Review fix

DESCRIPTION

@@ -1,36 +1,37 @@
 Package: TADAShiny
 Type: Package
-Title: WQP Data Discovery and Cleaning: First R Shiny App in the TADA (Tools for Automated Data Analysis) Series
+Title: Water Quality Portal Data Discovery and Cleaning: First R Shiny App in the TADA (Tools for Automated Data Analysis) Series
 Version: 0.0.0.9000
-Organization: U.S. Environmental Protection Agency
-Authors@R: 
-  c(person(given = "Cristina",
-           family = "Mullin",
-           role = c("aut", "cre"),
-           email = "[email protected]",
-           comment = c(ORCID = "0000-0002-0615-6087")),
-    person(given = "Trip",
-           family = "Hook",
-           role = "aut"),
-    person(given = "Elise",
-           family = "Hinman",
-           role = c("aut"),
-           email = "[email protected]"),
-    person(given = "Hui",
-           family = "Zhou",
-           role = c("aut"),
-           email = "[email protected]"),
-    person(given = "Shelly",
-           family = "Thawley",
-           role = "aut"))
-Description: Assists data partners in retrieving, wrangling, quality checking, and preparing data from the Water Quality Portal for subsequent analyses.
+Authors@R: c(
+  person(given = "U.S. Environmental Protection Agency", role = "aut"),
+  person(given = "Cristina",
+  family = "Mullin",
+  role = c("aut", "cre"),
+  email = "[email protected]",
+  comment = c(ORCID = "0000-0002-0615-6087")),
+  person(given = "Trip",
+  family = "Hook",
+  role = "aut"),
+  person(given = "Elise",
+  family = "Hinman",
+  role = "aut"),
+  person(given = "Hillary",
+  family = "Marler",
+  role = "aut"),
+  person(given = "Shelly",
+  family = "Thawley",
+  role = "aut"),
+  person(given = "Hui",
+  family = "Zhou",
+  role = "aut")
+  )
+Description: Assists data partners in retrieving, wrangling, quality checking, and harmonizing data from the Water Quality Portal for subsequent analyses.
 License: CC0
 Copyright: This software is in the public domain because it contains materials
     that originally came from the U.S. Environmental Protection Agency.
 Imports: 
-    config,
-    golem,
     magrittr,
+    golem,
     htmltools,
     readxl,
     writexl,
@@ -54,6 +55,7 @@ Imports:
 Remotes: 
     github::USEPA/TADA
 Suggests: 
+    config,
     testthat,
     remotes,
     covr,
@@ -73,6 +75,5 @@ 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$job_id = job_id
@@ -44,7 +45,7 @@ app_server <- function(input, output, session) {
   shiny::observeEvent(tadat$new, {
     shiny::showModal(shiny::modalDialog(
       title = "Data Loaded",
-      "Your data were successfully loaded into the app and are displayed on the Overview tab. The following data wrangling steps were performed automatically when data was loaded: 1) created TADA versions of a subset of columns for editing (originals are retained), 2) removed exact duplicates, 3) handled/flagged special characters and text in result values and units, 4) identified detection limit data and copied limit value to result value if blank, 5) harmonized result and depth units to TADA defaults, and 6) replaced retired characteristic names with current names. See summary information about your dataset in the gray box at the bottom of the app."
+      "Your data were successfully loaded into the app and are displayed on the Overview tab. The following data wrangling steps were performed automatically when data was loaded: 1) created TADA versions of a subset of columns for editing (originals are retained), 2) handled/flagged special characters and text in result values and units, 3) harmonized result and depth units to TADA defaults, and 4) replaced retired characteristic names with current names. See summary information about your dataset in the gray box at the bottom of the app."
     ))
     shiny::updateTabsetPanel(session = session, inputId = "tabbar", selected = "Overview")
     tadat$new <- NULL
@@ -57,27 +58,24 @@ app_server <- function(input, output, session) {
     }
   })
 
-  # 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

@@ -37,10 +37,10 @@ mod_TADA_summary_ui <- function(id) {
           "site_clean"
         )))),
         shiny::fluidRow(column(6, shiny::uiOutput(ns(
-          "dwn_all"
+          "dwn_working"
         )))),
         shiny::fluidRow(column(6, shiny::uiOutput(ns(
-          "dwn_ts"
+          "dwn_final"
         ))))#,
         # shiny::fluidRow(column(
         #   6,
@@ -169,16 +169,25 @@ mod_TADA_summary_server <- function(id, tadat) {
     })
 
     # download dataset button - only appears if there data exists in the app already
-    output$dwn_all <- shiny::renderUI({
+    output$dwn_working <- 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_final <- 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()
@@ -197,22 +206,28 @@ 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)
+
+        # Remove all rows flagged for removal
+        dfs <-
+          list(Data = TADA::TADA_OrderCols(tadat$raw[!tadat$raw$TADA.Remove,]), 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(