Merge pull request #162 from USEPA/cm-release-review-2

Cm release review 2
USEPA · Jun 12, 2024 · 48b7259 · 48b7259
2 parents 23a7fff + 96413be
commit 48b7259
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diff --git a/.devcontainer/Shiny/devcontainer.json b/.devcontainer/Shiny/devcontainer.json
@@ -3,7 +3,7 @@
     "image": "ghcr.io/rocker-org/devcontainer/geospatial:4",
     "features": {
         "ghcr.io/rocker-org/devcontainer-features/r-packages:1": {
-            "packages": "github::USEPA/TADA,config,golem,readxl,writexl,leaflet,shiny,shinyWidgets,shinyjs,shinycssloaders,DT,ggplot2,shinybusy,dplyr,plyr,tidyr,scales,forcats,RColorBrewer,lubridate,plotly",
+            "packages": "github::USEPA/EPATADA,config,golem,readxl,writexl,leaflet,shiny,shinyWidgets,shinyjs,shinycssloaders,DT,ggplot2,shinybusy,dplyr,plyr,tidyr,scales,forcats,RColorBrewer,lubridate,plotly",
             "installSystemRequirements": true
         }
     },

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -8,7 +8,7 @@
     "image": "ghcr.io/rocker-org/devcontainer/geospatial:4",
     "features": {
         "ghcr.io/rocker-org/devcontainer-features/r-packages:1": {
-            "packages": "github::USEPA/TADA,config,golem,readxl,writexl,leaflet,shiny,shinyWidgets,shinyjs,shinycssloaders,DT,ggplot2,shinybusy,dplyr,plyr,tidyr,scales,forcats,RColorBrewer,lubridate,plotly",
+            "packages": "github::USEPA/EPATADA,config,golem,readxl,writexl,leaflet,shiny,shinyWidgets,shinyjs,shinycssloaders,DT,ggplot2,shinybusy,dplyr,plyr,tidyr,scales,forcats,RColorBrewer,lubridate,plotly",
             "installSystemRequirements": true
         }
     },

diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -49,10 +49,18 @@ Add any other context about the problem here.
 
 **Reminders for TADA contributors addressing this issue**
 
-New features should include all of the following work:
+Bug fixes should include the following work:
 
--   [ ] Create the function/code.
+-   [ ] Create or edit the code.
 
--   [ ] Document all code using comments to describe what is does.
+-   [ ] Document all code using line/inline and/or multi-line/block comments
+    to describe what is does.
 
--   [ ] Create tests.
+-   [ ] Create or edit tests in tests/testthat folder to help prevent and/or 
+    troubleshoot potential future issues.
+
+-   [ ] If your code edits impact other functionality in the shiny 
+    app, ensure those are updated as well.
+
+-   [ ] Run styler::style_pkg(), devtools::document(), and devtools::check() 
+    and address any new notes or issues before creating a pull request.
diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md
@@ -35,10 +35,18 @@ Add any other context or screenshots about the feature request here.
 
 **Reminders for TADA contributors addressing this issue**
 
-New features should include all of the following work:
+New features and/or edits should include the following work:
 
--   [ ] Create the function/code.
+-   [ ] Create or edit the code.
 
--   [ ] Document all code using comments to describe what is does.
+-   [ ] Document all code using line/inline and/or multi-line/block comments
+    to describe what is does.
 
--   [ ] Create tests.
+-   [ ] Create or edit tests in tests/testthat folder to help prevent and/or 
+    troubleshoot potential future issues.
+
+-   [ ] If your code edits impact other functionality in the shiny 
+    app, ensure those are updated as well.
+
+-   [ ] Run styler::style_pkg(), devtools::document(), and devtools::check() 
+    and address any new notes or issues before creating a pull request.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -14,15 +14,6 @@ Authors@R: c(
   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.
@@ -41,7 +32,7 @@ Imports:
     shinycssloaders,
     DT,
     ggplot2,
-    TADA, 
+    EPATADA, 
     shinybusy, 
     dplyr, 
     plyr,
@@ -53,7 +44,7 @@ Imports:
     lubridate,
     plotly
 Remotes: 
-    github::USEPA/TADA
+    github::USEPA/EPATADA
 Suggests: 
     config,
     testthat,

diff --git a/R/app_server.R b/R/app_server.R
@@ -33,13 +33,13 @@ app_server <- function(input, output, session) {
   shinyjs::disable(selector = '.nav li a[data-value="Review"]')
 
