-items: flex-start; gap: 20px; margin-bottom: 150px; margin-top: 250px;",
-
-        div(
-          style = "display: flex; flex-direction: row; align-items: center; gap: 20px;",
-          shiny::conditionalPanel(
-            condition = sprintf("input['%s'] == 0 && input['%s'] == 0", ns("public_data_opts"), ns("show_upload_opts")),
-            shiny::actionButton(ns("show_upload_opts"), "Upload your data", class = "btn-primary upload-btn-large"),
-            shiny::actionButton(ns("public_data_opts"), "Retrieve public data", class = "btn-primary upload-btn-large")
-          )
-        ),
-        br(),
-
-        tags$style(HTML("
-          .upload-btn-large {
-            font-size: 1.6em;
-            padding: 20px 45px;
-            min-width: 260px;
-            border-radius: 8px;
-            margin-left: 20vw;
-            display: block;
-            box-shadow: 0 2px 16px rgba(0,0,0,0.13);
-          }
-          .upload-btn-wrapper {
-            width: 100%;
-            display: flex;
-            justify-content: flex-start;
-            margin: 60px 5vw 0 0;
-          }
-        ")),
-
-        shiny::conditionalPanel(
-          condition = sprintf("input['%s'] > 0", ns("show_upload_opts")),
-          div(
-            style = "display: flex; flex-direction: column; align-items: center; gap: 20px; margin-bottom: 150px; margin-top: 120px;",
-            div(
-              style = "width: 60%;",
-              bs_alert("To upload your own data, you should prepare at least two CSV files: an <b>counts.csv</b> file (containing your experiment data) and a <b>samples.csv</b> file (containing your sample information). A third <b>contrasts.csv</b> file (describing your comparisons) is optional. Read more about data preparation <a href='https://omicsplayground.readthedocs.io/en/latest/dataprep/dataprep/'><u>here</u></a>.",
-                closable = FALSE, translate = TRUE, html = TRUE)
-            ),
-            br(),
-
-            div(
-              p("Data type:", style = "text-align: left; margin: 0 0 2px 0; font-weight: bold;"),
-              shiny::selectInput(
-                ns("selected_datatype"), NULL,
-                choices = c("RNA-seq", "mRNA microarray", "proteomics", "scRNA-seq",
-                  "metabolomics (beta)" = "metabolomics", "multi-omics (beta)" = "multi-omics"),
-                selected = DEFAULTS$datatype, width = "400px"
-              )
-            ),
-
-            shiny::conditionalPanel(
-              condition = sprintf("input['%s'] == 'proteomics'", ns("selected_datatype")),
-              div(style = "width: 22%;",
-                shiny::selectInput(ns("proteomics_type"),
-                  label = tags$b("Proteomics type:"), choices = c("MS", "Olink NPX"),
-                  selected = "MS", width = "150px")
-              )
-            ),
-            
-            div(
-              p("Organism:", style = "text-align: left; margin: 0 0 2px 0; font-weight: bold;"),
-              shiny::selectInput(
-                inputId = ns("selected_organism"), label = NULL,
-                choices = NULL, multiple = FALSE, width = "400px"
-              )
-            ),
-            br(),
-
-            shiny::actionButton(ns("start_upload"), "Start upload", class = "btn-primary"),
-            br()
-          )
-        ),
-        
-        shiny::conditionalPanel(
-          condition = sprintf("input['%s'] > 0", ns("public_data_opts")),
-          div(
-            style = "display: flex; flex-direction: column; align-items: center; gap: 20px; margin-bottom: 150px; margin-top: 120px;",
-            div(
-              style = "width: 60%;",
-              bs_alert("The 'Retrieve public data' functionality in OPG allows to query large repositories of publically available data to retrieve a specific dataset. You will need the dataset's unique identifier, such as the GEO ID. At the moment, GEO, ReCount, and ArrayExpress repositories are queried.",
-                closable = FALSE, translate = TRUE, html = TRUE)
-            ),
-            br(),
-
-            div(
-              p("Data type:", style = "text-align: left; margin: 0 0 2px 0; font-weight: bold;"),
-              shiny::selectInput(
-                ns("selected_datatype"), NULL,
-                choices = c("RNA-seq", "mRNA microarray"),
-                selected = "RNA-seq", width = "400px"
-              )
-            ),
-
+        style = "margin-top: 40px;",
+        tabsetPanel(
+          id = ns("upload_tabs"),
+          type = "tabs",
+          # Upload your own data tab
+          tabPanel(
+            "Upload your data",
+            value = "upload",
             div(
-              p("Organism:", style = "text-align: left; margin: 0 0 2px 0; font-weight: bold;"),
-              shiny::selectInput(
-                inputId = ns("selected_organism"), label = NULL,
-                choices = playbase::SPECIES_TABLE$species_name, multiple = FALSE, width = "400px"
-              )
-            ),
-
-            br(),
