Review fix

DESCRIPTION

@@ -73,6 +73,6 @@ Config/testthat/load-all: list(export_all = FALSE, helpers = FALSE)
 LazyData: true
 URL: https://github.com/USEPA/TADAShiny
 BugReports: https://github.com/USEPA/TADAShiny/issues
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE)
 VignetteBuilder: knitr, rmarkdown

R/app_server.R

@@ -8,7 +8,7 @@
 # Below increases the max data upload size from the Shiny default of 5MB per file
 # to 30MB for file
 options(shiny.maxRequestSize = 30 * 1024^2)
-
+options(warn = 2)
 app_server <- function(input, output, session) {
   # Your application server logic
   tadat <- shiny::reactiveValues() # create a list object that holds reactive values passed between modules
@@ -35,6 +35,7 @@ app_server <- function(input, output, session) {
   # switch that indicates when a file is being loaded
   tadat$load_progress_file = NA
   tadat$save_progress_file = NA
+  tadat$flags_present = FALSE
   job_id = paste0("ts", format(Sys.time(), "%y%m%d%H%M%S"))
   tadat$default_outfile = paste0("tada_output_", job_id)
   tadat$job_id = job_id
@@ -52,32 +53,34 @@ app_server <- function(input, output, session) {
 
   # update the master 'Remove' column anytime data is added to the 'remove' table
   shiny::observeEvent(tadat$removals, {
+    print("Updating removals column")
+    print(dim(tadat$removals))
+    print(sum(tadat$raw$TADA.Remove))
     if (dim(tadat$removals)[2] > 0) {
+      print("Updating removals column")
       tadat$raw$TADA.Remove <- apply(tadat$removals, 1, any)
     }
+    print(sum(tadat$raw$TADA.Remove))
   })
 
-  # Update the default switches if a progress file is uploaded.
-  shiny::observeEvent(tadat$selected_flags, {
-    switch_defaults = tadat$selected_flags
-    })
-
-
-  # this observes when the user switches tabs and adds the current tab they're on as a column to their dataset.
   shiny::observe({
-    shiny::req(tadat$raw)
+    # JCH - is this necessary?
+    #shiny::req(tadat$raw)
     tadat$raw$TADAShiny.tab <- input$tabbar
     tadat$tab <- input$tabbar
   })
 
+  # JCH - disabling this for now. I think progress files provide this functionality
+  # this observes when the user switches tabs and adds the current tab they're on as a column to their dataset.
+
   # switch to tab user left off on when tadat$reup changes, which only happens when someone uploads a workbook with the column "Removed" in it
-  shiny::observeEvent(tadat$reup, {
-    shiny::showModal(shiny::modalDialog(
-      title = "Data Loaded",
-      "Your working dataset has been uploaded and the app switched to the tab where you left off."
-    ))
-    # the switch tab command
-    shiny::updateTabsetPanel(session = session, inputId = "tabbar", selected = unique(tadat$raw$tab))
-    tadat$reup <- NULL
-  })
+  #shiny::observeEvent(tadat$reup, {
+  #  shiny::showModal(shiny::modalDialog(
+  #    title = "Data Loaded",
+  #    "Your working dataset has been uploaded and the app switched to the tab where you left off."
+  #  ))
+  #  # the switch tab command
+  #  shiny::updateTabsetPanel(session = session, inputId = "tabbar", selected = unique(tadat$raw$tab))
+  #  tadat$reup <- NULL
+  #})
 }

R/mod_TADA_summary.R

@@ -81,6 +81,8 @@ mod_TADA_summary_server <- function(id, tadat) {
     # calculate the stats needed to fill the summary box
     shiny::observe({
       shiny::req(tadat$raw)
+      print("Updating summary stats")
+      print(nrow(tadat$raw))
       summary_things$rem_rec <-
         length(tadat$raw$ResultIdentifier[tadat$raw$TADA.Remove ==
                                             TRUE])
@@ -95,6 +97,7 @@ mod_TADA_summary_server <- function(id, tadat) {
         length(unique(tadat$raw$MonitoringLocationIdentifier[!tadat$raw$MonitoringLocationIdentifier %in%
                                                                clean_sites]))
       summary_things$removals <- sort_removals(tadat$removals)
+      print(nrow(tadat$raw))
     })
     summary_things$removals <- data.frame(matrix(
       ncol = 2,
@@ -118,6 +121,8 @@ mod_TADA_summary_server <- function(id, tadat) {
       if (is.null(tadat$raw)) {
         "Total Results in Dataset: 0"
       } else {
+        print("Updating result count")
+        print(nrow(tadat$raw))
         paste0("Total Results in Dataset: ", scales::comma(length(tadat$raw$ResultIdentifier)))
       }
     })
@@ -171,14 +176,23 @@ mod_TADA_summary_server <- function(id, tadat) {
     # download dataset button - only appears if there data exists in the app already
     output$dwn_all <- shiny::renderUI({
       shiny::req(tadat$raw)
-      shiny::downloadButton(ns("download_all"),
+      shiny::downloadButton(ns("download_working"),
                             "Download Working Dataset (.zip)",
-                            style = "color: #fff; background-color: #337ab7; border-color: #2e6da4")
+                            style = "color: #fff; background-color: #337ab7; border-color: #2e6da4",
+                            contentType = "application/zip")
     })
 