   # 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$job_id = job_id
-  
+  tadat$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
+
   # 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, {
@@ -60,22 +60,22 @@ app_server <- function(input, output, session) {
 
   shiny::observe({
     # JCH - is this necessary?
-    #shiny::req(tadat$raw)
+    # shiny::req(tadat$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::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
-  #})
+  # })
 }
diff --git a/R/app_ui.R b/R/app_ui.R
@@ -17,7 +17,7 @@ css <- "
 app_ui <- function(request) {
   tagList(
     # Leave this function for adding external resources
-    # This function automatically incorporates the epa styles.css file included 
+    # 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(),
@@ -80,7 +80,7 @@ app_ui <- function(request) {
       ),
       htmltools::hr(),
       mod_TADA_summary_ui("TADA_summary_1"),
-      # adds epa footer html 
+      # adds epa footer html
       shiny::includeHTML(app_sys("app/www/footer.html"))
     )
   )

diff --git a/R/mod_TADA_summary.R b/R/mod_TADA_summary.R
@@ -41,7 +41,7 @@ mod_TADA_summary_ui <- function(id) {
         )))),
         shiny::fluidRow(column(6, shiny::uiOutput(ns(
           "dwn_final"
-        ))))#,
+        )))) # ,
         # shiny::fluidRow(column(
         #   6,
         #   shiny::fileInput(
@@ -75,33 +75,33 @@ mod_TADA_summary_server <- function(id, tadat) {
   shiny::moduleServer(id, function(input, output, session) {
     ns <- session$ns
     # reactive list to hold reactive objects specific to this module
-    summary_things = shiny::reactiveValues()
-    
-    
+    summary_things <- shiny::reactiveValues()
+
+
     # calculate the stats needed to fill the summary box
     shiny::observe({
       shiny::req(tadat$raw)
       summary_things$rem_rec <-
         length(tadat$raw$ResultIdentifier[tadat$raw$TADA.Remove ==
-                                            TRUE])
+          TRUE])
       summary_things$clean_rec <-
         length(tadat$raw$ResultIdentifier[tadat$raw$TADA.Remove ==
-                                            FALSE])
+          FALSE])
       clean_sites <-
         unique(tadat$raw$MonitoringLocationIdentifier[tadat$raw$TADA.Remove ==
-                                                        FALSE])
+          FALSE])
       summary_things$clean_site <- length(clean_sites)
       summary_things$rem_site <-
         length(unique(tadat$raw$MonitoringLocationIdentifier[!tadat$raw$MonitoringLocationIdentifier %in%
-                                                               clean_sites]))
+          clean_sites]))
       summary_things$removals <- sort_removals(tadat$removals)
     })
     summary_things$removals <- data.frame(matrix(
       ncol = 2,
       nrow = 0,
       dimnames = list(NULL, c("Reason", "Count"))
     ))
-    
+
     # output$removal_summary = DT::renderDataTable(
     #   summary_things$removals,
     #   escape = FALSE,
@@ -112,7 +112,7 @@ mod_TADA_summary_server <- function(id, tadat) {
     #     language = list(zeroRecords = "No records removed")
     #   )
     # )
-    
+
     # summary text = total records
     output$rec_tot <- shiny::renderText({
       if (is.null(tadat$raw)) {
@@ -126,17 +126,21 @@ mod_TADA_summary_server <- function(id, tadat) {
       if (is.null(tadat$raw)) {
         "Total Results Flagged for Removal: 0"
       } else {
-        paste0("Total Results Flagged for Removal: ",
-               scales::comma(summary_things$rem_rec))
+        paste0(
+          "Total Results Flagged for Removal: ",
+          scales::comma(summary_things$rem_rec)
+        )
       }
     })
     # summary text = total records in clean
     output$rec_clean <- shiny::renderText({
       if (is.null(tadat$raw)) {
         "Total Results Retained: 0"
       } else {
-        paste0("Total Results Retained: ",
-               scales::comma(summary_things$clean_rec))
+        paste0(
+          "Total Results Retained: ",
+          scales::comma(summary_things$clean_rec)
+        )
       }
     })
     # summary text = total sites
@@ -154,37 +158,43 @@ mod_TADA_summary_server <- function(id, tadat) {
       if (is.null(tadat$raw)) {
         "Total Sites Flagged for Removal: 0"
       } else {
-        paste0("Total Sites Flagged for Removal: ",
-               scales::comma(summary_things$rem_site))
+        paste0(
+          "Total Sites Flagged for Removal: ",
+          scales::comma(summary_things$rem_site)
+        )
       }
     })
     # summary text = total sites in clean file