+              style = "display: flex; flex-direction: column; align-items: center; gap: 20px; margin-bottom: 150px; margin-top: 40px;",
+              div(
+                style = "width: 60%;",
+                bs_alert("To upload your own data, you should prepare at least two CSV files: an <b>counts.csv</b> file (containing your experiment data) and a <b>samples.csv</b> file (containing your sample information). A third <b>contrasts.csv</b> file (describing your comparisons) is optional. Read more about data preparation <a href='https://omicsplayground.readthedocs.io/en/latest/dataprep/dataprep/'><u>here</u></a>.", closable = FALSE, translate = TRUE, html = TRUE)
+              ),
+              br(),
+              div(
+                p("Data type:", style = "text-align: left; margin: 0 0 2px 0; font-weight: bold;"),
+                shiny::selectInput(
+                  ns("selected_datatype"), NULL,
+                  choices = c(
+                    "RNA-seq",
+                    "mRNA microarray",
+                    "proteomics",
+                    "scRNA-seq",
+                    "metabolomics (beta)" = "metabolomics",
+                    "multi-omics (beta)" = "multi-omics"
+                  ),
+                  selected = DEFAULTS$datatype,
+                  width = "400px"
+                ),
+                shiny::uiOutput(ns("proteomics_subtype_ui"))
+              ),
+              div(
+                p("Organism:", style = "text-align: left; margin: 0 0 2px 0; font-weight: bold;"),
+                shiny::selectInput(
+                  inputId = ns("selected_organism"),
+                  label = NULL,
+                  choices = NULL,
+                  multiple = FALSE,
+                  width = "400px"
+                )
+              ),
+              br(),
+              shiny::actionButton(
+                ns("start_upload"),
+                "Start upload",
+                class = "btn-primary"
+              ),
+              br()
+            )
+          ),
+          
+          # Retrieve public datasets tab
+          tabPanel(
+            "Retrieve public datasets",
+            value = "public",
             div(
-              p("Dataset identifier:", style = "text-align: left; margin: 0 0 2px 0; font-weight: bold;"),
-              shiny::textInput(ns("dataset_identifier"), label = NULL, width = "400px")
-            ),
-
-            br(),
-            shiny::actionButton(ns("start_search"), "Start search & download", class = "btn-primary"),
-            br()
+              style = "display: flex; flex-direction: column; align-items: center; gap: 20px; margin-bottom: 150px; margin-top: 40px;",
+              div(
+                style = "width: 60%;",
+                bs_alert("The 'Retrieve public data' functionality in OPG allows to query large repositories of publically available data to retrieve a specific dataset. You will need the dataset's unique identifier, such as the GEO ID. At the moment, <a href='https://www.ncbi.nlm.nih.gov/geo/' target='_blank'><u>GEO</u></a>, <a href='https://jhubiostatistics.shinyapps.io/recount3-study-explorer/' target='_blank'><u>recount3</u></a>, and <a href='https://www.ebi.ac.uk/biostudies/arrayexpress' target='_blank'><u>ArrayExpress</u></a> repositories are queried.", closable = FALSE, translate = TRUE, html = TRUE)
+              ),
+              br(),
+              div(
+                p("Data type:", style = "text-align: left; margin: 0 0 2px 0; font-weight: bold;"),
+                shiny::selectInput(
+                  ns("selected_datatype_public"), NULL,
+                  choices = c(
+                    "RNA-seq",
+                    "mRNA microarray"
+                  ),
+                  selected = "RNA-seq",
+                  width = "400px"
+                )
+              ),
+              div(
+                p("Organism:", style = "text-align: left; margin: 0 0 2px 0; font-weight: bold;"),
+                shiny::selectInput(
+                  inputId = ns("selected_organism_public"),
+                  label = NULL,
+                  choices = NULL,
+                  multiple = FALSE,
+                  width = "400px"
+                )
+              ),
+              div(
+                p("Dataset identifier:", style = "text-align: left; margin: 0 0 2px 0; font-weight: bold;"),
+                shiny::textInput(
+                  ns("dataset_identifier"),
+                  label = NULL,
+                  placeholder = "e.g., GSE12345, E-GEOD-12345",
+                  width = "400px"
+                ),
+                div(
+                  style = "font-size: 0.85em; color: #666; margin-top: 5px;",
+                  "Supported: GEO (GSE), ArrayExpress (E-), recount3 datasets"
+                )
+              ),
+              br(),
+              shiny::actionButton(
+                ns("start_search"),
+                "Retrieve dataset",
+                class = "btn-primary"
+              ),
+              br()
+            )
           )
-        ),
-
         )
+      )
     )
   )
 
