#46 Add a csv download for reports

DESCRIPTION

@@ -37,6 +37,7 @@ Imports:
   ggplot2,
   ggplotify,
   gridify,
+  jsonlite,
   junco,
   methods,
   openxlsx,
@@ -49,16 +50,17 @@ Imports:
   teal,
   teal.code,
   teal.modules.clinical,
+  teal.reporter,
   tern,
-  yaml
+  yaml,
+  zip
 Suggests:
   forcats,
   knitr,
   rAccess,
   rmarkdown,
   teal.data,
   teal.modules.general,
-  teal.reporter,
   teal.transform
 VignetteBuilder: knitr
 Config/Needs/website: insightsengineering/nesttemplate

NAMESPACE

@@ -103,4 +103,5 @@ importFrom(teal.code,eval_code)
 importFrom(teal.modules.clinical,add_expr)
 importFrom(teal.modules.clinical,bracket_expr)
 importFrom(tern,rtable2gg)
+importFrom(utils,write.csv)
 importFrom(yaml,as.yaml)

NEWS.md

@@ -6,6 +6,7 @@
 - Fixed ID conflict in `or_filtering_transformator` that caused errors when multiple instances were used in the same Shiny app. Removed a `shinyBS::bsModal()` block with fixed, non-module-scoped IDs (dead code — preview is handled by `shiny::showModal()`), resolving duplicate element IDs across instances.
 - Added `updateOn = "blur"` to all `textInput` controls so that reactive updates are only triggered when the user leaves the field, reducing unnecessary re-renders while typing. Requires `shiny >= 1.11.0`.
 - Refactored `title_footer_decorator` not to overwrite the first row of the TABLE.ID column in the imported file. This change allows for importing files that have meaningful data in the first row.
+- Added a button for CSV download for `tm_report_manager` module. #46
 
 # Version 0.0.3
 

R/ReportManager.R

@@ -484,6 +484,86 @@ ReportManager <- R6::R6Class("ReportManager", # nolint: object_name_linter
       }
     },
 
+    #' Set up CSV download observer
+    #' @description
+    #' Registers the `observeEvent` that handles CSV download clicks.
+    #' Call once from `moduleServer` after initialization.
+    #' @param input Shiny input object from `moduleServer`
+    setup_csv_download = function(input) {
+      shiny::observeEvent(input$csv_download_click, {
+        report_name <- input$csv_download_click
+        tmp_dir <- file.path(tempdir(), paste0("csv_export_", gsub("[^[:alnum:]]", "_", report_name)))
+        written <- tryCatch(
+          self$export_tables_to_csv(report_name, tmp_dir),
+          error = function(e) {
+            shiny::showNotification(
+              sprintf("Error exporting tables: %s", conditionMessage(e)),
+              type = "error"
+            )
+            character(0)
+          }
+        )
+        if (length(written) == 0) {
+          shiny::showNotification("No tables found in this report.", type = "warning")
+          return()
+        }
+        safe_title <- gsub("[^[:alnum:]_-]", "_", report_name)
+        if (length(written) == 1L) {
+          raw_bytes <- readBin(written[[1]], what = "raw", n = file.size(written[[1]]))
+          self$session$sendCustomMessage("trigger_csv_download", list(
+            b64 = jsonlite::base64_enc(raw_bytes),
+            filename = paste0(safe_title, "_tables.csv"),
+            type = "text/csv"
+          ))
+        } else {
+          zip_path <- file.path(tmp_dir, paste0(safe_title, "_tables.zip"))
+          zip::zip(zipfile = zip_path, files = written, mode = "cherry-pick")
+          raw_bytes <- readBin(zip_path, what = "raw", n = file.size(zip_path))
+          self$session$sendCustomMessage("trigger_csv_download", list(
+            b64 = jsonlite::base64_enc(raw_bytes),
+            filename = paste0(safe_title, "_tables.zip"),
+            type = "application/zip"
+          ))
+        }
+      })
+    },
+
+    #' Export all tables from a saved report as CSV files
+    #' @description
+    #' Loads the report from disk, extracts all table-type content from each card,
+    #' converts each to a `data.frame` and writes it as a CSV file in `output_dir`.
+    #' Returns the vector of written file paths, or an empty character vector when
+    #' no tables are found.
+    #' @param report_title (character) Title of the report to export.
+    #' @param output_dir (character) Directory where CSV files will be written.
+    #' @return character vector of written file paths.
+    export_tables_to_csv = function(report_title, output_dir) {
+      report_dir <- self$get_abs_report_path(report_title)
+      if (!file.exists(file.path(report_dir, "Report.json"))) {
+        return(character(0))
+      }
+
+      reporter <- teal.reporter::Reporter$new()
+      report_id <- jsonlite::read_json(file.path(report_dir, "Report.json"))$id
+      reporter$set_id(as.character(report_id))
+      reporter$from_jsondir(report_dir)
+
+      tables <- private$extract_tables_from_reporter(reporter)
+      if (length(tables) == 0) {
+        return(character(0))
+      }
+
+      if (!dir.exists(output_dir)) dir.create(output_dir, recursive = TRUE)
+
+      written <- character(length(tables))
+      for (i in seq_along(tables)) {
+        file_path <- file.path(output_dir, paste0(names(tables)[[i]], ".csv"))
+        utils::write.table(tables[[i]], file = file_path, sep = ",", col.names = FALSE, row.names = FALSE)
+        written[[i]] <- file_path
+      }
+      written
+    },
+
     #' Re-build reports
     #' @description
     #' Rebuild reports to include data that has changed.
@@ -599,6 +679,62 @@ ReportManager <- R6::R6Class("ReportManager", # nolint: object_name_linter
       saveRDS(unname(code_list), file.path(path, "code.rds"))
     },
 