     output$site_clean <- shiny::renderText({
       if (is.null(tadat$raw)) {
         "Total Sites Retained: 0"
       } else {
-        paste0("Total Sites Retained: ",
-               scales::comma(summary_things$clean_site))
+        paste0(
+          "Total Sites Retained: ",
+          scales::comma(summary_things$clean_site)
+        )
       }
     })
-    
+
     # download dataset button - only appears if there data exists in the app already
     output$dwn_working <- shiny::renderUI({
       shiny::req(tadat$raw)
       shiny::downloadButton(ns("download_working"),
-                            "Download Working Dataset (.zip)",
-                            style = "color: #fff; background-color: #337ab7; border-color: #2e6da4",
-                            contentType = "application/zip")
+        "Download Working Dataset (.zip)",
+        style = "color: #fff; background-color: #337ab7; border-color: #2e6da4",
+        contentType = "application/zip"
+      )
     })
-    
+
     output$dwn_final <- shiny::renderUI({
       shiny::req(tadat$raw)
       shiny::downloadButton(ns("download_final"),
-                            "Download Final Dataset (.zip)",
-                            style = "color: #fff; background-color: #337ab7; border-color: #2e6da4",
-                            contentType = "application/zip")
+        "Download Final Dataset (.zip)",
+        style = "color: #fff; background-color: #337ab7; border-color: #2e6da4",
+        contentType = "application/zip"
+      )
     })
-    
+
     output$download_working <- shiny::downloadHandler(
       filename = function() {
         paste0(tadat$default_outfile, "_working.zip")
@@ -193,19 +203,21 @@ mod_TADA_summary_server <- function(id, tadat) {
         fs <- c()
         tmpdir <- tempdir()
         setwd(tempdir())
-        datafile_name = paste0(tadat$default_outfile, ".xlsx")
-        progress_file_name = paste0(tadat$default_outfile, "_prog.RData")
+        datafile_name <- paste0(tadat$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)
+          list(Data = EPATADA::TADA_OrderCols(tadat$raw), Parameterization = desc)
         writeFile(tadat, progress_file_name)
         writexl::write_xlsx(dfs, path = datafile_name)
-        utils::zip(zipfile = fname,
-            files = c(datafile_name, progress_file_name))
+        utils::zip(
+          zipfile = fname,
+          files = c(datafile_name, progress_file_name)
+        )
       },
       contentType = "application/zip"
     )
-    
+
     output$download_final <- shiny::downloadHandler(
       filename = function() {
         paste0(tadat$default_outfile, "_final.zip")
@@ -214,21 +226,23 @@ mod_TADA_summary_server <- function(id, tadat) {
         fs <- c()
         tmpdir <- tempdir()
         setwd(tempdir())
-        datafile_name = paste0(tadat$default_outfile, ".xlsx")
-        progress_file_name = paste0(tadat$default_outfile, "_prog.RData")
+        datafile_name <- paste0(tadat$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)
+          list(Data = EPATADA::TADA_OrderCols(tadat$raw[!tadat$raw$TADA.Remove, ]), Parameterization = desc)
         writeFile(tadat, progress_file_name)
         writexl::write_xlsx(dfs, path = datafile_name)
-        utils::zip(zipfile = fname,
-                   files = c(datafile_name, progress_file_name))
+        utils::zip(
+          zipfile = fname,
+          files = c(datafile_name, progress_file_name)
+        )
       },
       contentType = "application/zip"
     )
-    
+
     shiny::observeEvent(input$disclaimer, {
       shiny::showModal(
         shiny::modalDialog(
@@ -251,7 +265,7 @@ sort_removals <- function(removal_table) {
       ))
     colnames(results) <- prefixes
     results[is.na(results)] <- FALSE
-    
+
     for (prefix in prefixes) {
       active_cols <- fields[dplyr::starts_with(prefix, vars = fields)]
       if (length(active_cols) > 0) {
@@ -264,13 +278,13 @@ sort_removals <- function(removal_table) {
     results["Flag and Filter"] <- (results$Flag & results$Filter)
     results["Filter only"] <- ((totals == 1) & results$Filter)
     results <-
-      dplyr::select(results,-intersect(prefixes, colnames(results)))
+      dplyr::select(results, -intersect(prefixes, colnames(results)))
     results$Many <- rowSums(results) > 2
     results$Retained <- !apply(results, 1, any)
     counts <- colSums(results)
     counts <-
       data.frame(Reason = names(counts), Count = as.vector(counts))
-    counts <- counts[(counts$Count > 0),]
+    counts <- counts[(counts$Count > 0), ]
     return(counts)
   }
 }