@@ -135,7 +129,5 @@ UploadUI <- function(id) {
     uiOutput(ns("upload_wizard")),
     body
   )
-
   return(ui)
-
 }

From 3810d0fdc6185351d8925352296b9158acd812c4 Mon Sep 17 00:00:00 2001
From: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: Thu, 11 Sep 2025 16:39:07 +0200
Subject: [PATCH 19/23] fix: maintain orig sample matrix for public data

---
 .../R/upload_module_preview_samples.R         | 30 ++++---------------
 1 file changed, 5 insertions(+), 25 deletions(-)

diff --git a/components/board.upload/R/upload_module_preview_samples.R b/components/board.upload/R/upload_module_preview_samples.R
index c61ae756d..09d4e5d9f 100644
--- a/components/board.upload/R/upload_module_preview_samples.R
+++ b/components/board.upload/R/upload_module_preview_samples.R
@@ -29,23 +29,15 @@ upload_table_preview_samples_server <- function(
 
     ns <- session$ns
 
-    public_metadata_full <- shiny::reactiveVal(NULL)
     shiny::observe({
-      if (public_dataset_id() != "" && !is.null(uploaded$samples.csv)) {
+      if (is.null(orig_sample_matrix()) && !is.null(uploaded$samples.csv)) {
         orig_sample_matrix(uploaded$samples.csv)
-        if (is.null(public_metadata_full())) {
-          public_metadata_full(orig_sample_matrix())
-        }
       }
     })
 
     table_data <- shiny::reactive({
       shiny::req(!is.null(uploaded$samples.csv))
-      dt <- if (public_dataset_id() != "" && !is.null(public_metadata_full())) {
-        public_metadata_full()
-      } else {
-        orig_sample_matrix()
-      }      
+      dt <- orig_sample_matrix()
       nrow0 <- nrow(dt)
       ncol0 <- ncol(dt)
       MAXSHOW <- 100
@@ -70,22 +62,14 @@ upload_table_preview_samples_server <- function(
     })
 
     shiny::observeEvent(input$vars_selected, {
-      dt_cols <- if (public_dataset_id() != "" && !is.null(public_metadata_full())) {
-        colnames(public_metadata_full())
-      } else {
-        colnames(orig_sample_matrix())
-      }
+      dt_cols <- colnames(orig_sample_matrix())
       if (all(input$vars_selected %in% dt_cols)) {
         vars_selected(input$vars_selected)
       }
     })
    
     shiny::observe({
-      cols <- if (public_dataset_id() != "" && !is.null(public_metadata_full())) {
-        colnames(public_metadata_full())
-      } else {
-        colnames(orig_sample_matrix())
-      }
+      cols <- colnames(orig_sample_matrix())
       current_selected <- vars_selected()
       if (is.null(current_selected) || length(current_selected) == 0 || !all(current_selected %in% cols)) {
         vars_selected(cols)
@@ -93,11 +77,7 @@ upload_table_preview_samples_server <- function(
     })
 
     output$col_sel <- renderUI({
-      choices <- if (public_dataset_id() != "" && !is.null(public_metadata_full())) {
-        colnames(public_metadata_full())
-      } else {
-        colnames(orig_sample_matrix())
-      }
+      choices <- colnames(orig_sample_matrix())
       shiny::checkboxGroupInput(
         ns("vars_selected"),
         label = "Retain variable:",

