Merge pull request #195 from USEPA/fix-option-C-#135

Fix option c #135

R/mod_query_data.R

@@ -305,8 +305,19 @@ mod_query_data_server <- function(id, tadat) {
       )
 
       # user uploaded data
-      raw <-
-        suppressWarnings(readxl::read_excel(input$file$datapath, sheet = 1))
+      raw <- readxl::read_excel(input$file$datapath, sheet = 1, col_types = "text")
+
+      # run autoclean
+      raw <- EPATADA::TADA_AutoClean(raw)
+
+      #####
+      # check that all TADA template columns are included (returns TRUE or FALSE)
+      # if FALSE, returns an error with names of specific columns that are missing but required
+      # this section needs to be updated to handle the error within the shiny app (instead of crashing) & display a message to users
+      EPATADA::TADA_CheckRequiredFields(raw)
+      #####
+
+      # other steps to prepare data for app
       raw$TADA.Remove <- NULL
       initializeTable(tadat, raw)
       if (!is.null(tadat$original_source)) {

R/utils_flag_functions.R

@@ -90,7 +90,7 @@ applyFlags <- function(in_table, orgs) {
   out <- EPATADA::TADA_FlagResultUnit(out, clean = "none")
 
   # QC rep/blank
-  out <- EPATADA::TADA_FindQCActivities(out, clean = FALSE)
+  out <- EPATADA::TADA_FindQCActivities(out, clean = FALSE, flaggedonly = FALSE)
 
   # Result is flagged as suspect by data submitter
   out <- EPATADA::TADA_FlagMeasureQualifierCode(out, clean = FALSE, define = TRUE)
@@ -116,8 +116,7 @@ applyFlags <- function(in_table, orgs) {
 
   # Continuous data
   out <- EPATADA::TADA_FlagContinuousData(out, clean = FALSE, 
-                                          flaggedonly = FALSE, 
-                                          time_difference = 4)
+                                          flaggedonly = FALSE)
 
   # Above WQX Upper Threshold
   out <- EPATADA::TADA_FlagAboveThreshold(out, clean = FALSE)