-    output$download_all <- shiny::downloadHandler(
+    output$dwn_ts <- shiny::renderUI({
+      shiny::req(tadat$raw)
+      shiny::downloadButton(ns("download_final"),
+                            "Download Final Dataset (.zip)",
+                            style = "color: #fff; background-color: #337ab7; border-color: #2e6da4",
+                            contentType = "application/zip")
+    })
+
+    output$download_working <- shiny::downloadHandler(
       filename = function() {
-        paste0(tadat$default_outfile, ".zip")
+        paste0(tadat$default_outfile, "_working.zip")
       },
       content = function(fname) {
         fs <- c()
@@ -187,6 +201,7 @@ mod_TADA_summary_server <- function(id, tadat) {
         datafile_name = paste0(tadat$default_outfile, ".xlsx")
         progress_file_name = paste0(tadat$default_outfile, "_prog.RData")
         desc <- writeNarrativeDataFrame(tadat)
+        out_data = TADA::TADA_OrderCols(tadat$raw[tadat$raw])
         dfs <-
           list(Data = TADA::TADA_OrderCols(tadat$raw), Parameterization = desc)
         writeFile(tadat, progress_file_name)
@@ -197,22 +212,26 @@ mod_TADA_summary_server <- function(id, tadat) {
       contentType = "application/zip"
     )
 
-    # # Download TADA progress file
-    # output$dwn_ts = shiny::renderUI({
-    #   shiny::req(tadat$raw)
-    #   shiny::downloadButton(ns("download_ts_file"),
-    #                         "Download Progress File (.Rdata)",
-    #                         style = "color: #fff; background-color: #337ab7; border-color: #2e6da4")
-    # })
-
-    # output$download_ts_file = shiny::downloadHandler(
-    #   filename = function() {
-    #     paste0(tadat$job_id, '.Rdata')
-    #   },
-    #   content = function(file) {
-    #     writeFile(tadat, file)
-    #   }
-    # )
+    output$download_final <- shiny::downloadHandler(
+      filename = function() {
+        paste0(tadat$default_outfile, "_final.zip")
+      },
+      content = function(fname) {
+        fs <- c()
+        tmpdir <- tempdir()
+        setwd(tempdir())
+        datafile_name = paste0(tadat$default_outfile, ".xlsx")
+        progress_file_name = paste0(tadat$default_outfile, "_prog.RData")
+        desc <- writeNarrativeDataFrame(tadat)
+        dfs <-
+          list(Data = TADA::TADA_OrderCols(tadat$raw), Parameterization = desc)
+        writeFile(tadat, progress_file_name)
+        writexl::write_xlsx(dfs, path = datafile_name)
+        utils::zip(zipfile = fname,
+                   files = c(datafile_name, progress_file_name))
+      },
+      contentType = "application/zip"
+    )
 
     shiny::observeEvent(input$disclaimer, {
       shiny::showModal(

R/mod_censored_data.R

@@ -299,7 +299,10 @@ mod_censored_data_server <- function(id, tadat) {
         ) # reset to detection quantitation limit value
       tadat$raw$TADA.ResultMeasureValueDataTypes.Flag[tadat$raw$TADA.ResultMeasureValueDataTypes.Flag == "Result Value/Unit Estimated from Detection Limit"] <-
         "Result Value/Unit Copied from Detection Limit" # reset data types flag to what it was before simpleCensoredMethods function run
+      # print(1234)
+      print(nrow(tadat$raw))
       tadat$raw <- tadat$raw %>% dplyr::select(-TADA.CensoredMethod)
+      print(nrow(tadat$raw))
       tadat$censor_applied = FALSE
     })