From 40552534d83bd0c6db0fc69a56f40271ed2f74ae Mon Sep 17 00:00:00 2001
From: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: Thu, 2 Oct 2025 14:21:19 +0200
Subject: [PATCH 20/23] fix merge

---
 .../R/upload_module_preview_counts.R          | 88 +------------------
 1 file changed, 1 insertion(+), 87 deletions(-)

diff --git a/components/board.upload/R/upload_module_preview_counts.R b/components/board.upload/R/upload_module_preview_counts.R
index 9dde1b975..78b0a1cba 100644
--- a/components/board.upload/R/upload_module_preview_counts.R
+++ b/components/board.upload/R/upload_module_preview_counts.R
@@ -141,92 +141,7 @@ upload_table_preview_counts_server <- function(
           cm <- intersect(colnames(GEO[["counts"]]), rownames(GEO[["samples"]]))
           GEO <- NULL
         }
-      div(
-        bslib::as_fill_carrier(),
-        style = "width: 100%; display: flex; ",
-        if (is.null(uploaded$counts.csv)) {
-          if (upload_datatype() == "proteomics") {
-            msg <- "The counts file (counts.csv) contains the gene counts for all samples. For proteomics data types other than Olink NPX, the file should be a tabular text file (.csv), where each row corresponds to a feature (i.e. genes) and each column corresponds to a sample. For Olink NPX, the uploaded file needs to be the standard Olink format."
-          } else {
-            msg <- "The counts file (counts.csv) contains the gene counts for all samples. The file should be a tabular text file (.csv), where each row corresponds to a feature (i.e. genes) and each column corresponds to a sample."
-          }
-          bslib::layout_columns(
-            col_widths = c(-3, 6, -3),
-            row_heights = list("auto", 8, 1, 2),
-            gap = "0.5rem",
-            bslib::as_fill_carrier(bs_alert(tspan(msg), closable = FALSE, translate_js = FALSE)),
-            bslib::card(
-              if (upload_datatype() == "multi-omics") {
-                shiny::radioButtons(
-                  ns("data_source"),
-                  label = "Select input files from:",
-                  choices = c("multi-csv", "pgx", "single-csv"),
-                  selected = "multi-csv",
-                  inline = TRUE
-                )
-              },
-              if (upload_datatype() == "multi-omics") {
-                shiny::conditionalPanel(
-                  condition = sprintf("input['%s'] == 'pgx'", ns("data_source")),
-                  div(
-                    div(
-                      style = "margin-bottom: 15px;",
-                      shiny::radioButtons(
-                        ns("data_processing"),
-                        label = "Select data processing level:",
-                        choices = c("Raw" = "raw", "Normalized (also batch corrected if selected on computation)" = "normalized"),
-                        selected = "raw",
-                        inline = TRUE
-                      )
-                    ),
-                    div(
-                      style = "display: flex; align-items: center; gap: 10px; margin-bottom: 10px;",
-                      span("Selected:", style = "font-weight: bold;"),
-                      textOutput(ns("selected_rows_text")),
-                    ),
-                    div(
-                      style = "height: 350px; overflow-y: auto;",
-                      DT::DTOutput(ns("available_data_table"))
-                    ),
-                    style = "width: 100%; max-height: 400px; overflow-y: auto;"
-                  ),
-                  selection = "multiple",
-                  options = list(pageLength = 5, dom = "tp", scrollY = TRUE)
-                )
-              },
-              if (upload_datatype() == "multi-omics") {
-                shiny::conditionalPanel(
-                  condition = sprintf("input['%s'] == 'multi-csv'", ns("data_source")),
-                  shiny::uiOutput(ns("dynamic_file_inputs")) # ,
-                )
-              },
-              if (upload_datatype() == "multi-omics") {
-                shiny::conditionalPanel(
-                  condition = sprintf("input['%s'] == 'single-csv'", ns("data_source")),
-                  fileInputArea(
-                    ns("counts_csv"),
-                    shiny::h4(tspan("Upload counts.csv", js = FALSE), class = "mb-0"),
-                    multiple = FALSE,
-                    accept = c(".csv"),
-                    width = "100%"
-                  )
-                )
-              },
-              if (upload_datatype() != "multi-omics") {
-                fileInputArea(
-                  ns("counts_csv"),
-                  shiny::h4(tspan("Upload counts.csv", js = FALSE), class = "mb-0"),
-                  multiple = FALSE,
-                  accept = c(".csv"),
-                  width = "100%"
-                )
-              },
-              style = "background-color: aliceblue; border: 0.07rem dashed steelblue;"
-            ),
-            action_buttons,
-            br()
-          )
-        },
+        
         if (!is.null(uploaded$counts.csv)) {
           bslib::layout_columns(
             col_widths = 12,
@@ -255,7 +170,6 @@ upload_table_preview_counts_server <- function(
         }
 
