Merge pull request #110 from USEPA/fix-epa-style

add css file

R/app_config.R

@@ -1,41 +1,40 @@
-#' 
-#' NOTE: If you manually change your package name in the DESCRIPTION, 
-#' don't forget to change it here too, and in the config file. 
+#'
+#' NOTE: If you manually change your package name in the DESCRIPTION,
+#' don't forget to change it here too, and in the config file.
 #' For a safer name change mechanism, use the `golem::set_golem_name()` function.
-#' 
-#' @param ... character vectors, specifying subdirectory and file(s) 
-#' within your package. The default, none, returns the root of the app. 
-#' 
+#'
+#' @param ... character vectors, specifying subdirectory and file(s)
+#' within your package. The default, none, returns the root of the app.
+#'
 #' @noRd
-app_sys <- function(...){
+app_sys <- function(...) {
   system.file(..., package = "TADAShiny")
 }
 
 
 #' Read App Config
-#' 
-#' @param value Value to retrieve from the config file. 
-#' @param config GOLEM_CONFIG_ACTIVE value. If unset, R_CONFIG_ACTIVE. 
+#'
+#' @param value Value to retrieve from the config file.
+#' @param config GOLEM_CONFIG_ACTIVE value. If unset, R_CONFIG_ACTIVE.
 #' If unset, "default".
 #' @param use_parent Logical, scan the parent directory for config file.
-#' 
+#'
 #' @noRd
 get_golem_config <- function(
-    value, 
+    value,
     config = Sys.getenv(
       "GOLEM_CONFIG_ACTIVE",
       Sys.getenv(
         "R_CONFIG_ACTIVE",
         "default"
       )
-    ), 
-    use_parent = TRUE
-){
+    ),
+    use_parent = TRUE) {
   config::get(
-    value = value, 
-    config = config, 
+    value = value,
+    config = config,
     # Modify this if your config file is somewhere else:
-    file = app_sys("golem-config.yml"), 
+    file = app_sys("golem-config.yml"),
     use_parent = use_parent
   )
 }

R/app_server.R

@@ -7,11 +7,11 @@
 
 # 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(shiny.maxRequestSize = 30 * 1024^2)
 
 app_server <- function(input, output, session) {
   # Your application server logic
-  tadat = shiny::reactiveValues() # create a list object that holds reactive values passed between modules
+  tadat <- shiny::reactiveValues() # create a list object that holds reactive values passed between modules
   mod_filtering_server("filtering_1", tadat)
   mod_query_data_server("query_data_1", tadat) # server call to the module servers with the name of the module and any dependencies (this one uses the tadat reactive values object)
   mod_data_flagging_server("data_flagging_1", tadat)
@@ -22,7 +22,7 @@ app_server <- function(input, output, session) {
   mod_review_data_server("review_data_1", tadat)
   mod_figures_server("figures_1", tadat)
   mod_TADA_summary_server("TADA_summary_1", tadat)
-  
+
   # this ensures all tabs except Upload are disabled upon app start
   shinyjs::disable(selector = '.nav li a[data-value="Overview"]')
   shinyjs::disable(selector = '.nav li a[data-value="Flag"]')
@@ -31,42 +31,40 @@ app_server <- function(input, output, session) {
   shinyjs::disable(selector = '.nav li a[data-value="Harmonize"]')
   shinyjs::disable(selector = '.nav li a[data-value="Figures"]')
   shinyjs::disable(selector = '.nav li a[data-value="Review"]')
-  
+
   # switch to overview tab when tadat$new changes and provide user with window letting them know how many records were automatically flagged for removal upon upload
   # move this to query_data?
-  shiny::observeEvent(tadat$new,{
-      shiny::showModal(shiny::modalDialog(
-        title = "Data Loaded",
-        "Your data were successfully loaded into the app and are displayed on the Overview tab. 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$new = NULL
+  shiny::observeEvent(tadat$new, {
+    shiny::showModal(shiny::modalDialog(
+      title = "Data Loaded",
+      "Your data were successfully loaded into the app and are displayed on the Overview tab. 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$new <- NULL
   })
-  
+
   # update the master 'Remove' column anytime data is added to the 'remove' table
-  shiny::observeEvent(tadat$removals,{
-    if(dim(tadat$removals)[2]>0){
-      tadat$raw$TADA.Remove = apply(tadat$removals, 1, any)
+  shiny::observeEvent(tadat$removals, {
+    if (dim(tadat$removals)[2] > 0) {
+      tadat$raw$TADA.Remove <- apply(tadat$removals, 1, any)
     }
   })
-  
-  # this observes when the user switches tabs and adds the current tab they're on as a column to their dataset. 
+
+  # this observes when the user switches tabs and adds the current tab they're on as a column to their dataset.
   shiny::observe({
     shiny::req(tadat$raw)
-    tadat$raw$TADAShiny.tab = input$tabbar
-    tadat$tab = input$tabbar
+    tadat$raw$TADAShiny.tab <- input$tabbar
+    tadat$tab <- input$tabbar
   })
-  
+
   # 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::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::updateTabsetPanel(session = session, inputId = "tabbar", selected = unique(tadat$raw$tab))
+    tadat$reup <- NULL
   })
-
-
 }