+    #' Extract all table-type content from a Reporter as a named list of data.frames
+    extract_tables_from_reporter = function(reporter) {
+      cards <- reporter$get_cards()
+      result <- list()
+      for (card_i in seq_along(cards)) {
+        card <- cards[[card_i]]
+        card_name <- names(cards)[[card_i]]
+        card_title <- tryCatch(
+          teal.reporter::metadata(card)$title,
+          error = function(e) NULL
+        )
+        if (is.null(card_title) || !nzchar(card_title)) card_title <- card_name
+        if (is.null(card_title) || !nzchar(card_title)) card_title <- paste0("card_", card_i)
+        safe_title <- gsub("[^[:alnum:]_-]", "_", card_title)
+
+        # Collect content elements: ReportCard R6 uses $get_content(), teal_card S3 is a plain list
+        elements <- if (inherits(card, "ReportCard")) card$get_content() else as.list(card)
+
+        tbl_count <- 0L
+        for (elem in elements) {
+          # Unwrap TableBlock (used by ReportCard$append_table)
+          if (inherits(elem, "TableBlock")) {
+            elem <- tryCatch(elem$get_content(), error = function(e) NULL)
+          }
+          df <- NULL
+          if (inherits(elem, c("TableTree", "ElementaryTable"))) {
+            df <- tryCatch(
+              {
+                as.data.frame(
+                  rtables::matrix_form(elem)$strings,
+                  stringsAsFactors = FALSE
+                )
+              },
+              error = function(e) NULL
+            )
+          } else if (inherits(elem, "chunk_output")) {
+            df <- tryCatch(as.data.frame(elem[[1]]), error = function(e) NULL)
+          } else if (inherits(elem, "listing_df") || is.data.frame(elem)) {
+            df <- as.data.frame(elem)
+          }
+          if (!is.null(df)) {
+            tbl_count <- tbl_count + 1L
+            key <- if (tbl_count == 1L) safe_title else paste0(safe_title, "_", tbl_count)
+            # Deduplicate key across all cards using a numeric suffix
+            if (key %in% names(result)) {
+              n <- 2L
+              while (paste0(key, "_", n) %in% names(result)) n <- n + 1L
+              key <- paste0(key, "_", n)
+            }
+            result[[key]] <- df
+          }
+        }
+      }
+      result
+    },
+
     #' Register `onSessionEnded` to unlock report when session is closed
     register_cleanup = function() {
       if (!is.null(self$session)) {

R/tm_report_manager.R

@@ -92,6 +92,17 @@ report_manager_ui <- function(id) {
       var reportName = $(this).data('report');
       Shiny.setInputValue('", ns("release_lock_click"), "', reportName, {priority: 'event'});
     });
+    Shiny.addCustomMessageHandler('trigger_csv_download', function(msg) {
+      var bytes = Uint8Array.from(atob(msg.b64), function(c) { return c.charCodeAt(0); });
+      var blob = new Blob([bytes], {type: msg.type});
+      var url = URL.createObjectURL(blob);
+      var a = document.createElement('a');
+      a.href = url;
+      a.download = msg.filename;
+      document.body.appendChild(a);
+      a.click();
+      setTimeout(function() { document.body.removeChild(a); URL.revokeObjectURL(url); }, 100);
+    });
   ")))
   )
 }
@@ -104,6 +115,7 @@ report_manager_ui <- function(id) {
 #' @import shiny teal
 #' @importFrom DT renderDT
 #' @importFrom shinyjs toggleState disable enable
+#' @importFrom utils write.csv
 #' @keywords internal
 report_manager_server <- function(id, reports_path = "reports", auto_save = TRUE, reporter) {
   moduleServer(id, function(input, output, session) {
@@ -114,6 +126,7 @@ report_manager_server <- function(id, reports_path = "reports", auto_save = TRUE
 
     # Initialize report manager object
     rm <- ReportManager$new(reports_path = reports_path, session)
+    rm$setup_csv_download(input)
     if (auto_save) {
       rm$auto_save_observer(reporter)
     }
@@ -473,6 +486,19 @@ report_manager_server <- function(id, reports_path = "reports", auto_save = TRUE
             lock_icon <- '<i class="fa fa-unlock" style="color: green; margin-right: 8px;" title="Unlocked"></i>'
           }
 
+          # CSV download button (available for all reports that have saved content)
+          report_json <- file.path(rm$get_abs_report_path(report_name), "Report.json")
+          has_content <- file.exists(report_json)
+          csv_btn <- if (has_content) {
+            create_action_button("csv_download_click", report_name, "download", "btn-default", "Download tables as CSV")
+          } else {
+            paste0(
+              '<button type="button" class="btn btn-sm btn-default" ',
+              'disabled title="No content to export" data-toggle="tooltip">',
+              '<i class="fa fa-download"></i></button>'
+            )
+          }
+
           # Action buttons based on state
           if (is_active) {
             # Active report: can edit title, cannot delete, can rebuild
@@ -535,7 +561,7 @@ report_manager_server <- function(id, reports_path = "reports", auto_save = TRUE
           }
 
           # Combine all elements with spacing
-          paste(lock_icon, edit_btn, load_btn, rebuild_btn, delete_btn, sep = " ")
+          paste(lock_icon, edit_btn, load_btn, rebuild_btn, delete_btn, csv_btn, sep = " ")
         }, character(1))
       } else {
         df$actions <- character(0)