       } else {
-
         div(
           bslib::as_fill_carrier(),
           style = "width: 100%; display: flex; ",

From beae8ca6db641099b07e164d5b7171c987dee31b Mon Sep 17 00:00:00 2001
From: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: Thu, 2 Oct 2025 14:27:37 +0200
Subject: [PATCH 21/23] fix merge2

---
 components/board.upload/R/upload_server.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/components/board.upload/R/upload_server.R b/components/board.upload/R/upload_server.R
index 1614339ab..227fcfecd 100644
--- a/components/board.upload/R/upload_server.R
+++ b/components/board.upload/R/upload_server.R
@@ -109,6 +109,7 @@ UploadBoard <- function(id,
       } else {
         shiny::updateSelectizeInput(session, "selected_datatype", choices = c("RNA-seq", "mRNA microarray", "proteomics", "scRNA-seq", "metabolomics (beta)" = "metabolomics"), selected = DEFAULTS$datatype)
       }
+    })
 
     output$proteomics_subtype_ui <- shiny::renderUI({
       if (upload_datatype() == "proteomics") {
@@ -329,7 +330,7 @@ UploadBoard <- function(id,
 
         return(list(res = res, olink = olink))
       }
-    )
+    })
 
     checked_counts <- shiny::eventReactive(
       {

From 6245f412d24623b64980122a2373569f3be402c0 Mon Sep 17 00:00:00 2001
From: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: Fri, 3 Oct 2025 11:51:59 +0200
Subject: [PATCH 22/23] fix: move return line, was missing olink case

---
 components/board.upload/R/upload_server.R | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/components/board.upload/R/upload_server.R b/components/board.upload/R/upload_server.R
index 227fcfecd..08c4f2769 100644
--- a/components/board.upload/R/upload_server.R
+++ b/components/board.upload/R/upload_server.R
@@ -327,9 +327,8 @@ UploadBoard <- function(id,
             checked_for_log(TRUE)
           }
         }
-
-        return(list(res = res, olink = olink))
       }
+      return(list(res = res, olink = olink))
     })
 
     checked_counts <- shiny::eventReactive(

From b71538e07d2dfbab8566b622153a197fd612ad45 Mon Sep 17 00:00:00 2001
From: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: Fri, 3 Oct 2025 11:52:15 +0200
Subject: [PATCH 23/23] fix: update loaded_samples when auto-filling them for
 olink

---
 components/board.upload/R/upload_module_preview_samples.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/components/board.upload/R/upload_module_preview_samples.R b/components/board.upload/R/upload_module_preview_samples.R
index 8c7133b37..1737420b7 100644
--- a/components/board.upload/R/upload_module_preview_samples.R
+++ b/components/board.upload/R/upload_module_preview_samples.R
@@ -31,6 +31,7 @@ upload_table_preview_samples_server <- function(
     shiny::observe({
       if (is.null(orig_sample_matrix()) && !is.null(uploaded$samples.csv)) {
         orig_sample_matrix(uploaded$samples.csv)
+        loaded_samples(TRUE)
       }
     })