R/app_ui.R

@@ -17,58 +17,71 @@ css <- "
 app_ui <- function(request) {
   tagList(
     # Leave this function for adding external resources
+    # This function automatically incorporates the epa styles.css file included 
+    # in the www folder. Downloaded from https://www.epa.gov/web-policies-and-procedures/web-standards-look-and-feel-template
+    # styles.css hosted locally in this app includes a fix (for compatibility with leaflet and plotly)
     golem_add_external_resources(),
     # Your application UI logic
     shiny::fluidPage(
-      tags$html(class = "no-js", lang="en"),
+      tags$html(class = "no-js", lang = "en"),
       HTML("<div id='eq-disclaimer-banner' class='padding-1 text-center text-white bg-secondary-dark'><strong>EPA development environment:</strong> The
       content on this page is not production ready. This site is being used
       for <strong>development</strong> and/or <strong>testing</strong> purposes
       only.</div>"),
-      epa_header,
-      #shiny::includeHTML(app_sys("app/www/header.html")),
+      # adds epa header html from here: https://www.epa.gov/themes/epa_theme/pattern-lab/patterns/pages-standalone-template/pages-standalone-template.rendered.html
+      shiny::includeHTML(app_sys("app/www/header.html")),
       shinyjs::useShinyjs(),
       shinyjs::inlineCSS(css),
       htmltools::br(),
       shiny::headerPanel(title = "Tools for Automated Data Analysis (TADA) Module 1: Water Quality Portal Data Discovery and Cleaning"),
       htmltools::br(),
       shiny::tabsetPanel( # create a navbar page with tabs at the top
         id = "tabbar",
-        shiny::tabPanel("1. Load", value = "Load",# each tabPanel represents a tab page at the top of the navbar
-                 htmltools::br(),
-                 mod_query_data_ui("query_data_1")), #,
-        shiny::tabPanel("2. Overview", value = "Overview",
-                 htmltools::br(),
-                 mod_overview_ui("overview_1")),
-                 # htmltools::hr()),
-                 # mod_summary_ui("summary_1")),
-        shiny::tabPanel("3. Flag", value = "Flag",
-                        htmltools::br(),
-                 mod_data_flagging_ui("data_flagging_1")),
-
-         shiny::tabPanel("4. Filter", value ="Filter",
-                         htmltools::br(),
-                         mod_filtering_ui("filtering_1")),
-        # shiny::tabPanel("Harmonize"),
-        shiny::tabPanel("5. Censored Data", value = "Censored",
-                        htmltools::br(),
-                        mod_censored_data_ui("censored_data_1")),
-        shiny::tabPanel("6. Harmonize and Calculate", value = "Harmonize",
-                        htmltools::br(),
-                        mod_harmonize_np_ui("harmonize_np_1")),
-        shiny::tabPanel("7. Explore", value = "Figures",
-                htmltools::br(),
-                mod_figures_ui("figures_1")),
-        shiny::tabPanel("8. Review", value = "Review",
-                        htmltools::br(),
-                        mod_review_data_ui("review_data_1"))#,
-        # shiny::tabPanel("Explore"),
-        # shiny::tabPanel("User Guide")
-
+        shiny::tabPanel("1. Load",
+          value = "Load", # each tabPanel represents a tab page at the top of the navbar
+          htmltools::br(),
+          mod_query_data_ui("query_data_1")
+        ), # ,
+        shiny::tabPanel("2. Overview",
+          value = "Overview",
+          htmltools::br(),
+          mod_overview_ui("overview_1")
+        ),
+        shiny::tabPanel("3. Flag",
+          value = "Flag",
+          htmltools::br(),
+          mod_data_flagging_ui("data_flagging_1")
+        ),
+        shiny::tabPanel("4. Filter",
+          value = "Filter",
+          htmltools::br(),
+          mod_filtering_ui("filtering_1")
+        ),
+        shiny::tabPanel("5. Censored Data",
+          value = "Censored",
+          htmltools::br(),
+          mod_censored_data_ui("censored_data_1")
+        ),
+        shiny::tabPanel("6. Harmonize and Calculate",
+          value = "Harmonize",
+          htmltools::br(),
+          mod_harmonize_np_ui("harmonize_np_1")
+        ),
+        shiny::tabPanel("7. Explore",
+          value = "Figures",
+          htmltools::br(),
+          mod_figures_ui("figures_1")
+        ),
+        shiny::tabPanel("8. Review",
+          value = "Review",
+          htmltools::br(),
+          mod_review_data_ui("review_data_1")
+        )
       ),
       htmltools::hr(),
       mod_TADA_summary_ui("TADA_summary_1"),
-      #shiny::includeHTML(app_sys("app/www/footer.html"))
+      # adds epa footer html 
+      shiny::includeHTML(app_sys("app/www/footer.html"))
     )
   )
 }

R/fct_helpers.R

@@ -1,4 +1,4 @@
-#' helpers 
+#' helpers
 #'
 #' @description A fct function
 #'

R/golem_utils_ui.R

@@ -9,7 +9,7 @@
 #' @examples
 #' list_to_li(c("a", "b"))
 #' @importFrom shiny tags tagAppendAttributes tagList
-#' 
+#'
 
 list_to_li <- function(list, class = NULL) {
   if (is.null(class)) {